Starting phenix.real_space_refine on Thu Sep 18 16:56:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk6_61545/09_2025/9jk6_61545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk6_61545/09_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_61545/09_2025/9jk6_61545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk6_61545/09_2025/9jk6_61545.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk6_61545/09_2025/9jk6_61545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk6_61545/09_2025/9jk6_61545.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F Time building chain proxies: 2.25, per 1000 atoms: 0.12 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 B 145 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 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: 1.54 Conformation dependent library (CDL) restraints added in 718.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.45 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: 3.23 Time building geometry restraints manager: 2.02 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' 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: 5.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 14.560 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.180 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.015 0.001 ARG F 301 TYR 0.023 0.002 TYR D 200 PHE 0.039 0.003 PHE D 153 TRP 0.029 0.003 TRP C 138 HIS 0.005 0.001 HIS D 340 Details of bonding type rmsd covalent geometry : bond 0.00472 (18924) covalent geometry : angle 0.86775 (25602) SS BOND : bond 0.00034 ( 6) SS BOND : angle 0.90721 ( 12) hydrogen bonds : bond 0.13449 ( 1057) hydrogen bonds : angle 5.90207 ( 3084) *********************** 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 : 0.726 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: 0.6172 time to fit residues: 347.9110 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 : 0.502 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.9990 chunk 98 optimal weight: 0.0670 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 0.0870 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 373 GLN A 426 HIS B 234 HIS B 245 GLN B 273 GLN B 305 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 GLN 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 = 0.3728 r_free = 0.3728 target = 0.139703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111222 restraints weight = 24508.071| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.20 r_work: 0.3220 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18930 Z= 0.132 Angle : 0.587 11.073 25614 Z= 0.303 Chirality : 0.041 0.136 2922 Planarity : 0.005 0.059 3186 Dihedral : 4.526 28.525 2518 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.38 % Allowed : 11.43 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.17), residues: 2220 helix: 0.72 (0.14), residues: 1308 sheet: 0.82 (0.35), residues: 180 loop : -1.51 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 176 TYR 0.020 0.002 TYR D 216 PHE 0.016 0.001 PHE B 264 TRP 0.016 0.002 TRP A 168 HIS 0.004 0.001 HIS A 269 Details of bonding type rmsd covalent geometry : bond 0.00312 (18924) covalent geometry : angle 0.58488 (25602) SS BOND : bond 0.00451 ( 6) SS BOND : angle 2.53905 ( 12) hydrogen bonds : bond 0.04092 ( 1057) hydrogen bonds : angle 4.15323 ( 3084) *********************** 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 412 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 325 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 156 MET cc_start: 0.8174 (ttt) cc_final: 0.7963 (ttp) REVERT: A 300 PHE cc_start: 0.7669 (m-10) cc_final: 0.6864 (t80) REVERT: A 337 ASP cc_start: 0.7408 (m-30) cc_final: 0.6925 (t0) REVERT: A 351 GLU cc_start: 0.8131 (mp0) cc_final: 0.7831 (mp0) REVERT: B 132 LEU cc_start: 0.7501 (mt) cc_final: 0.7151 (mt) REVERT: B 221 GLN cc_start: 0.7789 (mt0) cc_final: 0.7533 (mm110) REVERT: B 300 PHE cc_start: 0.7324 (m-10) cc_final: 0.6544 (t80) REVERT: B 442 GLU cc_start: 0.8157 (pp20) cc_final: 0.7746 (pp20) REVERT: C 132 LEU cc_start: 0.7546 (mt) cc_final: 0.7307 (mt) REVERT: C 198 VAL cc_start: 0.8511 (t) cc_final: 0.8251 (m) REVERT: C 209 LEU cc_start: 0.7607 (tp) cc_final: 0.7381 (tp) REVERT: C 251 THR cc_start: 0.8744 (t) cc_final: 0.8379 (m) REVERT: C 304 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7553 (mttt) REVERT: C 306 MET cc_start: 0.7777 (mmm) cc_final: 0.7183 (mtm) REVERT: C 329 ILE cc_start: 0.7041 (OUTLIER) cc_final: 0.6444 (tt) REVERT: D 128 ILE cc_start: 0.7947 (mt) cc_final: 0.7671 (pp) REVERT: D 304 LYS cc_start: 0.8325 (ttmm) cc_final: 0.7383 (mtmt) REVERT: D 306 MET cc_start: 0.7950 (mmm) cc_final: 0.6832 (mtm) REVERT: D 334 ARG cc_start: 0.7937 (mmm-85) cc_final: 0.7663 (tpt90) REVERT: D 373 GLN cc_start: 0.7720 (pt0) cc_final: 0.7481 (pt0) REVERT: D 442 GLU cc_start: 0.8168 (pp20) cc_final: 0.7743 (pp20) REVERT: E 128 ILE cc_start: 0.8209 (mt) cc_final: 0.7828 (mm) REVERT: E 132 LEU cc_start: 0.7485 (mt) cc_final: 0.7159 (mt) REVERT: E 222 TYR cc_start: 0.7294 (t80) cc_final: 0.6994 (t80) REVERT: E 251 THR cc_start: 0.8729 (t) cc_final: 0.8372 (m) REVERT: E 300 PHE cc_start: 0.7650 (m-10) cc_final: 0.7291 (t80) REVERT: E 329 ILE cc_start: 0.6905 (OUTLIER) cc_final: 0.6390 (tt) REVERT: E 353 ARG cc_start: 0.8120 (mtt90) cc_final: 0.7815 (mtt90) REVERT: E 373 GLN cc_start: 0.7211 (tt0) cc_final: 0.6932 (mt0) REVERT: F 300 PHE cc_start: 0.7270 (m-10) cc_final: 0.6613 (t80) REVERT: F 306 MET cc_start: 0.7307 (mmm) cc_final: 0.6762 (mtp) REVERT: F 329 ILE cc_start: 0.6828 (OUTLIER) cc_final: 0.6359 (tt) REVERT: F 455 LYS cc_start: 0.8860 (mtpp) cc_final: 0.8613 (mptm) outliers start: 87 outliers final: 37 residues processed: 365 average time/residue: 0.5266 time to fit residues: 215.4619 Evaluate side-chains 293 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 253 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 238 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 329 ILE Chi-restraints excluded: chain C residue 410 ARG 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 233 ILE Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 214 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 164 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 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 215 ASN 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 217 GLN E 305 HIS F 217 GLN F 269 HIS F 305 HIS F 462 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108888 restraints weight = 24449.468| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.18 r_work: 0.3193 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3200 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= 0.141 Angle : 0.582 13.708 25614 Z= 0.295 Chirality : 0.041 0.134 2922 Planarity : 0.005 0.054 3186 Dihedral : 4.327 29.773 2516 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.44 % Allowed : 13.49 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.18), residues: 2220 helix: 1.68 (0.15), residues: 1272 sheet: 1.17 (0.36), residues: 180 loop : -1.41 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 176 TYR 0.021 0.002 TYR D 222 PHE 0.014 0.001 PHE F 429 TRP 0.014 0.002 TRP D 138 HIS 0.003 0.001 HIS A 426 Details of bonding type rmsd covalent geometry : bond 0.00337 (18924) covalent geometry : angle 0.58171 (25602) SS BOND : bond 0.00405 ( 6) SS BOND : angle 1.34741 ( 12) hydrogen bonds : bond 0.04161 ( 1057) hydrogen bonds : angle 4.00096 ( 3084) *********************** 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 400 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 292 time to evaluate : 0.733 Fit side-chains REVERT: A 156 MET cc_start: 0.8208 (ttt) cc_final: 0.7979 (ttp) REVERT: A 233 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8011 (OUTLIER) REVERT: A 300 PHE cc_start: 0.7619 (m-10) cc_final: 0.6854 (t80) REVERT: A 304 LYS cc_start: 0.8386 (ttmm) cc_final: 0.7905 (tmtt) REVERT: A 306 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.6117 (mtp) REVERT: A 329 ILE cc_start: 0.6686 (OUTLIER) cc_final: 0.6202 (pp) REVERT: A 337 ASP cc_start: 0.7227 (m-30) cc_final: 0.6826 (t0) REVERT: A 351 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: B 132 LEU cc_start: 0.7388 (mt) cc_final: 0.7179 (mt) REVERT: B 300 PHE cc_start: 0.7463 (m-10) cc_final: 0.6745 (t80) REVERT: C 132 LEU cc_start: 0.7422 (mt) cc_final: 0.7178 (mt) REVERT: C 194 PHE cc_start: 0.7842 (t80) cc_final: 0.7526 (t80) REVERT: C 251 THR cc_start: 0.8746 (t) cc_final: 0.8397 (m) REVERT: C 300 PHE cc_start: 0.7691 (m-10) cc_final: 0.7297 (t80) REVERT: C 353 ARG cc_start: 0.8218 (mtt90) cc_final: 0.7913 (mtt90) REVERT: D 194 PHE cc_start: 0.8180 (t80) cc_final: 0.7831 (t80) REVERT: D 300 PHE cc_start: 0.7428 (m-10) cc_final: 0.6729 (t80) REVERT: D 334 ARG cc_start: 0.7973 (mmm-85) cc_final: 0.7590 (tpt90) REVERT: D 373 GLN cc_start: 0.7712 (OUTLIER) cc_final: 0.7417 (pt0) REVERT: E 132 LEU cc_start: 0.7578 (mt) cc_final: 0.7241 (mt) REVERT: E 179 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8405 (mtm) REVERT: E 194 PHE cc_start: 0.7972 (t80) cc_final: 0.7544 (t80) REVERT: E 222 TYR cc_start: 0.7462 (t80) cc_final: 0.7094 (t80) REVERT: E 251 THR cc_start: 0.8742 (t) cc_final: 0.8386 (m) REVERT: E 304 LYS cc_start: 0.8276 (ttmm) cc_final: 0.7432 (mttt) REVERT: E 353 ARG cc_start: 0.8224 (mtt90) cc_final: 0.7888 (mtt90) REVERT: E 373 GLN cc_start: 0.7199 (tt0) cc_final: 0.6743 (mt0) REVERT: F 132 LEU cc_start: 0.7665 (mt) cc_final: 0.7295 (mt) REVERT: F 304 LYS cc_start: 0.8426 (ttmm) cc_final: 0.7386 (mttt) REVERT: F 306 MET cc_start: 0.7773 (mmm) cc_final: 0.7043 (mtp) REVERT: F 455 LYS cc_start: 0.8816 (mtpp) cc_final: 0.8599 (mptm) outliers start: 108 outliers final: 46 residues processed: 339 average time/residue: 0.5175 time to fit residues: 198.3299 Evaluate side-chains 305 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 206 VAL 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 351 GLU 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 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 416 ASN 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 329 ILE Chi-restraints excluded: chain D residue 373 GLN Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 442 GLU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 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 487 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 57 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 125 optimal weight: 0.5980 chunk 198 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 chunk 189 optimal weight: 0.5980 chunk 165 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS B 221 GLN B 305 HIS ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 452 GLN C 305 HIS ** C 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 452 GLN E 215 ASN ** E 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 512 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.137482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108671 restraints weight = 24495.494| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.18 r_work: 0.3193 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18930 Z= 0.137 Angle : 0.565 15.390 25614 Z= 0.286 Chirality : 0.041 0.204 2922 Planarity : 0.004 0.049 3186 Dihedral : 4.196 30.452 2516 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 5.59 % Allowed : 14.90 % Favored : 79.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.18), residues: 2220 helix: 2.17 (0.15), residues: 1242 sheet: 1.57 (0.36), residues: 174 loop : -1.28 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 176 TYR 0.018 0.001 TYR C 200 PHE 0.014 0.001 PHE A 429 TRP 0.013 0.002 TRP A 138 HIS 0.004 0.001 HIS E 305 Details of bonding type rmsd covalent geometry : bond 0.00325 (18924) covalent geometry : angle 0.56522 (25602) SS BOND : bond 0.00308 ( 6) SS BOND : angle 0.97576 ( 12) hydrogen bonds : bond 0.04036 ( 1057) hydrogen bonds : angle 3.93451 ( 3084) *********************** 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 402 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 291 time to evaluate : 0.806 Fit side-chains REVERT: A 156 MET cc_start: 0.8196 (OUTLIER) cc_final: 0.7994 (ttp) REVERT: A 233 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8020 (OUTLIER) REVERT: A 300 PHE cc_start: 0.7633 (m-10) cc_final: 0.6864 (t80) REVERT: A 304 LYS cc_start: 0.8404 (ttmm) cc_final: 0.7950 (tmtt) REVERT: B 132 LEU cc_start: 0.7519 (mt) cc_final: 0.7211 (mt) REVERT: B 300 PHE cc_start: 0.7376 (m-10) cc_final: 0.6713 (t80) REVERT: B 306 MET cc_start: 0.7855 (tpt) cc_final: 0.7568 (mmm) REVERT: B 403 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7311 (tpp-160) REVERT: B 442 GLU cc_start: 0.8202 (pp20) cc_final: 0.7765 (pp20) REVERT: C 132 LEU cc_start: 0.7453 (mt) cc_final: 0.7147 (mt) REVERT: C 194 PHE cc_start: 0.7822 (t80) cc_final: 0.7531 (t80) REVERT: C 247 GLN cc_start: 0.8385 (tp40) cc_final: 0.8130 (tp40) REVERT: C 249 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8461 (mmm) REVERT: C 251 THR cc_start: 0.8706 (t) cc_final: 0.8363 (m) REVERT: C 285 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7902 (ttmt) REVERT: C 304 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7398 (mttt) REVERT: C 353 ARG cc_start: 0.8236 (mtt90) cc_final: 0.7940 (mtt90) REVERT: D 194 PHE cc_start: 0.8294 (t80) cc_final: 0.8042 (t80) REVERT: D 242 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: D 300 PHE cc_start: 0.7499 (m-10) cc_final: 0.6984 (t80) REVERT: D 304 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7853 (tmtt) REVERT: D 334 ARG cc_start: 0.7960 (mmm-85) cc_final: 0.7582 (tpt90) REVERT: E 132 LEU cc_start: 0.7598 (mt) cc_final: 0.7109 (mt) REVERT: E 179 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.8407 (mtm) REVERT: E 194 PHE cc_start: 0.7887 (t80) cc_final: 0.7583 (t80) REVERT: E 222 TYR cc_start: 0.7378 (t80) cc_final: 0.7023 (t80) REVERT: E 249 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8377 (mmp) REVERT: E 251 THR cc_start: 0.8715 (t) cc_final: 0.8352 (m) REVERT: E 304 LYS cc_start: 0.8338 (ttmm) cc_final: 0.7402 (mttt) REVERT: E 353 ARG cc_start: 0.8226 (mtt90) cc_final: 0.7907 (mtt90) REVERT: E 373 GLN cc_start: 0.7228 (tt0) cc_final: 0.6613 (mt0) REVERT: F 300 PHE cc_start: 0.7471 (m-10) cc_final: 0.6822 (OUTLIER) REVERT: F 304 LYS cc_start: 0.8404 (ttmm) cc_final: 0.7955 (tmtt) REVERT: F 306 MET cc_start: 0.7808 (mmm) cc_final: 0.7041 (mtp) REVERT: F 420 MET cc_start: 0.8068 (tmm) cc_final: 0.7827 (mmt) REVERT: F 455 LYS cc_start: 0.8746 (mtpp) cc_final: 0.8509 (mptm) REVERT: F 462 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8826 (mp10) outliers start: 111 outliers final: 51 residues processed: 340 average time/residue: 0.5640 time to fit residues: 216.1896 Evaluate side-chains 312 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 254 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 156 MET Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 148 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain 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 246 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 285 LYS 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 242 GLU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 206 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 461 THR 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 119 optimal weight: 3.9990 chunk 169 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 chunk 149 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 216 optimal weight: 0.9990 chunk 138 optimal weight: 0.0770 chunk 142 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 221 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 HIS ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN E 269 HIS E 340 HIS F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.139997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110936 restraints weight = 24503.094| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 2.17 r_work: 0.3232 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3629 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= 0.132 Angle : 0.571 15.681 25614 Z= 0.286 Chirality : 0.041 0.208 2922 Planarity : 0.004 0.048 3186 Dihedral : 4.122 33.235 2516 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.88 % Allowed : 16.26 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2220 helix: 2.35 (0.15), residues: 1236 sheet: 1.57 (0.35), residues: 174 loop : -1.20 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 176 TYR 0.015 0.001 TYR D 222 PHE 0.013 0.001 PHE F 429 TRP 0.013 0.002 TRP A 138 HIS 0.006 0.001 HIS D 305 Details of bonding type rmsd covalent geometry : bond 0.00317 (18924) covalent geometry : angle 0.57050 (25602) SS BOND : bond 0.00279 ( 6) SS BOND : angle 0.83315 ( 12) hydrogen bonds : bond 0.03948 ( 1057) hydrogen bonds : angle 3.89060 ( 3084) *********************** 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 376 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 279 time to evaluate : 0.708 Fit side-chains REVERT: A 233 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8064 (OUTLIER) REVERT: A 300 PHE cc_start: 0.7532 (m-10) cc_final: 0.6948 (t80) REVERT: A 304 LYS cc_start: 0.8410 (ttmm) cc_final: 0.7911 (tmtt) REVERT: B 132 LEU cc_start: 0.7675 (mt) cc_final: 0.7434 (mt) REVERT: B 174 LYS cc_start: 0.7550 (mmtm) cc_final: 0.7324 (mmtt) REVERT: B 300 PHE cc_start: 0.7500 (m-10) cc_final: 0.6916 (t80) REVERT: B 304 LYS cc_start: 0.8314 (ttmm) cc_final: 0.7870 (tmtt) REVERT: B 306 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7601 (mmm) REVERT: B 403 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7329 (tpp-160) REVERT: C 132 LEU cc_start: 0.7516 (mt) cc_final: 0.7214 (mt) REVERT: C 179 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8395 (mtm) REVERT: C 194 PHE cc_start: 0.7806 (t80) cc_final: 0.7555 (t80) REVERT: C 247 GLN cc_start: 0.8382 (tp40) cc_final: 0.8130 (tp40) REVERT: C 249 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8362 (mmm) REVERT: C 251 THR cc_start: 0.8713 (t) cc_final: 0.8401 (m) REVERT: C 285 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7921 (ttmt) REVERT: C 304 LYS cc_start: 0.8319 (ttmm) cc_final: 0.7449 (mttt) REVERT: C 353 ARG cc_start: 0.8266 (mtt90) cc_final: 0.7963 (mtt90) REVERT: D 194 PHE cc_start: 0.8230 (t80) cc_final: 0.7976 (t80) REVERT: D 242 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: D 247 GLN cc_start: 0.8294 (tp40) cc_final: 0.8059 (tp40) REVERT: D 300 PHE cc_start: 0.7396 (m-10) cc_final: 0.6769 (t80) REVERT: D 306 MET cc_start: 0.7899 (mmm) cc_final: 0.6658 (mtp) REVERT: D 334 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7546 (tpt90) REVERT: E 132 LEU cc_start: 0.7573 (mt) cc_final: 0.7185 (mt) REVERT: E 179 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8290 (mtm) REVERT: E 194 PHE cc_start: 0.7899 (t80) cc_final: 0.7616 (t80) REVERT: E 222 TYR cc_start: 0.7446 (t80) cc_final: 0.7089 (t80) REVERT: E 251 THR cc_start: 0.8737 (t) cc_final: 0.8402 (m) REVERT: E 304 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7395 (mttt) REVERT: E 306 MET cc_start: 0.7462 (tpt) cc_final: 0.6751 (ttm) REVERT: E 353 ARG cc_start: 0.8231 (mtt90) cc_final: 0.7895 (mtt90) REVERT: E 373 GLN cc_start: 0.7203 (tt0) cc_final: 0.6643 (mt0) REVERT: F 131 ILE cc_start: 0.6836 (OUTLIER) cc_final: 0.6517 (tt) REVERT: F 300 PHE cc_start: 0.7528 (m-10) cc_final: 0.7124 (t80) REVERT: F 306 MET cc_start: 0.7825 (mmm) cc_final: 0.7084 (mtp) REVERT: F 462 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8805 (mp10) outliers start: 97 outliers final: 59 residues processed: 325 average time/residue: 0.6015 time to fit residues: 220.5756 Evaluate side-chains 326 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 257 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 195 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain 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 306 MET 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 179 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 246 LEU Chi-restraints excluded: chain C residue 249 MET Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 179 MET Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 131 ILE 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 461 THR Chi-restraints excluded: chain F residue 462 GLN 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 104 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 chunk 7 optimal weight: 0.0980 chunk 73 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN B 247 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN E 245 GLN F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.137322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108716 restraints weight = 24354.666| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.12 r_work: 0.3207 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18930 Z= 0.162 Angle : 0.594 17.282 25614 Z= 0.299 Chirality : 0.042 0.153 2922 Planarity : 0.004 0.047 3186 Dihedral : 4.257 39.592 2516 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.29 % Allowed : 16.47 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2220 helix: 2.27 (0.15), residues: 1236 sheet: 1.66 (0.35), residues: 174 loop : -1.16 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 176 TYR 0.014 0.002 TYR C 222 PHE 0.016 0.002 PHE B 514 TRP 0.015 0.002 TRP C 458 HIS 0.005 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00398 (18924) covalent geometry : angle 0.59358 (25602) SS BOND : bond 0.00254 ( 6) SS BOND : angle 0.77037 ( 12) hydrogen bonds : bond 0.04389 ( 1057) hydrogen bonds : angle 3.98298 ( 3084) *********************** 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 380 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 275 time to evaluate : 0.791 Fit side-chains REVERT: A 233 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.8090 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8438 (ttmm) cc_final: 0.7526 (mtmt) REVERT: A 336 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7570 (ttm110) REVERT: B 132 LEU cc_start: 0.7743 (mt) cc_final: 0.7326 (mt) REVERT: B 242 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7634 (mp0) REVERT: B 300 PHE cc_start: 0.7412 (m-10) cc_final: 0.6779 (t80) REVERT: B 304 LYS cc_start: 0.8359 (ttmm) cc_final: 0.7905 (tmtt) REVERT: B 403 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7369 (tpp-160) REVERT: C 132 LEU cc_start: 0.7630 (mt) cc_final: 0.7283 (mt) REVERT: C 194 PHE cc_start: 0.7872 (t80) cc_final: 0.7606 (t80) REVERT: C 251 THR cc_start: 0.8747 (t) cc_final: 0.8442 (m) REVERT: C 304 LYS cc_start: 0.8386 (ttmm) cc_final: 0.7386 (mttt) REVERT: C 353 ARG cc_start: 0.8284 (mtt90) cc_final: 0.7992 (mtt90) REVERT: D 242 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: D 247 GLN cc_start: 0.8355 (tp40) cc_final: 0.8148 (tp40) REVERT: D 300 PHE cc_start: 0.7469 (m-10) cc_final: 0.6871 (t80) REVERT: D 334 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7561 (ttp80) REVERT: E 132 LEU cc_start: 0.7625 (mt) cc_final: 0.7188 (mt) REVERT: E 194 PHE cc_start: 0.7880 (t80) cc_final: 0.7598 (t80) REVERT: E 251 THR cc_start: 0.8788 (t) cc_final: 0.8458 (m) REVERT: E 306 MET cc_start: 0.7521 (tpt) cc_final: 0.6774 (ttm) REVERT: E 353 ARG cc_start: 0.8276 (mtt90) cc_final: 0.7970 (mtt90) REVERT: E 373 GLN cc_start: 0.7283 (tt0) cc_final: 0.6706 (mt0) REVERT: F 131 ILE cc_start: 0.7016 (OUTLIER) cc_final: 0.6789 (tt) REVERT: F 304 LYS cc_start: 0.8412 (ttmm) cc_final: 0.8195 (ttmm) REVERT: F 462 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8745 (mp10) outliers start: 105 outliers final: 62 residues processed: 328 average time/residue: 0.5497 time to fit residues: 204.9270 Evaluate side-chains 329 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 260 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 206 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 336 ARG 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 238 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 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 233 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 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 461 THR 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 169 optimal weight: 0.8980 chunk 211 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 134 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 212 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 GLN B 247 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN F 305 HIS ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109634 restraints weight = 24431.202| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.12 r_work: 0.3217 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3064 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 18930 Z= 0.145 Angle : 0.576 13.958 25614 Z= 0.291 Chirality : 0.041 0.151 2922 Planarity : 0.004 0.047 3186 Dihedral : 4.199 44.704 2516 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.88 % Allowed : 17.22 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.18), residues: 2220 helix: 2.33 (0.15), residues: 1236 sheet: 1.62 (0.35), residues: 174 loop : -1.16 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 176 TYR 0.014 0.001 TYR C 222 PHE 0.014 0.001 PHE F 429 TRP 0.015 0.002 TRP E 458 HIS 0.004 0.001 HIS B 305 Details of bonding type rmsd covalent geometry : bond 0.00353 (18924) covalent geometry : angle 0.57607 (25602) SS BOND : bond 0.00274 ( 6) SS BOND : angle 0.78351 ( 12) hydrogen bonds : bond 0.04139 ( 1057) hydrogen bonds : angle 3.92915 ( 3084) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 269 time to evaluate : 0.789 Fit side-chains REVERT: A 121 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6626 (pt) REVERT: A 233 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8109 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8425 (ttmm) cc_final: 0.7468 (mtmt) REVERT: A 329 ILE cc_start: 0.6667 (OUTLIER) cc_final: 0.6290 (mm) REVERT: A 336 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7571 (ttm110) REVERT: A 487 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6805 (t70) REVERT: B 132 LEU cc_start: 0.7741 (mt) cc_final: 0.7284 (mt) REVERT: B 221 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7456 (mm110) REVERT: B 242 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7598 (mp0) REVERT: B 300 PHE cc_start: 0.7512 (m-10) cc_final: 0.6947 (t80) REVERT: B 304 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7913 (tmtt) REVERT: B 403 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.7358 (tpp-160) REVERT: C 132 LEU cc_start: 0.7596 (mt) cc_final: 0.7276 (mt) REVERT: C 194 PHE cc_start: 0.7825 (t80) cc_final: 0.7592 (t80) REVERT: C 247 GLN cc_start: 0.8324 (tp40) cc_final: 0.8112 (tp40) REVERT: C 251 THR cc_start: 0.8722 (t) cc_final: 0.8421 (m) REVERT: C 285 LYS cc_start: 0.8311 (OUTLIER) cc_final: 0.7967 (ttmt) REVERT: C 304 LYS cc_start: 0.8402 (ttmm) cc_final: 0.7424 (mttt) REVERT: C 353 ARG cc_start: 0.8275 (mtt90) cc_final: 0.7985 (mtt90) REVERT: D 221 GLN cc_start: 0.7628 (mm110) cc_final: 0.7318 (mm110) REVERT: D 242 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: D 300 PHE cc_start: 0.7482 (m-10) cc_final: 0.6852 (t80) REVERT: D 334 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7564 (ttp80) REVERT: E 132 LEU cc_start: 0.7637 (mt) cc_final: 0.7198 (mt) REVERT: E 194 PHE cc_start: 0.7877 (t80) cc_final: 0.7600 (t80) REVERT: E 251 THR cc_start: 0.8740 (t) cc_final: 0.8427 (m) REVERT: E 304 LYS cc_start: 0.8391 (ttmm) cc_final: 0.7420 (mttt) REVERT: E 353 ARG cc_start: 0.8277 (mtt90) cc_final: 0.7982 (mtt90) REVERT: E 373 GLN cc_start: 0.7243 (tt0) cc_final: 0.6917 (tt0) REVERT: F 131 ILE cc_start: 0.7053 (OUTLIER) cc_final: 0.6825 (tt) REVERT: F 221 GLN cc_start: 0.7374 (mm110) cc_final: 0.7116 (mm110) REVERT: F 304 LYS cc_start: 0.8368 (ttmm) cc_final: 0.7490 (mtmt) REVERT: F 403 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.7386 (ttp80) REVERT: F 462 GLN cc_start: 0.8975 (OUTLIER) cc_final: 0.8694 (mp10) outliers start: 97 outliers final: 57 residues processed: 318 average time/residue: 0.5635 time to fit residues: 202.4707 Evaluate side-chains 324 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 255 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 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 336 ARG Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 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 285 LYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 342 GLU Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP 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 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 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 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 462 GLN 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 1 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 7.9990 chunk 159 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 247 GLN ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.136010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.107390 restraints weight = 24352.329| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.11 r_work: 0.3185 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 18930 Z= 0.189 Angle : 0.617 13.088 25614 Z= 0.312 Chirality : 0.043 0.154 2922 Planarity : 0.005 0.048 3186 Dihedral : 4.400 49.053 2516 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.73 % Allowed : 17.37 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.43 (0.18), residues: 2220 helix: 2.15 (0.15), residues: 1236 sheet: 1.67 (0.35), residues: 174 loop : -1.20 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 176 TYR 0.016 0.002 TYR C 222 PHE 0.018 0.002 PHE B 514 TRP 0.018 0.002 TRP C 458 HIS 0.005 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00466 (18924) covalent geometry : angle 0.61719 (25602) SS BOND : bond 0.00306 ( 6) SS BOND : angle 0.91967 ( 12) hydrogen bonds : bond 0.04724 ( 1057) hydrogen bonds : angle 4.08613 ( 3084) *********************** 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: 94 poor density : 270 time to evaluate : 0.789 Fit side-chains REVERT: A 121 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6512 (pt) REVERT: A 233 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8076 (OUTLIER) REVERT: A 336 ARG cc_start: 0.7850 (OUTLIER) cc_final: 0.7621 (ttm110) REVERT: A 487 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6817 (t70) REVERT: B 132 LEU cc_start: 0.7770 (mt) cc_final: 0.7281 (mt) REVERT: B 221 GLN cc_start: 0.7649 (mm-40) cc_final: 0.7382 (mm110) REVERT: B 242 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: B 251 THR cc_start: 0.8702 (t) cc_final: 0.8431 (m) REVERT: B 304 LYS cc_start: 0.8347 (ttmm) cc_final: 0.7319 (mtmt) REVERT: B 403 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7350 (tpp-160) REVERT: C 132 LEU cc_start: 0.7681 (mt) cc_final: 0.7315 (mt) REVERT: C 194 PHE cc_start: 0.7978 (t80) cc_final: 0.7593 (t80) REVERT: C 251 THR cc_start: 0.8787 (t) cc_final: 0.8461 (m) REVERT: C 285 LYS cc_start: 0.8343 (OUTLIER) cc_final: 0.8036 (ttmt) REVERT: C 304 LYS cc_start: 0.8445 (ttmm) cc_final: 0.7469 (mttt) REVERT: C 353 ARG cc_start: 0.8300 (mtt90) cc_final: 0.8020 (mtt90) REVERT: D 242 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 251 THR cc_start: 0.8705 (t) cc_final: 0.8432 (m) REVERT: D 304 LYS cc_start: 0.8355 (ttmm) cc_final: 0.7333 (mtmt) REVERT: D 334 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.7528 (ttp80) REVERT: D 442 GLU cc_start: 0.8336 (pp20) cc_final: 0.8035 (pp20) REVERT: E 132 LEU cc_start: 0.7614 (mt) cc_final: 0.7132 (mt) REVERT: E 194 PHE cc_start: 0.8050 (t80) cc_final: 0.7682 (t80) REVERT: E 251 THR cc_start: 0.8820 (t) cc_final: 0.8496 (m) REVERT: E 304 LYS cc_start: 0.8406 (ttmm) cc_final: 0.7463 (mttt) REVERT: E 353 ARG cc_start: 0.8305 (mtt90) cc_final: 0.8015 (mtt90) REVERT: E 373 GLN cc_start: 0.7320 (tt0) cc_final: 0.6691 (mt0) REVERT: F 304 LYS cc_start: 0.8388 (ttmm) cc_final: 0.7501 (mtmt) REVERT: F 403 ARG cc_start: 0.8200 (OUTLIER) cc_final: 0.7532 (ttp80) REVERT: F 462 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8716 (mp10) outliers start: 94 outliers final: 65 residues processed: 319 average time/residue: 0.5692 time to fit residues: 205.8859 Evaluate side-chains 325 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 250 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 306 MET Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 487 ASP Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 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 285 LYS 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 238 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 148 ILE 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 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 32 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 126 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 189 optimal weight: 1.9990 chunk 205 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 221 GLN D 221 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 425 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.137598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109014 restraints weight = 24258.353| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.11 r_work: 0.3197 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18930 Z= 0.154 Angle : 0.589 12.650 25614 Z= 0.298 Chirality : 0.042 0.155 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.278 48.883 2516 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 4.23 % Allowed : 18.13 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.18), residues: 2220 helix: 2.29 (0.15), residues: 1236 sheet: 1.60 (0.34), residues: 174 loop : -1.19 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 176 TYR 0.013 0.001 TYR C 222 PHE 0.014 0.001 PHE B 514 TRP 0.016 0.002 TRP E 458 HIS 0.005 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00376 (18924) covalent geometry : angle 0.58928 (25602) SS BOND : bond 0.00293 ( 6) SS BOND : angle 0.86344 ( 12) hydrogen bonds : bond 0.04258 ( 1057) hydrogen bonds : angle 3.98154 ( 3084) *********************** 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 345 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 261 time to evaluate : 0.806 Fit side-chains REVERT: A 121 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6505 (pt) REVERT: A 221 GLN cc_start: 0.7468 (mm110) cc_final: 0.7159 (mm110) REVERT: A 233 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8085 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8427 (ttmm) cc_final: 0.7459 (mtmt) REVERT: A 336 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7618 (ttm110) REVERT: A 487 ASP cc_start: 0.7032 (OUTLIER) cc_final: 0.6789 (t70) REVERT: B 132 LEU cc_start: 0.7777 (mt) cc_final: 0.7308 (mt) REVERT: B 221 GLN cc_start: 0.7555 (mm-40) cc_final: 0.7302 (mm110) REVERT: B 242 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: B 304 LYS cc_start: 0.8341 (ttmm) cc_final: 0.7315 (mtmt) REVERT: B 403 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7369 (tpp-160) REVERT: B 442 GLU cc_start: 0.8276 (pp20) cc_final: 0.7978 (pp20) REVERT: C 132 LEU cc_start: 0.7637 (mt) cc_final: 0.7311 (mt) REVERT: C 194 PHE cc_start: 0.7878 (t80) cc_final: 0.7598 (t80) REVERT: C 251 THR cc_start: 0.8744 (t) cc_final: 0.8440 (m) REVERT: C 285 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8024 (ttmt) REVERT: C 304 LYS cc_start: 0.8439 (ttmm) cc_final: 0.7455 (mttt) REVERT: C 353 ARG cc_start: 0.8275 (mtt90) cc_final: 0.7994 (mtt90) REVERT: D 221 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7456 (mm110) REVERT: D 242 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7620 (mp0) REVERT: D 304 LYS cc_start: 0.8413 (ttmm) cc_final: 0.7404 (mtmt) REVERT: D 334 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7543 (ttp80) REVERT: E 132 LEU cc_start: 0.7617 (mt) cc_final: 0.7157 (mt) REVERT: E 194 PHE cc_start: 0.7914 (t80) cc_final: 0.7691 (t80) REVERT: E 251 THR cc_start: 0.8750 (t) cc_final: 0.8441 (m) REVERT: E 304 LYS cc_start: 0.8396 (ttmm) cc_final: 0.7459 (mttt) REVERT: E 353 ARG cc_start: 0.8279 (mtt90) cc_final: 0.7985 (mtt90) REVERT: E 373 GLN cc_start: 0.7235 (tt0) cc_final: 0.6900 (tt0) REVERT: F 221 GLN cc_start: 0.7507 (mm110) cc_final: 0.7239 (mm110) REVERT: F 304 LYS cc_start: 0.8409 (ttmm) cc_final: 0.7443 (mttt) REVERT: F 403 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7412 (ttp80) REVERT: F 462 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8682 (mp10) REVERT: F 487 ASP cc_start: 0.7011 (OUTLIER) cc_final: 0.6747 (t70) outliers start: 84 outliers final: 61 residues processed: 303 average time/residue: 0.5227 time to fit residues: 180.6778 Evaluate side-chains 328 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 256 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LYS 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 233 ILE Chi-restraints excluded: chain D residue 238 ILE Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain D residue 487 ASP Chi-restraints excluded: chain E residue 138 TRP 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 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 183 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.9980 chunk 187 optimal weight: 0.0000 chunk 199 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 221 GLN ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.138483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.109988 restraints weight = 24309.089| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.12 r_work: 0.3224 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18930 Z= 0.136 Angle : 0.574 11.803 25614 Z= 0.288 Chirality : 0.041 0.145 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.163 48.668 2516 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.93 % Allowed : 18.53 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.18), residues: 2220 helix: 2.39 (0.15), residues: 1236 sheet: 1.58 (0.34), residues: 174 loop : -1.15 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 176 TYR 0.014 0.001 TYR C 222 PHE 0.016 0.001 PHE C 153 TRP 0.015 0.002 TRP E 458 HIS 0.005 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00328 (18924) covalent geometry : angle 0.57438 (25602) SS BOND : bond 0.00269 ( 6) SS BOND : angle 0.76611 ( 12) hydrogen bonds : bond 0.04004 ( 1057) hydrogen bonds : angle 3.89975 ( 3084) ********************** 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 344 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 266 time to evaluate : 0.777 Fit side-chains REVERT: A 121 LEU cc_start: 0.6789 (OUTLIER) cc_final: 0.6486 (pt) REVERT: A 221 GLN cc_start: 0.7462 (mm110) cc_final: 0.7165 (mm110) REVERT: A 233 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8098 (OUTLIER) REVERT: A 304 LYS cc_start: 0.8401 (ttmm) cc_final: 0.7408 (mtmt) REVERT: A 336 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7580 (ttm110) REVERT: A 487 ASP cc_start: 0.7041 (OUTLIER) cc_final: 0.6807 (t70) REVERT: B 132 LEU cc_start: 0.7803 (mt) cc_final: 0.7302 (mt) REVERT: B 221 GLN cc_start: 0.7545 (mm-40) cc_final: 0.7314 (mm110) REVERT: B 242 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.7599 (mp0) REVERT: B 300 PHE cc_start: 0.7535 (m-10) cc_final: 0.7008 (t80) REVERT: B 304 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7870 (tmtt) REVERT: B 403 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7392 (tpp-160) REVERT: B 442 GLU cc_start: 0.8258 (pp20) cc_final: 0.7848 (pp20) REVERT: C 132 LEU cc_start: 0.7739 (mt) cc_final: 0.7409 (mt) REVERT: C 194 PHE cc_start: 0.7914 (t80) cc_final: 0.7635 (t80) REVERT: C 251 THR cc_start: 0.8686 (t) cc_final: 0.8407 (m) REVERT: C 285 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.8000 (ttmt) REVERT: C 304 LYS cc_start: 0.8410 (ttmm) cc_final: 0.7436 (mttt) REVERT: C 353 ARG cc_start: 0.8266 (mtt90) cc_final: 0.7978 (mtt90) REVERT: D 221 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7336 (mm110) REVERT: D 242 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: D 300 PHE cc_start: 0.7577 (m-10) cc_final: 0.7094 (t80) REVERT: D 334 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7553 (ttp80) REVERT: D 442 GLU cc_start: 0.8283 (pp20) cc_final: 0.7964 (pp20) REVERT: E 132 LEU cc_start: 0.7721 (mt) cc_final: 0.7289 (mt) REVERT: E 192 LEU cc_start: 0.8655 (mt) cc_final: 0.8435 (mp) REVERT: E 194 PHE cc_start: 0.7917 (t80) cc_final: 0.7677 (t80) REVERT: E 251 THR cc_start: 0.8725 (t) cc_final: 0.8427 (m) REVERT: E 304 LYS cc_start: 0.8365 (ttmm) cc_final: 0.7487 (mttt) REVERT: E 353 ARG cc_start: 0.8263 (mtt90) cc_final: 0.7962 (mtt90) REVERT: E 373 GLN cc_start: 0.7187 (tt0) cc_final: 0.6857 (tt0) REVERT: F 221 GLN cc_start: 0.7496 (mm110) cc_final: 0.7237 (mm110) REVERT: F 304 LYS cc_start: 0.8384 (ttmm) cc_final: 0.7417 (mtmt) REVERT: F 403 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7403 (ttp80) REVERT: F 462 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.8693 (mp10) REVERT: F 487 ASP cc_start: 0.7029 (OUTLIER) cc_final: 0.6765 (t70) outliers start: 78 outliers final: 52 residues processed: 306 average time/residue: 0.5325 time to fit residues: 185.8243 Evaluate side-chains 318 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 255 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 142 LEU Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 416 ASN Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 487 ASP Chi-restraints excluded: chain B residue 138 TRP Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 242 GLU Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 416 ASN Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 206 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LYS Chi-restraints excluded: chain C residue 329 ILE Chi-restraints excluded: chain C residue 416 ASN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 206 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 242 GLU Chi-restraints excluded: chain D residue 334 ARG Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain D residue 461 THR Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 206 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 329 ILE Chi-restraints excluded: chain E residue 416 ASN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain E residue 461 THR Chi-restraints excluded: chain F residue 142 LEU Chi-restraints excluded: chain F residue 198 VAL Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 233 ILE Chi-restraints excluded: chain F residue 238 ILE Chi-restraints excluded: chain F residue 329 ILE Chi-restraints excluded: chain F residue 403 ARG Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 461 THR Chi-restraints excluded: chain F residue 462 GLN Chi-restraints excluded: chain F residue 487 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 87 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 chunk 73 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 204 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 172 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 221 GLN ** D 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.138376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.109821 restraints weight = 24413.421| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.13 r_work: 0.3220 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.4102 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= 0.140 Angle : 0.580 12.212 25614 Z= 0.292 Chirality : 0.041 0.158 2922 Planarity : 0.004 0.046 3186 Dihedral : 4.165 48.996 2516 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.42 % Allowed : 19.59 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.18), residues: 2220 helix: 2.41 (0.15), residues: 1236 sheet: 1.59 (0.34), residues: 174 loop : -1.13 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 176 TYR 0.015 0.001 TYR C 222 PHE 0.015 0.001 PHE C 153 TRP 0.016 0.002 TRP E 458 HIS 0.005 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00340 (18924) covalent geometry : angle 0.58001 (25602) SS BOND : bond 0.00245 ( 6) SS BOND : angle 0.71989 ( 12) hydrogen bonds : bond 0.04066 ( 1057) hydrogen bonds : angle 3.89792 ( 3084) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6268.68 seconds wall clock time: 107 minutes 27.14 seconds (6447.14 seconds total)