Starting phenix.real_space_refine on Mon Jun 16 10:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk9_61548/06_2025/9jk9_61548.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk9_61548/06_2025/9jk9_61548.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jk9_61548/06_2025/9jk9_61548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk9_61548/06_2025/9jk9_61548.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk9_61548/06_2025/9jk9_61548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk9_61548/06_2025/9jk9_61548.cif" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 78 5.16 5 C 12168 2.51 5 N 3204 2.21 5 O 3132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 18582 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3097 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 13, 'TRANS': 364} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 8.62, per 1000 atoms: 0.46 Number of scatterers: 18582 At special positions: 0 Unit cell: (103.79, 92.02, 221.49, 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 78 16.00 O 3132 8.00 N 3204 7.00 C 12168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.49 Conformation dependent library (CDL) restraints added in 2.1 seconds 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4380 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 13 sheets defined 63.3% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 114 through 138 Proline residue: A 127 - end of helix Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 146 through 172 removed outlier: 3.806A pdb=" N GLU A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER A 155 " --> pdb=" O GLY A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 Processing helix chain 'A' and resid 215 through 243 removed outlier: 3.589A pdb=" N ILE A 219 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 287 Processing helix chain 'A' and resid 291 through 294 Processing helix chain 'A' and resid 295 through 307 removed outlier: 3.562A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 339 Processing helix chain 'A' and resid 341 through 370 removed outlier: 3.916A 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 433 Processing helix chain 'A' and resid 436 through 446 removed outlier: 4.700A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N TYR A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 453 Processing helix chain 'A' and resid 508 through 512 removed outlier: 3.941A pdb=" N HIS A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 138 Proline residue: B 127 - end of helix Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 146 through 172 removed outlier: 3.806A pdb=" N GLU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER B 155 " --> pdb=" O GLY B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 207 Processing helix chain 'B' and resid 215 through 243 removed outlier: 3.589A pdb=" N ILE B 219 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 287 Processing helix chain 'B' and resid 291 through 294 Processing helix chain 'B' and resid 295 through 307 removed outlier: 3.562A pdb=" N LYS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 339 Processing helix chain 'B' and resid 341 through 370 removed outlier: 3.917A 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 433 Processing helix chain 'B' and resid 436 through 446 removed outlier: 4.700A pdb=" N ARG B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 453 Processing helix chain 'B' and resid 508 through 512 removed outlier: 3.942A pdb=" N HIS B 512 " --> pdb=" O PRO B 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 138 Proline residue: C 127 - end of helix Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 146 through 172 removed outlier: 3.806A pdb=" N GLU C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER C 155 " --> pdb=" O GLY C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 207 Processing helix chain 'C' and resid 215 through 243 removed outlier: 3.589A pdb=" N ILE C 219 " --> pdb=" O ASN C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 287 Processing helix chain 'C' and resid 291 through 294 Processing helix chain 'C' and resid 295 through 307 removed outlier: 3.563A pdb=" N LYS C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 339 Processing helix chain 'C' and resid 341 through 370 removed outlier: 3.916A 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 433 Processing helix chain 'C' and resid 436 through 446 removed outlier: 4.700A pdb=" N ARG C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER C 446 " --> pdb=" O GLU C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 453 Processing helix chain 'C' and resid 508 through 512 removed outlier: 3.941A pdb=" N HIS C 512 " --> pdb=" O PRO C 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 138 Proline residue: D 127 - end of helix Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 146 through 172 removed outlier: 3.807A pdb=" N GLU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER D 155 " --> pdb=" O GLY D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 207 Processing helix chain 'D' and resid 215 through 243 removed outlier: 3.590A pdb=" N ILE D 219 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 287 Processing helix chain 'D' and resid 291 through 294 Processing helix chain 'D' and resid 295 through 307 removed outlier: 3.562A pdb=" N LYS D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 339 Processing helix chain 'D' and resid 341 through 370 removed outlier: 3.917A 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 433 Processing helix chain 'D' and resid 436 through 446 removed outlier: 4.699A pdb=" N ARG D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER D 446 " --> pdb=" O GLU D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 453 Processing helix chain 'D' and resid 508 through 512 removed outlier: 3.941A pdb=" N HIS D 512 " --> pdb=" O PRO D 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 115 through 138 Proline residue: E 127 - end of helix Proline residue: E 134 - end of helix Processing helix chain 'E' and resid 146 through 172 removed outlier: 3.806A pdb=" N GLU E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 207 Processing helix chain 'E' and resid 215 through 243 removed outlier: 3.590A pdb=" N ILE E 219 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 287 Processing helix chain 'E' and resid 291 through 294 Processing helix chain 'E' and resid 295 through 307 removed outlier: 3.562A pdb=" N LYS E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 339 Processing helix chain 'E' and resid 341 through 370 removed outlier: 3.917A 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 433 Processing helix chain 'E' and resid 436 through 446 removed outlier: 4.700A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N TYR E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER E 446 " --> pdb=" O GLU E 442 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 453 Processing helix chain 'E' and resid 508 through 512 removed outlier: 3.942A pdb=" N HIS E 512 " --> pdb=" O PRO E 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 138 Proline residue: F 127 - end of helix Proline residue: F 134 - end of helix Processing helix chain 'F' and resid 146 through 172 removed outlier: 3.807A pdb=" N GLU F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER F 155 " --> pdb=" O GLY F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 207 Processing helix chain 'F' and resid 215 through 243 removed outlier: 3.589A pdb=" N ILE F 219 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 287 Processing helix chain 'F' and resid 291 through 294 Processing helix chain 'F' and resid 295 through 307 removed outlier: 3.562A pdb=" N LYS F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 339 Processing helix chain 'F' and resid 341 through 370 removed outlier: 3.916A 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 433 Processing helix chain 'F' and resid 436 through 446 removed outlier: 4.700A pdb=" N ARG F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N TYR F 444 " --> pdb=" O PHE F 440 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER F 446 " --> pdb=" O GLU F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 453 Processing helix chain 'F' and resid 508 through 512 removed outlier: 3.942A pdb=" N HIS F 512 " --> pdb=" O PRO F 509 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 177 through 178 removed outlier: 6.174A pdb=" N ASP A 178 " --> pdb=" O LEU B 502 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLU B 504 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP A 463 " --> pdb=" O ILE B 501 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA3, first strand: chain 'C' and resid 177 through 178 removed outlier: 6.278A pdb=" N ILE A 501 " --> pdb=" O TRP C 463 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU C 465 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N SER A 503 " --> pdb=" O LEU C 465 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N SER C 467 " --> pdb=" O SER A 503 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 375 Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 178 removed outlier: 6.273A pdb=" N ASP B 178 " --> pdb=" O LEU C 502 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N GLU C 504 " --> pdb=" O ASP B 178 " (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 Processing sheet with id=AA8, first strand: chain 'D' and resid 262 through 267 Processing sheet with id=AA9, first strand: chain 'D' and resid 373 through 375 Processing sheet with id=AB1, first strand: chain 'F' and resid 177 through 178 removed outlier: 6.116A pdb=" N ILE D 501 " --> pdb=" O TRP F 463 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N LEU F 465 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N SER D 503 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER F 467 " --> pdb=" O SER D 503 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 373 through 375 Processing sheet with id=AB3, first strand: chain 'E' and resid 177 through 178 removed outlier: 6.048A pdb=" N ASP E 178 " --> pdb=" O LEU F 502 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N GLU F 504 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP E 463 " --> pdb=" O ILE F 501 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 373 through 375 removed outlier: 3.556A pdb=" N GLN F 373 " --> pdb=" O VAL E 515 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL E 515 " --> pdb=" O GLN F 373 " (cutoff:3.500A) 1157 hydrogen bonds defined for protein. 3342 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.75 Time building geometry restraints manager: 5.25 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: 5551 1.34 - 1.46: 3488 1.46 - 1.58: 9831 1.58 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 19002 Sorted by residual: bond pdb=" CB GLN A 273 " pdb=" CG GLN A 273 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.67e+00 bond pdb=" CB GLN E 273 " pdb=" CG GLN E 273 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.62e+00 bond pdb=" CB GLN C 273 " pdb=" CG GLN C 273 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.60e+00 bond pdb=" CB GLN B 273 " pdb=" CG GLN B 273 " ideal model delta sigma weight residual 1.520 1.463 0.057 3.00e-02 1.11e+03 3.59e+00 bond pdb=" CB GLN F 273 " pdb=" CG GLN F 273 " ideal model delta sigma weight residual 1.520 1.464 0.056 3.00e-02 1.11e+03 3.54e+00 ... (remaining 18997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.96: 24411 1.96 - 3.92: 1051 3.92 - 5.88: 176 5.88 - 7.84: 54 7.84 - 9.80: 12 Bond angle restraints: 25704 Sorted by residual: angle pdb=" C ARG D 214 " pdb=" N ASN D 215 " pdb=" CA ASN D 215 " ideal model delta sigma weight residual 122.82 129.09 -6.27 1.42e+00 4.96e-01 1.95e+01 angle pdb=" C ARG B 214 " pdb=" N ASN B 215 " pdb=" CA ASN B 215 " ideal model delta sigma weight residual 122.82 129.05 -6.23 1.42e+00 4.96e-01 1.93e+01 angle pdb=" C ARG A 214 " pdb=" N ASN A 215 " pdb=" CA ASN A 215 " ideal model delta sigma weight residual 122.82 129.03 -6.21 1.42e+00 4.96e-01 1.91e+01 angle pdb=" C ARG C 214 " pdb=" N ASN C 215 " pdb=" CA ASN C 215 " ideal model delta sigma weight residual 122.82 129.00 -6.18 1.42e+00 4.96e-01 1.90e+01 angle pdb=" C ARG E 214 " pdb=" N ASN E 215 " pdb=" CA ASN E 215 " ideal model delta sigma weight residual 122.82 129.00 -6.18 1.42e+00 4.96e-01 1.89e+01 ... (remaining 25699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.16: 10337 12.16 - 24.31: 859 24.31 - 36.47: 162 36.47 - 48.63: 42 48.63 - 60.78: 6 Dihedral angle restraints: 11406 sinusoidal: 4686 harmonic: 6720 Sorted by residual: dihedral pdb=" CA GLU A 504 " pdb=" C GLU A 504 " pdb=" N GLU A 505 " pdb=" CA GLU A 505 " ideal model delta harmonic sigma weight residual 180.00 155.08 24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLU E 504 " pdb=" C GLU E 504 " pdb=" N GLU E 505 " pdb=" CA GLU E 505 " ideal model delta harmonic sigma weight residual 180.00 155.10 24.90 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA GLU C 504 " pdb=" C GLU C 504 " pdb=" N GLU C 505 " pdb=" CA GLU C 505 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 ... (remaining 11403 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2086 0.052 - 0.104: 668 0.104 - 0.155: 153 0.155 - 0.207: 21 0.207 - 0.259: 6 Chirality restraints: 2934 Sorted by residual: chirality pdb=" CA ASN A 215 " pdb=" N ASN A 215 " pdb=" C ASN A 215 " pdb=" CB ASN A 215 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ASN E 215 " pdb=" N ASN E 215 " pdb=" C ASN E 215 " pdb=" CB ASN E 215 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASN D 215 " pdb=" N ASN D 215 " pdb=" C ASN D 215 " pdb=" CB ASN D 215 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 2931 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 264 " 0.017 2.00e-02 2.50e+03 2.31e-02 9.38e+00 pdb=" CG PHE B 264 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE B 264 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE B 264 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 264 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B 264 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 264 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 264 " -0.017 2.00e-02 2.50e+03 2.30e-02 9.27e+00 pdb=" CG PHE A 264 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE A 264 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE A 264 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 264 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE A 264 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 264 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 264 " 0.017 2.00e-02 2.50e+03 2.29e-02 9.22e+00 pdb=" CG PHE E 264 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE E 264 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 PHE E 264 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE E 264 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE E 264 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE E 264 " 0.011 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3938 2.78 - 3.31: 16947 3.31 - 3.84: 32228 3.84 - 4.37: 38030 4.37 - 4.90: 64304 Nonbonded interactions: 155447 Sorted by model distance: nonbonded pdb=" O ALA B 447 " pdb=" OH TYR B 453 " model vdw 2.249 3.040 nonbonded pdb=" O ALA D 447 " pdb=" OH TYR D 453 " model vdw 2.249 3.040 nonbonded pdb=" O ALA A 447 " pdb=" OH TYR A 453 " model vdw 2.249 3.040 nonbonded pdb=" O ALA F 447 " pdb=" OH TYR F 453 " model vdw 2.250 3.040 nonbonded pdb=" O ALA C 447 " pdb=" OH TYR C 453 " model vdw 2.250 3.040 ... (remaining 155442 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 38.060 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 73.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 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 : 0.006 0.057 19008 Z= 0.278 Angle : 0.970 9.797 25716 Z= 0.542 Chirality : 0.055 0.259 2934 Planarity : 0.007 0.059 3198 Dihedral : 9.351 60.783 7008 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.30 % Allowed : 1.20 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.48 (0.14), residues: 2232 helix: -1.94 (0.11), residues: 1344 sheet: 0.64 (0.37), residues: 180 loop : -1.23 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 168 HIS 0.010 0.003 HIS F 418 PHE 0.049 0.006 PHE D 153 TYR 0.024 0.003 TYR B 283 ARG 0.013 0.001 ARG E 256 Details of bonding type rmsd hydrogen bonds : bond 0.15595 ( 1157) hydrogen bonds : angle 6.75605 ( 3342) SS BOND : bond 0.00566 ( 6) SS BOND : angle 0.60818 ( 12) covalent geometry : bond 0.00643 (19002) covalent geometry : angle 0.97060 (25704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 440 time to evaluate : 2.268 Fit side-chains revert: symmetry clash REVERT: A 347 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6715 (mt-10) REVERT: A 459 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6661 (mp) REVERT: B 150 GLU cc_start: 0.6478 (mt-10) cc_final: 0.6241 (tp30) REVERT: B 207 ARG cc_start: 0.7846 (mmm-85) cc_final: 0.7563 (mmt-90) REVERT: B 300 PHE cc_start: 0.7635 (m-80) cc_final: 0.6882 (t80) REVERT: B 367 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6838 (mm-30) REVERT: B 373 GLN cc_start: 0.8251 (tt0) cc_final: 0.8037 (tt0) REVERT: C 222 TYR cc_start: 0.7869 (t80) cc_final: 0.7571 (t80) REVERT: C 228 ASP cc_start: 0.7822 (m-30) cc_final: 0.7482 (m-30) REVERT: C 298 SER cc_start: 0.8097 (p) cc_final: 0.7889 (t) REVERT: C 346 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7309 (tp30) REVERT: C 347 GLU cc_start: 0.7347 (mt-10) cc_final: 0.7128 (mt-10) REVERT: C 389 ASP cc_start: 0.7754 (p0) cc_final: 0.7505 (p0) REVERT: C 435 MET cc_start: 0.8494 (mtp) cc_final: 0.8234 (mtm) REVERT: D 207 ARG cc_start: 0.7867 (mmm-85) cc_final: 0.7614 (mmt-90) REVERT: D 228 ASP cc_start: 0.7918 (m-30) cc_final: 0.7592 (m-30) REVERT: D 247 GLN cc_start: 0.7596 (tt0) cc_final: 0.7335 (tt0) REVERT: D 347 GLU cc_start: 0.7144 (mt-10) cc_final: 0.6730 (pt0) REVERT: D 373 GLN cc_start: 0.8448 (tt0) cc_final: 0.8158 (tt0) REVERT: D 388 MET cc_start: 0.7527 (ptt) cc_final: 0.6920 (ptt) REVERT: D 389 ASP cc_start: 0.7882 (p0) cc_final: 0.7394 (p0) REVERT: D 459 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6745 (mp) REVERT: E 150 GLU cc_start: 0.6778 (mt-10) cc_final: 0.6464 (tp30) REVERT: E 158 PHE cc_start: 0.7962 (m-10) cc_final: 0.7687 (m-80) REVERT: E 207 ARG cc_start: 0.7674 (mmm-85) cc_final: 0.7318 (mmt-90) REVERT: E 226 LEU cc_start: 0.8662 (tp) cc_final: 0.8449 (tt) REVERT: F 304 LYS cc_start: 0.7698 (tttt) cc_final: 0.7155 (mttp) REVERT: F 306 MET cc_start: 0.6408 (mmp) cc_final: 0.6143 (mmp) REVERT: F 347 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6831 (mt-10) outliers start: 6 outliers final: 0 residues processed: 442 average time/residue: 1.4523 time to fit residues: 711.1632 Evaluate side-chains 275 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 273 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain D residue 459 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 0.4980 chunk 168 optimal weight: 9.9990 chunk 93 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 201 optimal weight: 0.6980 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 234 HIS A 247 GLN A 273 GLN A 406 GLN A 512 HIS B 234 HIS ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 HIS B 406 GLN B 414 GLN B 416 ASN B 512 HIS C 234 HIS C 247 GLN C 273 GLN C 416 ASN C 512 HIS D 234 HIS D 273 GLN D 406 GLN D 414 GLN D 512 HIS E 234 HIS E 406 GLN E 414 GLN E 416 ASN E 512 HIS F 234 HIS F 247 GLN F 273 GLN F 416 ASN F 512 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116417 restraints weight = 18899.656| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.69 r_work: 0.3310 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19008 Z= 0.158 Angle : 0.582 10.627 25716 Z= 0.310 Chirality : 0.042 0.170 2934 Planarity : 0.005 0.044 3198 Dihedral : 5.026 54.500 2530 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.16 % Allowed : 7.28 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.17), residues: 2232 helix: 0.30 (0.13), residues: 1362 sheet: 1.26 (0.39), residues: 174 loop : -0.43 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 458 HIS 0.005 0.001 HIS C 305 PHE 0.024 0.002 PHE C 183 TYR 0.018 0.002 TYR B 453 ARG 0.005 0.001 ARG B 263 Details of bonding type rmsd hydrogen bonds : bond 0.03983 ( 1157) hydrogen bonds : angle 4.70119 ( 3342) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.46885 ( 12) covalent geometry : bond 0.00360 (19002) covalent geometry : angle 0.58212 (25704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 338 time to evaluate : 2.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8388 (mt) REVERT: A 186 ARG cc_start: 0.7333 (mtt-85) cc_final: 0.7046 (mtp180) REVERT: A 328 MET cc_start: 0.5048 (OUTLIER) cc_final: 0.4442 (pmt) REVERT: A 341 ASN cc_start: 0.7086 (p0) cc_final: 0.6009 (t0) REVERT: A 347 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 373 GLN cc_start: 0.8459 (tt0) cc_final: 0.8077 (tt0) REVERT: A 459 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6944 (mp) REVERT: A 516 LEU cc_start: 0.8367 (tp) cc_final: 0.8023 (tm) REVERT: B 150 GLU cc_start: 0.6978 (mt-10) cc_final: 0.6319 (tp30) REVERT: B 186 ARG cc_start: 0.7351 (mtt-85) cc_final: 0.7004 (mtp180) REVERT: B 190 LEU cc_start: 0.8293 (mt) cc_final: 0.8083 (mm) REVERT: B 194 PHE cc_start: 0.7876 (t80) cc_final: 0.7495 (t80) REVERT: B 207 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7488 (mmt-90) REVERT: B 300 PHE cc_start: 0.7920 (m-80) cc_final: 0.6766 (t80) REVERT: B 306 MET cc_start: 0.7055 (mmp) cc_final: 0.6683 (mmp) REVERT: B 328 MET cc_start: 0.4744 (OUTLIER) cc_final: 0.3910 (pp-130) REVERT: B 334 ARG cc_start: 0.6668 (ttm-80) cc_final: 0.6415 (ttt-90) REVERT: B 341 ASN cc_start: 0.6989 (p0) cc_final: 0.5935 (t0) REVERT: B 367 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7327 (mm-30) REVERT: B 373 GLN cc_start: 0.8440 (tt0) cc_final: 0.8230 (tt0) REVERT: B 392 GLU cc_start: 0.7840 (mt-10) cc_final: 0.7627 (mt-10) REVERT: B 421 GLU cc_start: 0.8731 (tp30) cc_final: 0.8059 (tp30) REVERT: B 451 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8339 (mp) REVERT: B 516 LEU cc_start: 0.8550 (tp) cc_final: 0.8295 (tm) REVERT: C 181 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7333 (mmm-85) REVERT: C 228 ASP cc_start: 0.8351 (m-30) cc_final: 0.8031 (m-30) REVERT: C 298 SER cc_start: 0.8333 (p) cc_final: 0.8096 (t) REVERT: C 341 ASN cc_start: 0.7363 (p0) cc_final: 0.6125 (t0) REVERT: C 346 GLU cc_start: 0.8397 (mm-30) cc_final: 0.8060 (tp30) REVERT: C 347 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C 392 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7572 (mt-10) REVERT: C 435 MET cc_start: 0.8798 (mtp) cc_final: 0.8589 (mtm) REVERT: D 150 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6858 (mt-10) REVERT: D 186 ARG cc_start: 0.7373 (mtt-85) cc_final: 0.7124 (mtp180) REVERT: D 328 MET cc_start: 0.5333 (OUTLIER) cc_final: 0.4895 (pmt) REVERT: D 341 ASN cc_start: 0.7051 (p0) cc_final: 0.5982 (t0) REVERT: D 347 GLU cc_start: 0.7731 (mt-10) cc_final: 0.7437 (mt-10) REVERT: D 349 GLU cc_start: 0.8219 (tp30) cc_final: 0.7585 (mm-30) REVERT: D 373 GLN cc_start: 0.8482 (tt0) cc_final: 0.8153 (tt0) REVERT: D 459 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.6923 (mp) REVERT: E 150 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6370 (tp30) REVERT: E 179 MET cc_start: 0.8409 (mtm) cc_final: 0.8091 (mtp) REVERT: E 186 ARG cc_start: 0.7347 (mtt-85) cc_final: 0.7079 (mtm-85) REVERT: E 207 ARG cc_start: 0.7563 (mmm-85) cc_final: 0.7189 (mmt-90) REVERT: E 226 LEU cc_start: 0.8568 (tp) cc_final: 0.8258 (tt) REVERT: E 328 MET cc_start: 0.5318 (OUTLIER) cc_final: 0.4957 (pmt) REVERT: E 341 ASN cc_start: 0.6947 (p0) cc_final: 0.6013 (t0) REVERT: E 392 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7662 (mt-10) REVERT: E 456 ASP cc_start: 0.8509 (p0) cc_final: 0.8282 (p0) REVERT: F 181 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7485 (mmm-85) REVERT: F 186 ARG cc_start: 0.7312 (mtt-85) cc_final: 0.7086 (mtp180) REVERT: F 213 ASP cc_start: 0.6272 (t0) cc_final: 0.5883 (t0) REVERT: F 306 MET cc_start: 0.6798 (mmp) cc_final: 0.6581 (mmp) REVERT: F 341 ASN cc_start: 0.7414 (p0) cc_final: 0.6320 (t0) REVERT: F 347 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7802 (mt-10) REVERT: F 392 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7633 (mt-10) outliers start: 63 outliers final: 12 residues processed: 371 average time/residue: 1.3887 time to fit residues: 572.4277 Evaluate side-chains 310 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 288 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 181 ARG Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain F residue 181 ARG Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 504 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 220 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 chunk 202 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN B 247 GLN B 273 GLN B 416 ASN B 462 GLN C 416 ASN C 493 ASN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS D 406 GLN E 247 GLN E 273 GLN E 305 HIS E 406 GLN E 416 ASN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN F 512 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.153761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111382 restraints weight = 18791.364| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.67 r_work: 0.3240 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19008 Z= 0.210 Angle : 0.622 10.073 25716 Z= 0.331 Chirality : 0.044 0.169 2934 Planarity : 0.006 0.055 3198 Dihedral : 5.160 58.026 2530 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.77 % Allowed : 8.84 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2232 helix: 1.07 (0.13), residues: 1356 sheet: 1.70 (0.39), residues: 174 loop : -0.14 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 458 HIS 0.007 0.002 HIS F 234 PHE 0.029 0.003 PHE E 183 TYR 0.023 0.003 TYR E 453 ARG 0.008 0.001 ARG F 256 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 1157) hydrogen bonds : angle 4.71465 ( 3342) SS BOND : bond 0.00084 ( 6) SS BOND : angle 0.33776 ( 12) covalent geometry : bond 0.00490 (19002) covalent geometry : angle 0.62249 (25704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 2.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7453 (mtt-85) cc_final: 0.7101 (mtp180) REVERT: A 194 PHE cc_start: 0.7865 (t80) cc_final: 0.7486 (t80) REVERT: A 213 ASP cc_start: 0.6174 (t0) cc_final: 0.5901 (t0) REVERT: A 328 MET cc_start: 0.5149 (OUTLIER) cc_final: 0.4351 (pp-130) REVERT: A 347 GLU cc_start: 0.7787 (mt-10) cc_final: 0.7516 (mt-10) REVERT: A 373 GLN cc_start: 0.8494 (tt0) cc_final: 0.8133 (tt0) REVERT: A 451 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 516 LEU cc_start: 0.8411 (tp) cc_final: 0.8019 (tm) REVERT: B 150 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6445 (mt-10) REVERT: B 181 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7369 (mmt-90) REVERT: B 186 ARG cc_start: 0.7579 (mtt-85) cc_final: 0.7144 (mtp180) REVERT: B 190 LEU cc_start: 0.8316 (mt) cc_final: 0.8101 (mm) REVERT: B 194 PHE cc_start: 0.7912 (t80) cc_final: 0.7543 (t80) REVERT: B 300 PHE cc_start: 0.7996 (m-80) cc_final: 0.6827 (t80) REVERT: B 306 MET cc_start: 0.6992 (mmp) cc_final: 0.6693 (mmp) REVERT: B 328 MET cc_start: 0.4920 (OUTLIER) cc_final: 0.4058 (pp-130) REVERT: B 334 ARG cc_start: 0.6623 (ttm-80) cc_final: 0.6417 (ttt-90) REVERT: B 367 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7406 (mm-30) REVERT: B 421 GLU cc_start: 0.8663 (tp30) cc_final: 0.8151 (tp30) REVERT: B 425 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8429 (mt0) REVERT: B 451 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8475 (mp) REVERT: B 459 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7356 (pp) REVERT: B 516 LEU cc_start: 0.8472 (tp) cc_final: 0.8190 (tm) REVERT: C 228 ASP cc_start: 0.8363 (m-30) cc_final: 0.8110 (m-30) REVERT: C 298 SER cc_start: 0.8446 (p) cc_final: 0.8208 (t) REVERT: C 328 MET cc_start: 0.5473 (OUTLIER) cc_final: 0.3766 (pp-130) REVERT: C 347 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7549 (mt-10) REVERT: C 351 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: C 392 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7583 (mt-10) REVERT: C 435 MET cc_start: 0.8854 (mtp) cc_final: 0.8649 (mtm) REVERT: C 506 PHE cc_start: 0.7055 (m-10) cc_final: 0.6268 (t80) REVERT: D 150 GLU cc_start: 0.7264 (mt-10) cc_final: 0.6827 (mt-10) REVERT: D 186 ARG cc_start: 0.7516 (mtt-85) cc_final: 0.7162 (mtp180) REVERT: D 194 PHE cc_start: 0.7886 (t80) cc_final: 0.7439 (t80) REVERT: D 328 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.4943 (pp-130) REVERT: D 347 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7460 (mt-10) REVERT: D 373 GLN cc_start: 0.8605 (tt0) cc_final: 0.8163 (tt0) REVERT: E 150 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6596 (mt-10) REVERT: E 186 ARG cc_start: 0.7552 (mtt-85) cc_final: 0.7109 (mtp180) REVERT: E 194 PHE cc_start: 0.7882 (t80) cc_final: 0.7444 (t80) REVERT: E 207 ARG cc_start: 0.7893 (mmm-85) cc_final: 0.7356 (mmt-90) REVERT: E 226 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8286 (tt) REVERT: E 306 MET cc_start: 0.7014 (mmp) cc_final: 0.6650 (mmp) REVERT: E 328 MET cc_start: 0.5236 (OUTLIER) cc_final: 0.4095 (pp-130) REVERT: E 367 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7446 (mm-30) REVERT: E 392 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7612 (mt-10) REVERT: E 486 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7334 (mm) REVERT: F 186 ARG cc_start: 0.7580 (mtt-85) cc_final: 0.7170 (mtp180) REVERT: F 192 LEU cc_start: 0.8251 (tp) cc_final: 0.7904 (tt) REVERT: F 213 ASP cc_start: 0.6286 (t0) cc_final: 0.5883 (t0) REVERT: F 306 MET cc_start: 0.7054 (mmp) cc_final: 0.6839 (mmp) REVERT: F 328 MET cc_start: 0.5598 (OUTLIER) cc_final: 0.3842 (pp-130) REVERT: F 347 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7309 (mt-10) REVERT: F 351 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: F 371 HIS cc_start: 0.8356 (m170) cc_final: 0.8065 (m-70) REVERT: F 392 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7576 (mt-10) outliers start: 75 outliers final: 17 residues processed: 337 average time/residue: 1.3157 time to fit residues: 496.5215 Evaluate side-chains 318 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 486 LEU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 102 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 184 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 55 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 130 optimal weight: 0.0870 chunk 142 optimal weight: 0.9990 chunk 215 optimal weight: 0.9980 chunk 131 optimal weight: 3.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS E 416 ASN F 247 GLN F 273 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.155362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113279 restraints weight = 18838.273| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.68 r_work: 0.3267 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19008 Z= 0.146 Angle : 0.552 8.514 25716 Z= 0.290 Chirality : 0.041 0.163 2934 Planarity : 0.005 0.042 3198 Dihedral : 4.814 55.170 2530 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.61 % Allowed : 9.94 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2232 helix: 1.49 (0.14), residues: 1356 sheet: 1.98 (0.40), residues: 174 loop : 0.04 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 458 HIS 0.005 0.001 HIS E 371 PHE 0.025 0.002 PHE F 196 TYR 0.018 0.002 TYR E 453 ARG 0.009 0.000 ARG D 175 Details of bonding type rmsd hydrogen bonds : bond 0.03735 ( 1157) hydrogen bonds : angle 4.52071 ( 3342) SS BOND : bond 0.00045 ( 6) SS BOND : angle 0.47090 ( 12) covalent geometry : bond 0.00333 (19002) covalent geometry : angle 0.55234 (25704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 284 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7405 (mtt-85) cc_final: 0.7049 (mtp180) REVERT: A 194 PHE cc_start: 0.7840 (t80) cc_final: 0.7476 (t80) REVERT: A 213 ASP cc_start: 0.6477 (t0) cc_final: 0.6143 (t0) REVERT: A 256 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8529 (ttp-170) REVERT: A 328 MET cc_start: 0.4992 (OUTLIER) cc_final: 0.4492 (pmt) REVERT: A 341 ASN cc_start: 0.7035 (p0) cc_final: 0.6716 (p0) REVERT: A 347 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7540 (mt-10) REVERT: A 373 GLN cc_start: 0.8483 (tt0) cc_final: 0.8070 (tt0) REVERT: A 451 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8671 (mp) REVERT: A 516 LEU cc_start: 0.8398 (tp) cc_final: 0.8020 (tm) REVERT: B 181 ARG cc_start: 0.7836 (mmm-85) cc_final: 0.7377 (mtt-85) REVERT: B 186 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.7066 (mtp180) REVERT: B 194 PHE cc_start: 0.7892 (t80) cc_final: 0.7494 (t80) REVERT: B 300 PHE cc_start: 0.8073 (m-80) cc_final: 0.6873 (t80) REVERT: B 306 MET cc_start: 0.6845 (mmp) cc_final: 0.6589 (mmp) REVERT: B 328 MET cc_start: 0.4889 (OUTLIER) cc_final: 0.4015 (pp-130) REVERT: B 334 ARG cc_start: 0.6596 (ttm-80) cc_final: 0.6392 (ttt-90) REVERT: B 341 ASN cc_start: 0.7026 (p0) cc_final: 0.6044 (t0) REVERT: B 421 GLU cc_start: 0.8678 (tp30) cc_final: 0.8306 (tp30) REVERT: B 451 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8479 (mp) REVERT: B 459 LEU cc_start: 0.7565 (OUTLIER) cc_final: 0.6960 (pp) REVERT: B 486 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.7080 (mm) REVERT: B 504 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7605 (tp30) REVERT: B 516 LEU cc_start: 0.8464 (tp) cc_final: 0.8180 (tm) REVERT: C 228 ASP cc_start: 0.8348 (m-30) cc_final: 0.8099 (m-30) REVERT: C 298 SER cc_start: 0.8354 (p) cc_final: 0.8131 (t) REVERT: C 306 MET cc_start: 0.7086 (mmp) cc_final: 0.6883 (mmp) REVERT: C 328 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.3782 (pp-130) REVERT: C 341 ASN cc_start: 0.7342 (p0) cc_final: 0.6237 (t0) REVERT: C 347 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7557 (mt-10) REVERT: C 351 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7519 (mp0) REVERT: C 392 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7519 (mt-10) REVERT: C 506 PHE cc_start: 0.7019 (m-10) cc_final: 0.6279 (t80) REVERT: D 186 ARG cc_start: 0.7562 (mtt-85) cc_final: 0.7100 (mtp180) REVERT: D 194 PHE cc_start: 0.7886 (t80) cc_final: 0.7466 (t80) REVERT: D 256 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8616 (ttp-170) REVERT: D 328 MET cc_start: 0.5397 (OUTLIER) cc_final: 0.4842 (pmt) REVERT: D 341 ASN cc_start: 0.7070 (p0) cc_final: 0.6058 (t0) REVERT: D 347 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7530 (mt-10) REVERT: D 451 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8696 (mp) REVERT: E 150 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6608 (mt-10) REVERT: E 186 ARG cc_start: 0.7607 (mtt-85) cc_final: 0.7133 (mtp180) REVERT: E 194 PHE cc_start: 0.7890 (t80) cc_final: 0.7459 (t80) REVERT: E 306 MET cc_start: 0.7013 (mmp) cc_final: 0.6776 (mmp) REVERT: E 328 MET cc_start: 0.5219 (OUTLIER) cc_final: 0.4106 (pp-130) REVERT: E 341 ASN cc_start: 0.7068 (p0) cc_final: 0.6102 (t0) REVERT: E 392 GLU cc_start: 0.7796 (mt-10) cc_final: 0.7558 (mt-10) REVERT: F 186 ARG cc_start: 0.7447 (mtt-85) cc_final: 0.7034 (mtp180) REVERT: F 192 LEU cc_start: 0.8198 (tp) cc_final: 0.7907 (tt) REVERT: F 306 MET cc_start: 0.6935 (mmp) cc_final: 0.6700 (mmp) REVERT: F 328 MET cc_start: 0.5532 (OUTLIER) cc_final: 0.3789 (pp-130) REVERT: F 341 ASN cc_start: 0.7338 (p0) cc_final: 0.6281 (t0) REVERT: F 346 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7665 (mt-10) REVERT: F 347 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7294 (mt-10) REVERT: F 351 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7293 (mp0) REVERT: F 392 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7627 (mt-10) outliers start: 72 outliers final: 21 residues processed: 326 average time/residue: 1.3604 time to fit residues: 495.5682 Evaluate side-chains 309 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 272 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 425 GLN Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 486 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 459 LEU Chi-restraints excluded: chain F residue 504 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 87 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 136 optimal weight: 0.0050 chunk 211 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN B 462 GLN B 512 HIS C 247 GLN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 HIS E 305 HIS E 416 ASN E 512 HIS F 414 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.154131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111933 restraints weight = 19118.820| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.68 r_work: 0.3250 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19008 Z= 0.162 Angle : 0.563 8.193 25716 Z= 0.296 Chirality : 0.042 0.157 2934 Planarity : 0.005 0.049 3198 Dihedral : 4.728 52.706 2530 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.71 % Allowed : 10.49 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.18), residues: 2232 helix: 1.60 (0.14), residues: 1368 sheet: 2.14 (0.41), residues: 174 loop : 0.19 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 458 HIS 0.005 0.001 HIS C 234 PHE 0.028 0.002 PHE F 196 TYR 0.018 0.002 TYR A 453 ARG 0.010 0.000 ARG C 175 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1157) hydrogen bonds : angle 4.50550 ( 3342) SS BOND : bond 0.00061 ( 6) SS BOND : angle 0.45764 ( 12) covalent geometry : bond 0.00371 (19002) covalent geometry : angle 0.56291 (25704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 283 time to evaluate : 2.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7931 (mmm-85) cc_final: 0.7380 (mtt-85) REVERT: A 186 ARG cc_start: 0.7375 (mtt-85) cc_final: 0.7024 (mtp180) REVERT: A 194 PHE cc_start: 0.7864 (t80) cc_final: 0.7516 (t80) REVERT: A 213 ASP cc_start: 0.6490 (t0) cc_final: 0.6140 (t0) REVERT: A 256 ARG cc_start: 0.8998 (OUTLIER) cc_final: 0.8753 (mtm-85) REVERT: A 306 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6115 (mmp) REVERT: A 328 MET cc_start: 0.5270 (OUTLIER) cc_final: 0.4482 (pp-130) REVERT: A 347 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7519 (mt-10) REVERT: A 373 GLN cc_start: 0.8500 (tt0) cc_final: 0.8085 (tt0) REVERT: A 451 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 150 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6257 (mt-10) REVERT: B 181 ARG cc_start: 0.7847 (mmm-85) cc_final: 0.7373 (mtt-85) REVERT: B 186 ARG cc_start: 0.7626 (mtt-85) cc_final: 0.7070 (mtp180) REVERT: B 194 PHE cc_start: 0.7957 (t80) cc_final: 0.7526 (t80) REVERT: B 300 PHE cc_start: 0.8062 (m-80) cc_final: 0.6876 (t80) REVERT: B 306 MET cc_start: 0.6840 (mmp) cc_final: 0.6556 (mmp) REVERT: B 328 MET cc_start: 0.4922 (OUTLIER) cc_final: 0.4027 (pp-130) REVERT: B 451 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 459 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7249 (pp) REVERT: B 504 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7711 (tp30) REVERT: C 150 GLU cc_start: 0.6046 (tp30) cc_final: 0.5659 (pt0) REVERT: C 228 ASP cc_start: 0.8385 (m-30) cc_final: 0.8153 (m-30) REVERT: C 298 SER cc_start: 0.8416 (p) cc_final: 0.8200 (t) REVERT: C 306 MET cc_start: 0.7083 (mmp) cc_final: 0.6871 (mmp) REVERT: C 328 MET cc_start: 0.5468 (OUTLIER) cc_final: 0.3775 (pp-130) REVERT: C 347 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7513 (mt-10) REVERT: C 351 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: C 506 PHE cc_start: 0.7278 (m-10) cc_final: 0.6571 (t80) REVERT: D 181 ARG cc_start: 0.7972 (mmm-85) cc_final: 0.7425 (mmt-90) REVERT: D 186 ARG cc_start: 0.7397 (mtt-85) cc_final: 0.7057 (mtp180) REVERT: D 194 PHE cc_start: 0.7926 (t80) cc_final: 0.7538 (t80) REVERT: D 256 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8737 (mtm-85) REVERT: D 306 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6367 (mmp) REVERT: D 341 ASN cc_start: 0.7112 (p0) cc_final: 0.6039 (t0) REVERT: D 347 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7511 (mt-10) REVERT: D 373 GLN cc_start: 0.8456 (tt0) cc_final: 0.8086 (tt0) REVERT: D 451 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8713 (mp) REVERT: E 150 GLU cc_start: 0.7260 (mt-10) cc_final: 0.6665 (mt-10) REVERT: E 186 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.7122 (mtp180) REVERT: E 194 PHE cc_start: 0.7928 (t80) cc_final: 0.7466 (t80) REVERT: E 306 MET cc_start: 0.6877 (mmp) cc_final: 0.6644 (mmp) REVERT: E 328 MET cc_start: 0.5178 (OUTLIER) cc_final: 0.4059 (pp-130) REVERT: E 341 ASN cc_start: 0.7026 (p0) cc_final: 0.6081 (t0) REVERT: E 392 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7604 (mt-10) REVERT: E 451 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8621 (mp) REVERT: F 150 GLU cc_start: 0.6124 (tp30) cc_final: 0.5618 (mt-10) REVERT: F 186 ARG cc_start: 0.7511 (mtt-85) cc_final: 0.7140 (mtp180) REVERT: F 192 LEU cc_start: 0.8154 (tp) cc_final: 0.7878 (tt) REVERT: F 213 ASP cc_start: 0.6468 (t0) cc_final: 0.6106 (t0) REVERT: F 306 MET cc_start: 0.7038 (mmp) cc_final: 0.6812 (mmp) REVERT: F 328 MET cc_start: 0.5564 (OUTLIER) cc_final: 0.3815 (pp-130) REVERT: F 347 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7260 (mt-10) REVERT: F 351 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7291 (mp0) REVERT: F 392 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7514 (mt-10) outliers start: 74 outliers final: 23 residues processed: 324 average time/residue: 1.3831 time to fit residues: 500.2125 Evaluate side-chains 317 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 451 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 504 GLU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 306 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 126 optimal weight: 1.9990 chunk 180 optimal weight: 0.9990 chunk 193 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 73 optimal weight: 0.0370 chunk 16 optimal weight: 0.6980 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 406 GLN B 416 ASN C 493 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 305 HIS E 305 HIS E 406 GLN E 416 ASN F 247 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.155356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.113422 restraints weight = 19060.904| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.67 r_work: 0.3270 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19008 Z= 0.138 Angle : 0.537 8.296 25716 Z= 0.281 Chirality : 0.041 0.152 2934 Planarity : 0.005 0.038 3198 Dihedral : 4.497 39.879 2530 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.56 % Allowed : 11.30 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.18), residues: 2232 helix: 1.68 (0.14), residues: 1374 sheet: 2.27 (0.39), residues: 180 loop : 0.31 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 458 HIS 0.004 0.001 HIS F 234 PHE 0.029 0.002 PHE F 196 TYR 0.016 0.002 TYR B 453 ARG 0.007 0.000 ARG E 175 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 1157) hydrogen bonds : angle 4.40500 ( 3342) SS BOND : bond 0.00039 ( 6) SS BOND : angle 0.52764 ( 12) covalent geometry : bond 0.00312 (19002) covalent geometry : angle 0.53743 (25704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 283 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7911 (mmm-85) cc_final: 0.7240 (mmt-90) REVERT: A 186 ARG cc_start: 0.7364 (mtt-85) cc_final: 0.7078 (mtp180) REVERT: A 194 PHE cc_start: 0.7880 (t80) cc_final: 0.7544 (t80) REVERT: A 213 ASP cc_start: 0.6416 (t0) cc_final: 0.6053 (t0) REVERT: A 328 MET cc_start: 0.5205 (OUTLIER) cc_final: 0.4487 (pp-130) REVERT: A 341 ASN cc_start: 0.7040 (p0) cc_final: 0.6096 (t0) REVERT: A 347 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7534 (mt-10) REVERT: A 373 GLN cc_start: 0.8483 (tt0) cc_final: 0.8096 (tt0) REVERT: A 451 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8687 (mp) REVERT: B 150 GLU cc_start: 0.7066 (mt-10) cc_final: 0.6184 (mt-10) REVERT: B 181 ARG cc_start: 0.7822 (mmm-85) cc_final: 0.7332 (mtt-85) REVERT: B 186 ARG cc_start: 0.7597 (mtt-85) cc_final: 0.7111 (mtp180) REVERT: B 194 PHE cc_start: 0.7950 (t80) cc_final: 0.7586 (t80) REVERT: B 300 PHE cc_start: 0.8058 (m-80) cc_final: 0.6847 (t80) REVERT: B 306 MET cc_start: 0.6785 (mmp) cc_final: 0.6521 (mmp) REVERT: B 328 MET cc_start: 0.4965 (OUTLIER) cc_final: 0.4045 (pp-130) REVERT: B 341 ASN cc_start: 0.7038 (p0) cc_final: 0.6191 (t0) REVERT: C 228 ASP cc_start: 0.8338 (m-30) cc_final: 0.8124 (m-30) REVERT: C 298 SER cc_start: 0.8257 (p) cc_final: 0.8056 (t) REVERT: C 306 MET cc_start: 0.7050 (mmp) cc_final: 0.6720 (mmp) REVERT: C 328 MET cc_start: 0.5442 (OUTLIER) cc_final: 0.3751 (pp-130) REVERT: C 341 ASN cc_start: 0.7324 (p0) cc_final: 0.6322 (t0) REVERT: C 347 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7252 (mt-10) REVERT: C 351 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: C 451 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8579 (mp) REVERT: C 506 PHE cc_start: 0.7280 (m-10) cc_final: 0.6572 (t80) REVERT: D 181 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7345 (mmt-90) REVERT: D 186 ARG cc_start: 0.7356 (mtt-85) cc_final: 0.7090 (mtp180) REVERT: D 194 PHE cc_start: 0.7865 (t80) cc_final: 0.7480 (t80) REVERT: D 256 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8746 (mtm-85) REVERT: D 328 MET cc_start: 0.5541 (OUTLIER) cc_final: 0.5005 (pp-130) REVERT: D 341 ASN cc_start: 0.7175 (p0) cc_final: 0.6079 (t0) REVERT: D 347 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7524 (mt-10) REVERT: D 373 GLN cc_start: 0.8485 (tt0) cc_final: 0.8109 (tt0) REVERT: D 421 GLU cc_start: 0.8633 (tp30) cc_final: 0.8381 (tp30) REVERT: D 451 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8686 (mp) REVERT: E 150 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6642 (mt-10) REVERT: E 156 MET cc_start: 0.8812 (ttt) cc_final: 0.8557 (ttt) REVERT: E 186 ARG cc_start: 0.7642 (mtt-85) cc_final: 0.7133 (mtp180) REVERT: E 194 PHE cc_start: 0.7894 (t80) cc_final: 0.7422 (t80) REVERT: E 306 MET cc_start: 0.6910 (mmp) cc_final: 0.6616 (mmp) REVERT: E 328 MET cc_start: 0.5201 (OUTLIER) cc_final: 0.4092 (pp-130) REVERT: E 341 ASN cc_start: 0.6957 (p0) cc_final: 0.6137 (t0) REVERT: E 392 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7558 (mt-10) REVERT: E 451 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8537 (mp) REVERT: E 504 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7567 (tp30) REVERT: F 186 ARG cc_start: 0.7472 (mtt-85) cc_final: 0.7074 (mtp180) REVERT: F 192 LEU cc_start: 0.8132 (tp) cc_final: 0.7868 (tt) REVERT: F 213 ASP cc_start: 0.6580 (t0) cc_final: 0.6145 (t0) REVERT: F 306 MET cc_start: 0.7013 (mmp) cc_final: 0.6785 (mmp) REVERT: F 341 ASN cc_start: 0.7318 (p0) cc_final: 0.6373 (t0) REVERT: F 347 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7180 (mt-10) REVERT: F 351 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7241 (mp0) REVERT: F 392 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7525 (mt-10) REVERT: F 451 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8557 (mp) REVERT: F 513 LYS cc_start: 0.7998 (mmmt) cc_final: 0.7607 (mmtm) outliers start: 71 outliers final: 23 residues processed: 323 average time/residue: 1.3958 time to fit residues: 506.2927 Evaluate side-chains 319 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 282 time to evaluate : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 147 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 178 optimal weight: 0.5980 chunk 155 optimal weight: 1.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 191 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN B 406 GLN B 416 ASN C 247 GLN D 215 ASN D 253 GLN E 406 GLN E 416 ASN F 247 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.113611 restraints weight = 19043.053| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 1.67 r_work: 0.3274 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19008 Z= 0.133 Angle : 0.535 10.739 25716 Z= 0.278 Chirality : 0.041 0.148 2934 Planarity : 0.005 0.037 3198 Dihedral : 4.399 34.280 2530 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.21 % Allowed : 12.10 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.18), residues: 2232 helix: 1.76 (0.14), residues: 1374 sheet: 2.24 (0.39), residues: 180 loop : 0.36 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 458 HIS 0.007 0.001 HIS A 305 PHE 0.030 0.002 PHE F 196 TYR 0.015 0.002 TYR A 453 ARG 0.008 0.000 ARG C 175 Details of bonding type rmsd hydrogen bonds : bond 0.03552 ( 1157) hydrogen bonds : angle 4.35567 ( 3342) SS BOND : bond 0.00061 ( 6) SS BOND : angle 0.54412 ( 12) covalent geometry : bond 0.00300 (19002) covalent geometry : angle 0.53528 (25704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 2.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7912 (mmm-85) cc_final: 0.7383 (mtt-85) REVERT: A 186 ARG cc_start: 0.7382 (mtt-85) cc_final: 0.7083 (mtp180) REVERT: A 194 PHE cc_start: 0.7873 (t80) cc_final: 0.7542 (t80) REVERT: A 213 ASP cc_start: 0.6366 (t0) cc_final: 0.5978 (t0) REVERT: A 328 MET cc_start: 0.5208 (OUTLIER) cc_final: 0.4556 (pp-130) REVERT: A 341 ASN cc_start: 0.6991 (p0) cc_final: 0.6133 (t0) REVERT: A 347 GLU cc_start: 0.7757 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 373 GLN cc_start: 0.8462 (tt0) cc_final: 0.8083 (tt0) REVERT: A 451 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8704 (mp) REVERT: B 150 GLU cc_start: 0.7064 (mt-10) cc_final: 0.6253 (mt-10) REVERT: B 181 ARG cc_start: 0.7827 (mmm-85) cc_final: 0.7350 (mtt-85) REVERT: B 186 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7127 (mtp180) REVERT: B 194 PHE cc_start: 0.7923 (t80) cc_final: 0.7562 (t80) REVERT: B 215 ASN cc_start: 0.6941 (OUTLIER) cc_final: 0.6673 (t0) REVERT: B 300 PHE cc_start: 0.8069 (m-80) cc_final: 0.6841 (t80) REVERT: B 306 MET cc_start: 0.6990 (mmp) cc_final: 0.6725 (mmp) REVERT: B 328 MET cc_start: 0.4946 (OUTLIER) cc_final: 0.4023 (pp-130) REVERT: B 341 ASN cc_start: 0.6898 (p0) cc_final: 0.6134 (t0) REVERT: C 228 ASP cc_start: 0.8348 (m-30) cc_final: 0.8102 (m-30) REVERT: C 306 MET cc_start: 0.7140 (mmp) cc_final: 0.6828 (mmp) REVERT: C 328 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.3688 (pp-130) REVERT: C 341 ASN cc_start: 0.7336 (p0) cc_final: 0.6386 (t0) REVERT: C 347 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7317 (mt-10) REVERT: C 351 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: C 451 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8577 (mp) REVERT: C 506 PHE cc_start: 0.7306 (m-10) cc_final: 0.6666 (t80) REVERT: D 131 ILE cc_start: 0.7405 (mm) cc_final: 0.7189 (tp) REVERT: D 181 ARG cc_start: 0.7902 (mmm-85) cc_final: 0.7334 (mmt-90) REVERT: D 186 ARG cc_start: 0.7394 (mtt-85) cc_final: 0.7101 (mtp180) REVERT: D 194 PHE cc_start: 0.7864 (t80) cc_final: 0.7488 (t80) REVERT: D 256 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8739 (mtm-85) REVERT: D 328 MET cc_start: 0.5466 (OUTLIER) cc_final: 0.4999 (pp-130) REVERT: D 341 ASN cc_start: 0.7130 (p0) cc_final: 0.6118 (t0) REVERT: D 347 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7573 (mt-10) REVERT: D 373 GLN cc_start: 0.8415 (tt0) cc_final: 0.8080 (tt0) REVERT: D 421 GLU cc_start: 0.8659 (tp30) cc_final: 0.8416 (tp30) REVERT: D 451 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8695 (mp) REVERT: E 150 GLU cc_start: 0.7203 (mt-10) cc_final: 0.6725 (mt-10) REVERT: E 156 MET cc_start: 0.8858 (ttt) cc_final: 0.8599 (ttt) REVERT: E 186 ARG cc_start: 0.7639 (mtt-85) cc_final: 0.7158 (mtp180) REVERT: E 194 PHE cc_start: 0.7921 (t80) cc_final: 0.7513 (t80) REVERT: E 306 MET cc_start: 0.7141 (mmp) cc_final: 0.6869 (mmp) REVERT: E 328 MET cc_start: 0.5161 (OUTLIER) cc_final: 0.4074 (pp-130) REVERT: E 341 ASN cc_start: 0.6896 (p0) cc_final: 0.6244 (t0) REVERT: E 392 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7629 (mt-10) REVERT: E 451 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8536 (mp) REVERT: E 504 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7582 (tp30) REVERT: F 186 ARG cc_start: 0.7488 (mtt-85) cc_final: 0.7096 (mtp180) REVERT: F 192 LEU cc_start: 0.8121 (tp) cc_final: 0.7865 (tt) REVERT: F 213 ASP cc_start: 0.6576 (t0) cc_final: 0.6083 (t0) REVERT: F 306 MET cc_start: 0.7029 (mmp) cc_final: 0.6798 (mmp) REVERT: F 328 MET cc_start: 0.5518 (OUTLIER) cc_final: 0.3840 (pp-130) REVERT: F 341 ASN cc_start: 0.7332 (p0) cc_final: 0.6430 (t0) REVERT: F 347 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7216 (mt-10) REVERT: F 351 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: F 392 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7530 (mt-10) REVERT: F 451 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8565 (mp) outliers start: 64 outliers final: 25 residues processed: 321 average time/residue: 1.2927 time to fit residues: 467.7880 Evaluate side-chains 320 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 279 time to evaluate : 2.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 454 ASP Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain D residue 459 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 126 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 116 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 198 optimal weight: 0.6980 chunk 80 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 196 optimal weight: 0.5980 chunk 197 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 406 GLN B 416 ASN C 215 ASN C 247 GLN E 406 GLN E 416 ASN F 247 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.113915 restraints weight = 19132.348| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.68 r_work: 0.3276 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19008 Z= 0.131 Angle : 0.537 8.224 25716 Z= 0.278 Chirality : 0.041 0.159 2934 Planarity : 0.004 0.036 3198 Dihedral : 4.353 33.980 2530 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.06 % Allowed : 12.70 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.18), residues: 2232 helix: 1.78 (0.14), residues: 1374 sheet: 2.21 (0.39), residues: 180 loop : 0.38 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 458 HIS 0.004 0.001 HIS A 305 PHE 0.030 0.002 PHE F 196 TYR 0.015 0.002 TYR B 453 ARG 0.008 0.000 ARG C 175 Details of bonding type rmsd hydrogen bonds : bond 0.03515 ( 1157) hydrogen bonds : angle 4.33574 ( 3342) SS BOND : bond 0.00067 ( 6) SS BOND : angle 0.55123 ( 12) covalent geometry : bond 0.00294 (19002) covalent geometry : angle 0.53663 (25704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 284 time to evaluate : 1.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7894 (mmm-85) cc_final: 0.7361 (mtt-85) REVERT: A 186 ARG cc_start: 0.7378 (mtt-85) cc_final: 0.7071 (mtp180) REVERT: A 194 PHE cc_start: 0.7920 (t80) cc_final: 0.7597 (t80) REVERT: A 213 ASP cc_start: 0.6399 (t0) cc_final: 0.6096 (t0) REVERT: A 328 MET cc_start: 0.5179 (OUTLIER) cc_final: 0.4528 (pp-130) REVERT: A 341 ASN cc_start: 0.6922 (p0) cc_final: 0.6132 (t0) REVERT: A 347 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7538 (mt-10) REVERT: A 373 GLN cc_start: 0.8460 (tt0) cc_final: 0.8087 (tt0) REVERT: A 451 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8696 (mp) REVERT: B 150 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6188 (mt-10) REVERT: B 181 ARG cc_start: 0.7812 (mmm-85) cc_final: 0.7298 (mtt-85) REVERT: B 186 ARG cc_start: 0.7615 (mtt-85) cc_final: 0.7133 (mtp180) REVERT: B 194 PHE cc_start: 0.7931 (t80) cc_final: 0.7614 (t80) REVERT: B 300 PHE cc_start: 0.8068 (m-80) cc_final: 0.6821 (t80) REVERT: B 306 MET cc_start: 0.7029 (mmp) cc_final: 0.6759 (mmp) REVERT: B 328 MET cc_start: 0.4929 (OUTLIER) cc_final: 0.4005 (pp-130) REVERT: B 341 ASN cc_start: 0.6843 (p0) cc_final: 0.6144 (t0) REVERT: C 150 GLU cc_start: 0.6196 (tp30) cc_final: 0.5787 (pt0) REVERT: C 215 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6616 (t0) REVERT: C 228 ASP cc_start: 0.8396 (m-30) cc_final: 0.8160 (m-30) REVERT: C 306 MET cc_start: 0.7113 (mmp) cc_final: 0.6817 (mmp) REVERT: C 328 MET cc_start: 0.5456 (OUTLIER) cc_final: 0.3675 (pp-130) REVERT: C 341 ASN cc_start: 0.7477 (p0) cc_final: 0.6340 (t0) REVERT: C 347 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7290 (mt-10) REVERT: C 351 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: C 451 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8570 (mp) REVERT: C 506 PHE cc_start: 0.7471 (m-10) cc_final: 0.6734 (t80) REVERT: D 181 ARG cc_start: 0.7886 (mmm-85) cc_final: 0.7313 (mmt-90) REVERT: D 186 ARG cc_start: 0.7392 (mtt-85) cc_final: 0.7089 (mtp180) REVERT: D 194 PHE cc_start: 0.7860 (t80) cc_final: 0.7498 (t80) REVERT: D 256 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8731 (mtm-85) REVERT: D 306 MET cc_start: 0.6906 (mmp) cc_final: 0.6537 (mmp) REVERT: D 328 MET cc_start: 0.5457 (OUTLIER) cc_final: 0.5048 (pp-130) REVERT: D 341 ASN cc_start: 0.7070 (p0) cc_final: 0.6206 (t0) REVERT: D 347 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7594 (mt-10) REVERT: D 373 GLN cc_start: 0.8427 (tt0) cc_final: 0.8088 (tt0) REVERT: D 421 GLU cc_start: 0.8657 (tp30) cc_final: 0.8423 (tp30) REVERT: D 451 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8694 (mp) REVERT: E 150 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6756 (mt-10) REVERT: E 156 MET cc_start: 0.8868 (ttt) cc_final: 0.8612 (ttt) REVERT: E 186 ARG cc_start: 0.7627 (mtt-85) cc_final: 0.7132 (mtp180) REVERT: E 194 PHE cc_start: 0.7948 (t80) cc_final: 0.7554 (t80) REVERT: E 306 MET cc_start: 0.7160 (mmp) cc_final: 0.6904 (mmp) REVERT: E 328 MET cc_start: 0.5160 (OUTLIER) cc_final: 0.4078 (pp-130) REVERT: E 341 ASN cc_start: 0.7047 (p0) cc_final: 0.6185 (t0) REVERT: E 392 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7630 (mt-10) REVERT: E 451 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8535 (mp) REVERT: E 504 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7575 (tp30) REVERT: F 186 ARG cc_start: 0.7481 (mtt-85) cc_final: 0.7091 (mtp180) REVERT: F 192 LEU cc_start: 0.8116 (tp) cc_final: 0.7863 (tt) REVERT: F 213 ASP cc_start: 0.6307 (t0) cc_final: 0.5845 (t0) REVERT: F 306 MET cc_start: 0.7074 (mmp) cc_final: 0.6846 (mmp) REVERT: F 328 MET cc_start: 0.5517 (OUTLIER) cc_final: 0.3807 (pp-130) REVERT: F 341 ASN cc_start: 0.7472 (p0) cc_final: 0.6365 (t0) REVERT: F 347 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7190 (mt-10) REVERT: F 351 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: F 392 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7518 (mt-10) REVERT: F 451 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8553 (mp) REVERT: F 513 LYS cc_start: 0.7985 (mmmt) cc_final: 0.7669 (mmtm) outliers start: 61 outliers final: 22 residues processed: 315 average time/residue: 1.5363 time to fit residues: 542.5373 Evaluate side-chains 316 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 278 time to evaluate : 2.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 451 LEU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 72 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 66 optimal weight: 0.3980 chunk 182 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 197 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 512 HIS B 414 GLN B 416 ASN C 215 ASN C 247 GLN C 512 HIS D 253 GLN D 493 ASN D 512 HIS E 215 ASN E 406 GLN E 416 ASN F 247 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.153443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110970 restraints weight = 19035.243| |-----------------------------------------------------------------------------| r_work (start): 0.3399 rms_B_bonded: 1.67 r_work: 0.3238 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19008 Z= 0.181 Angle : 0.589 8.041 25716 Z= 0.307 Chirality : 0.043 0.167 2934 Planarity : 0.005 0.041 3198 Dihedral : 4.489 36.282 2528 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.86 % Allowed : 13.10 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.18), residues: 2232 helix: 1.73 (0.14), residues: 1368 sheet: 2.22 (0.39), residues: 180 loop : 0.36 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 458 HIS 0.005 0.001 HIS F 234 PHE 0.030 0.002 PHE F 196 TYR 0.019 0.002 TYR B 453 ARG 0.008 0.000 ARG C 175 Details of bonding type rmsd hydrogen bonds : bond 0.04004 ( 1157) hydrogen bonds : angle 4.47796 ( 3342) SS BOND : bond 0.00076 ( 6) SS BOND : angle 0.47559 ( 12) covalent geometry : bond 0.00418 (19002) covalent geometry : angle 0.58862 (25704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 280 time to evaluate : 2.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7418 (mtt-85) cc_final: 0.7075 (mtp180) REVERT: A 213 ASP cc_start: 0.6411 (t0) cc_final: 0.6039 (t0) REVERT: A 306 MET cc_start: 0.6673 (mmt) cc_final: 0.6364 (mmp) REVERT: A 328 MET cc_start: 0.5321 (OUTLIER) cc_final: 0.4693 (pp-130) REVERT: A 373 GLN cc_start: 0.8512 (tt0) cc_final: 0.8095 (tt0) REVERT: A 451 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8728 (mp) REVERT: B 150 GLU cc_start: 0.7083 (mt-10) cc_final: 0.6171 (mt-10) REVERT: B 181 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7345 (mtt-85) REVERT: B 194 PHE cc_start: 0.7944 (t80) cc_final: 0.7526 (t80) REVERT: B 300 PHE cc_start: 0.8076 (m-80) cc_final: 0.6851 (t80) REVERT: B 306 MET cc_start: 0.6870 (mmp) cc_final: 0.6614 (mmp) REVERT: B 328 MET cc_start: 0.5044 (OUTLIER) cc_final: 0.4127 (pp-130) REVERT: C 228 ASP cc_start: 0.8392 (m-30) cc_final: 0.8137 (m-30) REVERT: C 306 MET cc_start: 0.7167 (mmp) cc_final: 0.6956 (mmp) REVERT: C 328 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.3755 (pp-130) REVERT: C 347 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7352 (mt-10) REVERT: C 351 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: C 451 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8615 (mp) REVERT: C 506 PHE cc_start: 0.7540 (m-10) cc_final: 0.6878 (t80) REVERT: D 186 ARG cc_start: 0.7433 (mtt-85) cc_final: 0.7107 (mtp180) REVERT: D 256 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8753 (mtm-85) REVERT: D 306 MET cc_start: 0.6990 (mmp) cc_final: 0.6584 (mmp) REVERT: D 328 MET cc_start: 0.5492 (OUTLIER) cc_final: 0.5077 (pp-130) REVERT: D 341 ASN cc_start: 0.7012 (p0) cc_final: 0.6094 (t0) REVERT: D 373 GLN cc_start: 0.8450 (tt0) cc_final: 0.8075 (tt0) REVERT: D 421 GLU cc_start: 0.8629 (tp30) cc_final: 0.8397 (tp30) REVERT: D 451 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8708 (mp) REVERT: E 150 GLU cc_start: 0.7177 (mt-10) cc_final: 0.6587 (mt-10) REVERT: E 156 MET cc_start: 0.8829 (ttt) cc_final: 0.8587 (ttt) REVERT: E 186 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7111 (mtp180) REVERT: E 194 PHE cc_start: 0.7947 (t80) cc_final: 0.7506 (t80) REVERT: E 215 ASN cc_start: 0.7040 (OUTLIER) cc_final: 0.6790 (t0) REVERT: E 306 MET cc_start: 0.7099 (mmp) cc_final: 0.6842 (mmp) REVERT: E 328 MET cc_start: 0.5188 (OUTLIER) cc_final: 0.4099 (pp-130) REVERT: E 341 ASN cc_start: 0.6948 (p0) cc_final: 0.6068 (t0) REVERT: E 451 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8603 (mp) REVERT: E 504 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7723 (tp30) REVERT: F 192 LEU cc_start: 0.8139 (tp) cc_final: 0.7854 (tt) REVERT: F 213 ASP cc_start: 0.6587 (t0) cc_final: 0.6099 (t0) REVERT: F 328 MET cc_start: 0.5536 (OUTLIER) cc_final: 0.3829 (pp-130) REVERT: F 347 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7209 (mt-10) REVERT: F 351 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7175 (mp0) outliers start: 57 outliers final: 23 residues processed: 307 average time/residue: 1.2809 time to fit residues: 442.1470 Evaluate side-chains 307 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 31 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 104 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 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 406 GLN B 416 ASN C 247 GLN C 493 ASN ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 462 GLN E 215 ASN E 416 ASN F 247 GLN F 493 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.154945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.112874 restraints weight = 19067.068| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.67 r_work: 0.3263 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19008 Z= 0.144 Angle : 0.559 8.147 25716 Z= 0.289 Chirality : 0.041 0.163 2934 Planarity : 0.005 0.038 3198 Dihedral : 4.369 34.502 2528 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.21 % Allowed : 13.86 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.18), residues: 2232 helix: 1.71 (0.14), residues: 1374 sheet: 2.17 (0.39), residues: 180 loop : 0.43 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 458 HIS 0.004 0.001 HIS C 234 PHE 0.033 0.002 PHE F 196 TYR 0.015 0.002 TYR B 453 ARG 0.009 0.000 ARG C 175 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 1157) hydrogen bonds : angle 4.39084 ( 3342) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.52597 ( 12) covalent geometry : bond 0.00328 (19002) covalent geometry : angle 0.55951 (25704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4464 Ramachandran restraints generated. 2232 Oldfield, 0 Emsley, 2232 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 277 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.7081 (mtp180) REVERT: A 213 ASP cc_start: 0.6313 (t0) cc_final: 0.5938 (t0) REVERT: A 306 MET cc_start: 0.6626 (mmt) cc_final: 0.6288 (mmp) REVERT: A 328 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.4729 (pp-130) REVERT: A 373 GLN cc_start: 0.8482 (tt0) cc_final: 0.8100 (tt0) REVERT: A 451 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 150 GLU cc_start: 0.7079 (mt-10) cc_final: 0.6167 (mt-10) REVERT: B 181 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7302 (mtt-85) REVERT: B 194 PHE cc_start: 0.7935 (t80) cc_final: 0.7520 (t80) REVERT: B 300 PHE cc_start: 0.8070 (m-80) cc_final: 0.6842 (t80) REVERT: B 306 MET cc_start: 0.6888 (mmp) cc_final: 0.6640 (mmp) REVERT: B 328 MET cc_start: 0.5147 (OUTLIER) cc_final: 0.4211 (pp-130) REVERT: B 341 ASN cc_start: 0.7226 (p0) cc_final: 0.6358 (t0) REVERT: C 228 ASP cc_start: 0.8396 (m-30) cc_final: 0.8151 (m-30) REVERT: C 306 MET cc_start: 0.7103 (mmp) cc_final: 0.6885 (mmp) REVERT: C 328 MET cc_start: 0.5474 (OUTLIER) cc_final: 0.3689 (pp-130) REVERT: C 341 ASN cc_start: 0.7465 (p0) cc_final: 0.6340 (t0) REVERT: C 347 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7275 (mt-10) REVERT: C 351 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 451 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8588 (mp) REVERT: C 506 PHE cc_start: 0.7512 (m-10) cc_final: 0.6787 (t80) REVERT: D 186 ARG cc_start: 0.7471 (mtt-85) cc_final: 0.7103 (mtp180) REVERT: D 256 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8723 (mtm-85) REVERT: D 306 MET cc_start: 0.6950 (mmp) cc_final: 0.6497 (mmp) REVERT: D 328 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.5028 (pp-130) REVERT: D 341 ASN cc_start: 0.7177 (p0) cc_final: 0.6156 (t0) REVERT: D 373 GLN cc_start: 0.8488 (tt0) cc_final: 0.8120 (tt0) REVERT: D 421 GLU cc_start: 0.8642 (tp30) cc_final: 0.8398 (tp30) REVERT: D 451 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8703 (mp) REVERT: E 150 GLU cc_start: 0.7180 (mt-10) cc_final: 0.6659 (mt-10) REVERT: E 156 MET cc_start: 0.8822 (ttt) cc_final: 0.8589 (ttt) REVERT: E 186 ARG cc_start: 0.7637 (mtt-85) cc_final: 0.7127 (mtp180) REVERT: E 194 PHE cc_start: 0.7940 (t80) cc_final: 0.7472 (t80) REVERT: E 306 MET cc_start: 0.7050 (mmp) cc_final: 0.6847 (mmp) REVERT: E 328 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.3920 (pp-130) REVERT: E 341 ASN cc_start: 0.6946 (p0) cc_final: 0.6186 (t0) REVERT: E 451 LEU cc_start: 0.8828 (OUTLIER) cc_final: 0.8547 (mp) REVERT: E 504 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: F 192 LEU cc_start: 0.8112 (tp) cc_final: 0.7840 (tt) REVERT: F 213 ASP cc_start: 0.6589 (t0) cc_final: 0.6132 (t0) REVERT: F 306 MET cc_start: 0.6746 (mmp) cc_final: 0.6010 (mtm) REVERT: F 328 MET cc_start: 0.5513 (OUTLIER) cc_final: 0.3804 (pp-130) REVERT: F 341 ASN cc_start: 0.7458 (p0) cc_final: 0.6366 (t0) REVERT: F 347 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7200 (mt-10) REVERT: F 351 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: F 392 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7512 (mt-10) REVERT: F 513 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7655 (mmtm) outliers start: 44 outliers final: 22 residues processed: 298 average time/residue: 1.2386 time to fit residues: 415.8790 Evaluate side-chains 307 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 271 time to evaluate : 2.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 176 ARG Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 446 SER Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 328 MET Chi-restraints excluded: chain C residue 351 GLU Chi-restraints excluded: chain C residue 451 LEU Chi-restraints excluded: chain C residue 452 GLN Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 ARG Chi-restraints excluded: chain D residue 256 ARG Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 451 LEU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 328 MET Chi-restraints excluded: chain E residue 351 GLU Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain E residue 451 LEU Chi-restraints excluded: chain E residue 457 ARG Chi-restraints excluded: chain E residue 504 GLU Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 328 MET Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 459 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 91 optimal weight: 0.6980 chunk 137 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 67 optimal weight: 0.0270 chunk 162 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 192 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 406 GLN B 416 ASN B 519 GLN C 247 GLN D 253 GLN E 416 ASN F 247 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.155524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.113800 restraints weight = 19031.961| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 1.69 r_work: 0.3276 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3149 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19008 Z= 0.131 Angle : 0.544 8.149 25716 Z= 0.281 Chirality : 0.041 0.188 2934 Planarity : 0.004 0.036 3198 Dihedral : 4.188 18.022 2526 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.11 % Allowed : 14.06 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.18), residues: 2232 helix: 1.75 (0.14), residues: 1380 sheet: 1.62 (0.39), residues: 192 loop : 0.45 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 458 HIS 0.005 0.001 HIS F 305 PHE 0.033 0.002 PHE F 196 TYR 0.014 0.002 TYR A 453 ARG 0.009 0.000 ARG C 175 Details of bonding type rmsd hydrogen bonds : bond 0.03513 ( 1157) hydrogen bonds : angle 4.32658 ( 3342) SS BOND : bond 0.00098 ( 6) SS BOND : angle 0.53486 ( 12) covalent geometry : bond 0.00294 (19002) covalent geometry : angle 0.54406 (25704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18807.03 seconds wall clock time: 323 minutes 28.02 seconds (19408.02 seconds total)