Starting phenix.real_space_refine on Thu Sep 18 17:02:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk9_61548/09_2025/9jk9_61548.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk9_61548/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jk9_61548/09_2025/9jk9_61548.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk9_61548/09_2025/9jk9_61548.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jk9_61548/09_2025/9jk9_61548.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk9_61548/09_2025/9jk9_61548.map" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D, E, F Time building chain proxies: 2.78, per 1000 atoms: 0.15 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 B 145 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 149 " distance=2.02 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 748.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.72 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: 3.15 Time building geometry restraints manager: 1.67 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.410 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: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.370 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.860 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (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 ARG 0.013 0.001 ARG E 256 TYR 0.024 0.003 TYR B 283 PHE 0.049 0.006 PHE D 153 TRP 0.027 0.003 TRP B 168 HIS 0.010 0.003 HIS F 418 Details of bonding type rmsd covalent geometry : bond 0.00643 (19002) covalent geometry : angle 0.97060 (25704) SS BOND : bond 0.00566 ( 6) SS BOND : angle 0.60818 ( 12) hydrogen bonds : bond 0.15595 ( 1157) hydrogen bonds : angle 6.75605 ( 3342) *********************** 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 : 0.732 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: 0.6486 time to fit residues: 317.4208 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 : 0.966 ------------------------------------------------------------------------------- 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 216 optimal weight: 0.5980 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 305 HIS 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.158368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.116420 restraints weight = 18907.762| |-----------------------------------------------------------------------------| 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: 0.3186 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2383 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (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 ARG 0.005 0.001 ARG B 263 TYR 0.018 0.002 TYR B 453 PHE 0.024 0.002 PHE C 183 TRP 0.019 0.002 TRP C 458 HIS 0.005 0.001 HIS C 305 Details of bonding type rmsd covalent geometry : bond 0.00360 (19002) covalent geometry : angle 0.58212 (25704) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.46885 ( 12) hydrogen bonds : bond 0.03983 ( 1157) hydrogen bonds : angle 4.70119 ( 3342) *********************** 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 : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8387 (mt) REVERT: A 186 ARG cc_start: 0.7333 (mtt-85) cc_final: 0.7046 (mtp180) REVERT: A 328 MET cc_start: 0.5058 (OUTLIER) cc_final: 0.4448 (pmt) REVERT: A 341 ASN cc_start: 0.7087 (p0) cc_final: 0.6009 (t0) REVERT: A 347 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7470 (mt-10) REVERT: A 373 GLN cc_start: 0.8462 (tt0) cc_final: 0.8079 (tt0) REVERT: A 459 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.6941 (mp) REVERT: A 516 LEU cc_start: 0.8368 (tp) cc_final: 0.8026 (tm) REVERT: B 150 GLU cc_start: 0.6981 (mt-10) cc_final: 0.6322 (tp30) REVERT: B 186 ARG cc_start: 0.7351 (mtt-85) cc_final: 0.7003 (mtp180) REVERT: B 190 LEU cc_start: 0.8291 (mt) cc_final: 0.8081 (mm) REVERT: B 194 PHE cc_start: 0.7875 (t80) cc_final: 0.7494 (t80) REVERT: B 207 ARG cc_start: 0.8046 (mmm-85) cc_final: 0.7487 (mmt-90) REVERT: B 300 PHE cc_start: 0.7917 (m-80) cc_final: 0.6762 (t80) REVERT: B 306 MET cc_start: 0.7055 (mmp) cc_final: 0.6684 (mmp) REVERT: B 328 MET cc_start: 0.4752 (OUTLIER) cc_final: 0.3919 (pp-130) REVERT: B 334 ARG cc_start: 0.6680 (ttm-80) cc_final: 0.6426 (ttt-90) REVERT: B 341 ASN cc_start: 0.6988 (p0) cc_final: 0.5934 (t0) REVERT: B 367 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7324 (mm-30) REVERT: B 373 GLN cc_start: 0.8441 (tt0) cc_final: 0.8232 (tt0) REVERT: B 392 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 421 GLU cc_start: 0.8728 (tp30) cc_final: 0.8057 (tp30) REVERT: B 451 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8340 (mp) REVERT: B 516 LEU cc_start: 0.8549 (tp) cc_final: 0.8297 (tm) REVERT: C 181 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7332 (mmm-85) REVERT: C 228 ASP cc_start: 0.8352 (m-30) cc_final: 0.8031 (m-30) REVERT: C 298 SER cc_start: 0.8331 (p) cc_final: 0.8094 (t) REVERT: C 341 ASN cc_start: 0.7364 (p0) cc_final: 0.6125 (t0) REVERT: C 346 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8062 (tp30) REVERT: C 347 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7793 (mt-10) REVERT: C 392 GLU cc_start: 0.7786 (mt-10) cc_final: 0.7570 (mt-10) REVERT: C 435 MET cc_start: 0.8798 (mtp) cc_final: 0.8588 (mtm) REVERT: D 150 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6859 (mt-10) REVERT: D 186 ARG cc_start: 0.7372 (mtt-85) cc_final: 0.7123 (mtp180) REVERT: D 328 MET cc_start: 0.5341 (OUTLIER) cc_final: 0.4901 (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: 0.8218 (tp30) cc_final: 0.7584 (mm-30) REVERT: D 373 GLN cc_start: 0.8483 (tt0) cc_final: 0.8154 (tt0) REVERT: D 459 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.6921 (mp) REVERT: E 150 GLU cc_start: 0.6994 (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: 0.7345 (mtt-85) cc_final: 0.7077 (mtm-85) REVERT: E 207 ARG cc_start: 0.7562 (mmm-85) cc_final: 0.7188 (mmt-90) REVERT: E 226 LEU cc_start: 0.8569 (tp) cc_final: 0.8259 (tt) REVERT: E 328 MET cc_start: 0.5328 (OUTLIER) cc_final: 0.4965 (pmt) REVERT: E 341 ASN cc_start: 0.6948 (p0) cc_final: 0.6013 (t0) REVERT: E 392 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7661 (mt-10) REVERT: E 456 ASP cc_start: 0.8509 (p0) cc_final: 0.8281 (p0) REVERT: F 181 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7484 (mmm-85) REVERT: F 186 ARG cc_start: 0.7311 (mtt-85) cc_final: 0.7083 (mtp180) REVERT: F 213 ASP cc_start: 0.6271 (t0) cc_final: 0.5882 (t0) REVERT: F 306 MET cc_start: 0.6798 (mmp) cc_final: 0.6581 (mmp) REVERT: F 341 ASN cc_start: 0.7415 (p0) cc_final: 0.6320 (t0) REVERT: F 347 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7804 (mt-10) REVERT: F 392 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7630 (mt-10) outliers start: 63 outliers final: 12 residues processed: 371 average time/residue: 0.6511 time to fit residues: 268.1203 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 : 0.562 ------------------------------------------------------------------------------- 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 205 optimal weight: 0.9980 chunk 221 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 193 optimal weight: 1.9990 chunk 164 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.155678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.114038 restraints weight = 19001.965| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.67 r_work: 0.3276 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2770 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= 0.163 Angle : 0.570 10.108 25716 Z= 0.302 Chirality : 0.042 0.167 2934 Planarity : 0.005 0.039 3198 Dihedral : 4.871 54.306 2530 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.77 % Allowed : 8.73 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.15 (0.17), residues: 2232 helix: 1.14 (0.14), residues: 1362 sheet: 1.70 (0.39), residues: 174 loop : -0.08 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 175 TYR 0.020 0.002 TYR B 453 PHE 0.024 0.002 PHE D 183 TRP 0.021 0.002 TRP C 458 HIS 0.005 0.002 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00373 (19002) covalent geometry : angle 0.57046 (25704) SS BOND : bond 0.00072 ( 6) SS BOND : angle 0.42235 ( 12) hydrogen bonds : bond 0.03974 ( 1157) hydrogen bonds : angle 4.60621 ( 3342) *********************** 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 378 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 303 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7501 (mtt-85) cc_final: 0.7100 (mtp180) REVERT: A 194 PHE cc_start: 0.7841 (t80) cc_final: 0.7532 (t80) REVERT: A 213 ASP cc_start: 0.6192 (t0) cc_final: 0.5925 (t0) REVERT: A 328 MET cc_start: 0.5062 (OUTLIER) cc_final: 0.4539 (pmt) REVERT: A 341 ASN cc_start: 0.7071 (p0) cc_final: 0.6068 (t0) REVERT: A 347 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7518 (mt-10) REVERT: A 451 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8680 (mp) REVERT: A 459 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.6864 (mp) REVERT: A 516 LEU cc_start: 0.8410 (tp) cc_final: 0.8043 (tm) REVERT: B 179 MET cc_start: 0.8644 (mtm) cc_final: 0.8408 (mtp) REVERT: B 181 ARG cc_start: 0.7781 (mmm-85) cc_final: 0.7272 (mmt-90) REVERT: B 186 ARG cc_start: 0.7505 (mtt-85) cc_final: 0.7084 (mtp180) REVERT: B 194 PHE cc_start: 0.7872 (t80) cc_final: 0.7479 (t80) REVERT: B 207 ARG cc_start: 0.8112 (mmm-85) cc_final: 0.7560 (mmt-90) REVERT: B 300 PHE cc_start: 0.8070 (m-80) cc_final: 0.6883 (t80) REVERT: B 306 MET cc_start: 0.7072 (mmp) cc_final: 0.6664 (mmp) REVERT: B 328 MET cc_start: 0.4823 (OUTLIER) cc_final: 0.3969 (pp-130) REVERT: B 334 ARG cc_start: 0.6599 (ttm-80) cc_final: 0.6394 (ttt-90) REVERT: B 341 ASN cc_start: 0.6972 (p0) cc_final: 0.6044 (t0) REVERT: B 367 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7409 (mm-30) REVERT: B 392 GLU cc_start: 0.7835 (mt-10) cc_final: 0.7628 (mt-10) REVERT: B 421 GLU cc_start: 0.8683 (tp30) cc_final: 0.8164 (tp30) REVERT: B 425 GLN cc_start: 0.8679 (OUTLIER) cc_final: 0.8427 (mt0) REVERT: B 451 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8436 (mp) REVERT: B 459 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7181 (pp) REVERT: B 516 LEU cc_start: 0.8449 (tp) cc_final: 0.8176 (tm) REVERT: C 228 ASP cc_start: 0.8350 (m-30) cc_final: 0.8068 (m-30) REVERT: C 285 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7678 (ttpt) REVERT: C 298 SER cc_start: 0.8344 (p) cc_final: 0.8130 (t) REVERT: C 328 MET cc_start: 0.5479 (OUTLIER) cc_final: 0.3774 (pp-130) REVERT: C 341 ASN cc_start: 0.7487 (p0) cc_final: 0.6215 (t0) REVERT: C 347 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7575 (mt-10) REVERT: C 351 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7511 (mp0) REVERT: C 392 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7530 (mt-10) REVERT: C 506 PHE cc_start: 0.6840 (m-10) cc_final: 0.6140 (t80) REVERT: D 150 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6834 (mt-10) REVERT: D 186 ARG cc_start: 0.7556 (mtt-85) cc_final: 0.7170 (mtp180) REVERT: D 194 PHE cc_start: 0.7766 (t80) cc_final: 0.7366 (t80) REVERT: D 328 MET cc_start: 0.5375 (OUTLIER) cc_final: 0.4889 (pmt) REVERT: D 341 ASN cc_start: 0.6974 (p0) cc_final: 0.5933 (t0) REVERT: D 347 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7498 (mt-10) REVERT: D 349 GLU cc_start: 0.8171 (tp30) cc_final: 0.7447 (mm-30) REVERT: D 373 GLN cc_start: 0.8559 (tt0) cc_final: 0.8162 (tt0) REVERT: E 150 GLU cc_start: 0.7211 (mt-10) cc_final: 0.6400 (tp30) REVERT: E 179 MET cc_start: 0.8543 (mtm) cc_final: 0.8288 (mtp) REVERT: E 186 ARG cc_start: 0.7528 (mtt-85) cc_final: 0.7104 (mtp180) REVERT: E 194 PHE cc_start: 0.7816 (t80) cc_final: 0.7437 (t80) REVERT: E 207 ARG cc_start: 0.7735 (mmm-85) cc_final: 0.7354 (mmt-90) REVERT: E 226 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8250 (tt) REVERT: E 306 MET cc_start: 0.6952 (mmp) cc_final: 0.6669 (mmp) REVERT: E 328 MET cc_start: 0.5278 (OUTLIER) cc_final: 0.5036 (pmt) REVERT: E 341 ASN cc_start: 0.7034 (p0) cc_final: 0.6180 (t0) REVERT: E 367 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7427 (mm-30) REVERT: E 392 GLU cc_start: 0.7857 (mt-10) cc_final: 0.7652 (mt-10) REVERT: E 486 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.7161 (mm) REVERT: F 186 ARG cc_start: 0.7467 (mtt-85) cc_final: 0.7104 (mtp180) REVERT: F 192 LEU cc_start: 0.8221 (tp) cc_final: 0.7906 (tt) REVERT: F 213 ASP cc_start: 0.6219 (t0) cc_final: 0.5809 (t0) REVERT: F 306 MET cc_start: 0.6970 (mmp) cc_final: 0.6765 (mmp) REVERT: F 328 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.3888 (pp-130) REVERT: F 341 ASN cc_start: 0.7482 (p0) cc_final: 0.6313 (t0) REVERT: F 347 GLU cc_start: 0.7991 (mt-10) cc_final: 0.7789 (mt-10) REVERT: F 392 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7622 (mt-10) outliers start: 75 outliers final: 16 residues processed: 337 average time/residue: 0.5964 time to fit residues: 224.6247 Evaluate side-chains 319 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 188 LEU 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 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 459 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 285 LYS 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 446 SER Chi-restraints excluded: chain E residue 459 LEU 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 459 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 129 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 chunk 216 optimal weight: 0.6980 chunk 130 optimal weight: 10.0000 chunk 170 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 188 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN C 416 ASN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS E 416 ASN F 247 GLN F 273 GLN F 416 ASN F 512 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.154888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.113019 restraints weight = 19126.994| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 1.68 r_work: 0.3262 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2982 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= 0.161 Angle : 0.562 7.809 25716 Z= 0.296 Chirality : 0.042 0.161 2934 Planarity : 0.005 0.041 3198 Dihedral : 4.753 48.725 2530 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.46 % Allowed : 9.94 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (0.18), residues: 2232 helix: 1.48 (0.14), residues: 1362 sheet: 1.95 (0.40), residues: 174 loop : 0.10 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 175 TYR 0.019 0.002 TYR E 453 PHE 0.023 0.002 PHE F 196 TRP 0.022 0.002 TRP C 458 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00368 (19002) covalent geometry : angle 0.56173 (25704) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.43828 ( 12) hydrogen bonds : bond 0.03858 ( 1157) hydrogen bonds : angle 4.53493 ( 3342) *********************** 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 357 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 288 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7430 (mtt-85) cc_final: 0.7071 (mtp180) REVERT: A 194 PHE cc_start: 0.7825 (t80) cc_final: 0.7473 (t80) REVERT: A 213 ASP cc_start: 0.6531 (t0) cc_final: 0.6245 (t0) REVERT: A 328 MET cc_start: 0.5033 (OUTLIER) cc_final: 0.4525 (pmt) REVERT: A 341 ASN cc_start: 0.7075 (p0) cc_final: 0.6063 (t0) REVERT: A 347 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7542 (mt-10) REVERT: A 373 GLN cc_start: 0.8450 (tt0) cc_final: 0.8065 (tt0) REVERT: A 451 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8709 (mp) REVERT: B 150 GLU cc_start: 0.7088 (mt-10) cc_final: 0.6271 (mt-10) REVERT: B 179 MET cc_start: 0.8762 (mtm) cc_final: 0.8562 (mtp) REVERT: B 181 ARG cc_start: 0.7806 (mmm-85) cc_final: 0.7337 (mtt-85) REVERT: B 186 ARG cc_start: 0.7595 (mtt-85) cc_final: 0.7097 (mtp180) REVERT: B 194 PHE cc_start: 0.7906 (t80) cc_final: 0.7516 (t80) REVERT: B 300 PHE cc_start: 0.8079 (m-80) cc_final: 0.6873 (t80) REVERT: B 328 MET cc_start: 0.4841 (OUTLIER) cc_final: 0.3981 (pp-130) REVERT: B 334 ARG cc_start: 0.6605 (ttm-80) cc_final: 0.6400 (ttt-90) REVERT: B 341 ASN cc_start: 0.7001 (p0) cc_final: 0.6115 (t0) REVERT: B 451 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8489 (mp) REVERT: B 459 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7111 (pp) REVERT: B 486 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7232 (mm) REVERT: B 504 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7631 (tp30) REVERT: C 228 ASP cc_start: 0.8367 (m-30) cc_final: 0.8118 (m-30) REVERT: C 298 SER cc_start: 0.8362 (p) cc_final: 0.8136 (t) REVERT: C 328 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.3739 (pp-130) REVERT: C 341 ASN cc_start: 0.7478 (p0) cc_final: 0.6199 (t0) REVERT: C 347 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 351 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: C 392 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7469 (mt-10) REVERT: C 506 PHE cc_start: 0.7054 (m-10) cc_final: 0.6299 (t80) REVERT: D 176 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7343 (mmm160) REVERT: D 186 ARG cc_start: 0.7429 (mtt-85) cc_final: 0.7114 (mtp180) REVERT: D 194 PHE cc_start: 0.7809 (t80) cc_final: 0.7379 (t80) REVERT: D 341 ASN cc_start: 0.7104 (p0) cc_final: 0.6028 (t0) REVERT: D 347 GLU cc_start: 0.7790 (mt-10) cc_final: 0.7508 (mt-10) REVERT: D 349 GLU cc_start: 0.8169 (tp30) cc_final: 0.7407 (mm-30) REVERT: D 451 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8701 (mp) REVERT: E 150 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6518 (mt-10) REVERT: E 186 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.7150 (mtp180) REVERT: E 194 PHE cc_start: 0.7900 (t80) cc_final: 0.7451 (t80) REVERT: E 306 MET cc_start: 0.7001 (mmp) cc_final: 0.6678 (mmp) REVERT: E 328 MET cc_start: 0.5287 (OUTLIER) cc_final: 0.4984 (pmt) REVERT: E 341 ASN cc_start: 0.7030 (p0) cc_final: 0.6197 (t0) REVERT: F 186 ARG cc_start: 0.7481 (mtt-85) cc_final: 0.7070 (mtp180) REVERT: F 192 LEU cc_start: 0.8114 (tp) cc_final: 0.7817 (tt) REVERT: F 213 ASP cc_start: 0.6403 (t0) cc_final: 0.5970 (t0) REVERT: F 328 MET cc_start: 0.5529 (OUTLIER) cc_final: 0.3781 (pp-130) REVERT: F 341 ASN cc_start: 0.7489 (p0) cc_final: 0.6259 (t0) REVERT: F 392 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7561 (mt-10) outliers start: 69 outliers final: 18 residues processed: 322 average time/residue: 0.5997 time to fit residues: 215.5149 Evaluate side-chains 309 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 278 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 451 LEU 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 176 ARG 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 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 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 151 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 134 optimal weight: 0.8980 chunk 161 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN B 462 GLN B 512 HIS C 247 GLN D 253 GLN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 416 ASN F 416 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.113082 restraints weight = 19036.888| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.68 r_work: 0.3265 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3095 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= 0.151 Angle : 0.552 8.201 25716 Z= 0.290 Chirality : 0.041 0.157 2934 Planarity : 0.005 0.049 3198 Dihedral : 4.698 59.777 2530 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.56 % Allowed : 10.94 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.78 (0.18), residues: 2232 helix: 1.63 (0.14), residues: 1368 sheet: 2.06 (0.40), residues: 174 loop : 0.15 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 175 TYR 0.017 0.002 TYR B 453 PHE 0.029 0.002 PHE F 196 TRP 0.022 0.002 TRP C 458 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00344 (19002) covalent geometry : angle 0.55246 (25704) SS BOND : bond 0.00040 ( 6) SS BOND : angle 0.48156 ( 12) hydrogen bonds : bond 0.03754 ( 1157) hydrogen bonds : angle 4.47075 ( 3342) *********************** 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 359 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 288 time to evaluate : 0.723 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7371 (mtt-85) cc_final: 0.7029 (mtp180) REVERT: A 194 PHE cc_start: 0.7869 (t80) cc_final: 0.7529 (t80) REVERT: A 213 ASP cc_start: 0.6454 (t0) cc_final: 0.6113 (t0) REVERT: A 256 ARG cc_start: 0.9013 (OUTLIER) cc_final: 0.8690 (mtm-85) REVERT: A 328 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4404 (pp-130) REVERT: A 341 ASN cc_start: 0.6977 (p0) cc_final: 0.6052 (t0) REVERT: A 347 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7525 (mt-10) REVERT: A 373 GLN cc_start: 0.8445 (tt0) cc_final: 0.8073 (tt0) REVERT: A 451 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8707 (mp) REVERT: A 504 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7560 (tm-30) REVERT: B 150 GLU cc_start: 0.7047 (mt-10) cc_final: 0.6281 (mt-10) REVERT: B 181 ARG cc_start: 0.7810 (mmm-85) cc_final: 0.7342 (mtt-85) REVERT: B 186 ARG cc_start: 0.7592 (mtt-85) cc_final: 0.7062 (mtp180) REVERT: B 194 PHE cc_start: 0.7953 (t80) cc_final: 0.7528 (t80) REVERT: B 300 PHE cc_start: 0.8093 (m-80) cc_final: 0.6875 (t80) REVERT: B 328 MET cc_start: 0.4901 (OUTLIER) cc_final: 0.4019 (pp-130) REVERT: B 341 ASN cc_start: 0.7083 (p0) cc_final: 0.6186 (t0) REVERT: B 451 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8497 (mp) REVERT: B 459 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7175 (pp) REVERT: B 504 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: C 228 ASP cc_start: 0.8359 (m-30) cc_final: 0.8123 (m-30) REVERT: C 285 LYS cc_start: 0.7945 (OUTLIER) cc_final: 0.7695 (ttpt) REVERT: C 298 SER cc_start: 0.8250 (p) cc_final: 0.8044 (t) REVERT: C 328 MET cc_start: 0.5443 (OUTLIER) cc_final: 0.3742 (pp-130) REVERT: C 341 ASN cc_start: 0.7477 (p0) cc_final: 0.6242 (t0) REVERT: C 347 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7516 (mt-10) REVERT: C 351 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: C 451 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8494 (mp) REVERT: C 506 PHE cc_start: 0.7239 (m-10) cc_final: 0.6546 (t80) REVERT: D 176 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.7389 (mmm160) REVERT: D 181 ARG cc_start: 0.7954 (mmm-85) cc_final: 0.7396 (mmt-90) REVERT: D 186 ARG cc_start: 0.7402 (mtt-85) cc_final: 0.7069 (mtp180) REVERT: D 194 PHE cc_start: 0.7850 (t80) cc_final: 0.7449 (t80) REVERT: D 256 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8708 (mtm-85) REVERT: D 306 MET cc_start: 0.6565 (mmm) cc_final: 0.6336 (mmp) REVERT: D 328 MET cc_start: 0.5496 (OUTLIER) cc_final: 0.4953 (pp-130) REVERT: D 341 ASN cc_start: 0.7033 (p0) cc_final: 0.6213 (t0) REVERT: D 347 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7518 (mt-10) REVERT: D 349 GLU cc_start: 0.8155 (tp30) cc_final: 0.7395 (mm-30) REVERT: D 373 GLN cc_start: 0.8514 (tt0) cc_final: 0.8109 (tt0) REVERT: D 421 GLU cc_start: 0.8600 (tp30) cc_final: 0.8378 (tp30) REVERT: D 451 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8710 (mp) REVERT: E 150 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6699 (mt-10) REVERT: E 186 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.7120 (mtp180) REVERT: E 194 PHE cc_start: 0.7883 (t80) cc_final: 0.7472 (t80) REVERT: E 207 ARG cc_start: 0.7961 (mmm-85) cc_final: 0.7474 (mmt-90) REVERT: E 306 MET cc_start: 0.7064 (mmp) cc_final: 0.6766 (mmp) REVERT: E 328 MET cc_start: 0.5215 (OUTLIER) cc_final: 0.4919 (pmt) REVERT: E 341 ASN cc_start: 0.6939 (p0) cc_final: 0.6209 (t0) REVERT: E 451 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8640 (mp) REVERT: F 150 GLU cc_start: 0.6073 (tp30) cc_final: 0.5568 (mt-10) REVERT: F 186 ARG cc_start: 0.7460 (mtt-85) cc_final: 0.7088 (mtp180) REVERT: F 192 LEU cc_start: 0.8130 (tp) cc_final: 0.7859 (tt) REVERT: F 213 ASP cc_start: 0.6405 (t0) cc_final: 0.5923 (t0) REVERT: F 306 MET cc_start: 0.6796 (mmp) cc_final: 0.6267 (mtm) REVERT: F 328 MET cc_start: 0.5543 (OUTLIER) cc_final: 0.3780 (pp-130) REVERT: F 341 ASN cc_start: 0.7482 (p0) cc_final: 0.6283 (t0) REVERT: F 392 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7527 (mt-10) outliers start: 71 outliers final: 18 residues processed: 328 average time/residue: 0.6569 time to fit residues: 239.4085 Evaluate side-chains 313 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 276 time to evaluate : 0.745 ------------------------------------------------------------------------------- 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 459 LEU Chi-restraints excluded: chain A residue 504 GLU 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 285 LYS 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 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 446 SER Chi-restraints excluded: chain E residue 451 LEU 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 459 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 50 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 199 optimal weight: 0.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 512 HIS B 215 ASN B 414 GLN B 416 ASN D 215 ASN ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 HIS E 406 GLN E 416 ASN E 512 HIS F 215 ASN F 247 GLN F 414 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.153307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.110957 restraints weight = 19010.285| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.67 r_work: 0.3236 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19008 Z= 0.187 Angle : 0.586 8.048 25716 Z= 0.309 Chirality : 0.043 0.153 2934 Planarity : 0.005 0.051 3198 Dihedral : 4.773 52.107 2530 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.71 % Allowed : 11.70 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.18), residues: 2232 helix: 1.63 (0.14), residues: 1368 sheet: 2.19 (0.41), residues: 174 loop : 0.22 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG F 175 TYR 0.020 0.002 TYR E 453 PHE 0.029 0.002 PHE F 196 TRP 0.027 0.003 TRP C 458 HIS 0.006 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00433 (19002) covalent geometry : angle 0.58580 (25704) SS BOND : bond 0.00036 ( 6) SS BOND : angle 0.44504 ( 12) hydrogen bonds : bond 0.04075 ( 1157) hydrogen bonds : angle 4.53710 ( 3342) *********************** 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 358 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 284 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 186 ARG cc_start: 0.7410 (mtt-85) cc_final: 0.7032 (mtp180) REVERT: A 194 PHE cc_start: 0.7945 (t80) cc_final: 0.7575 (t80) REVERT: A 213 ASP cc_start: 0.6453 (t0) cc_final: 0.6174 (t0) REVERT: A 256 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8702 (mtm-85) REVERT: A 306 MET cc_start: 0.6742 (mmm) cc_final: 0.6471 (mmp) REVERT: A 328 MET cc_start: 0.5269 (OUTLIER) cc_final: 0.4532 (pp-130) REVERT: A 347 GLU cc_start: 0.7751 (mt-10) cc_final: 0.7508 (mt-10) REVERT: A 373 GLN cc_start: 0.8528 (tt0) cc_final: 0.8124 (tt0) REVERT: A 451 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8733 (mp) REVERT: A 504 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7643 (tm-30) REVERT: A 516 LEU cc_start: 0.8396 (tp) cc_final: 0.8128 (tm) REVERT: B 150 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6079 (mt-10) REVERT: B 181 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7384 (mtt-85) REVERT: B 186 ARG cc_start: 0.7644 (mtt-85) cc_final: 0.7120 (mtp180) REVERT: B 194 PHE cc_start: 0.7980 (t80) cc_final: 0.7536 (t80) REVERT: B 215 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6732 (t0) REVERT: B 300 PHE cc_start: 0.8086 (m-80) cc_final: 0.6875 (t80) REVERT: B 328 MET cc_start: 0.4949 (OUTLIER) cc_final: 0.4065 (pp-130) REVERT: B 451 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 459 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7353 (pp) REVERT: B 504 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7715 (tp30) REVERT: C 150 GLU cc_start: 0.6093 (tp30) cc_final: 0.5678 (pt0) REVERT: C 228 ASP cc_start: 0.8388 (m-30) cc_final: 0.8161 (m-30) REVERT: C 328 MET cc_start: 0.5478 (OUTLIER) cc_final: 0.3777 (pp-130) REVERT: C 347 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7542 (mt-10) REVERT: C 351 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: C 451 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8565 (mp) REVERT: C 506 PHE cc_start: 0.7376 (m-10) cc_final: 0.6712 (t80) REVERT: D 181 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7461 (mmt-90) REVERT: D 186 ARG cc_start: 0.7426 (mtt-85) cc_final: 0.7074 (mtp180) REVERT: D 194 PHE cc_start: 0.7934 (t80) cc_final: 0.7521 (t80) REVERT: D 328 MET cc_start: 0.5566 (OUTLIER) cc_final: 0.5082 (pp-130) REVERT: D 341 ASN cc_start: 0.7137 (p0) cc_final: 0.6168 (t0) REVERT: D 347 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7557 (mt-10) REVERT: D 373 GLN cc_start: 0.8553 (tt0) cc_final: 0.8160 (tt0) REVERT: D 421 GLU cc_start: 0.8564 (tp30) cc_final: 0.8322 (tp30) REVERT: D 451 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8718 (mp) REVERT: E 150 GLU cc_start: 0.7213 (mt-10) cc_final: 0.6606 (mt-10) REVERT: E 156 MET cc_start: 0.8864 (ttt) cc_final: 0.8616 (ttt) REVERT: E 186 ARG cc_start: 0.7665 (mtt-85) cc_final: 0.7142 (mtp180) REVERT: E 194 PHE cc_start: 0.7947 (t80) cc_final: 0.7500 (t80) REVERT: E 306 MET cc_start: 0.6996 (mmp) cc_final: 0.6706 (mmp) REVERT: E 328 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4058 (pp-130) REVERT: E 341 ASN cc_start: 0.6941 (p0) cc_final: 0.5952 (t0) REVERT: E 451 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8617 (mp) REVERT: F 186 ARG cc_start: 0.7520 (mtt-85) cc_final: 0.7142 (mtp180) REVERT: F 192 LEU cc_start: 0.8154 (tp) cc_final: 0.7869 (tt) REVERT: F 213 ASP cc_start: 0.6358 (t0) cc_final: 0.6153 (t0) REVERT: F 306 MET cc_start: 0.6811 (mmp) cc_final: 0.6225 (mtm) REVERT: F 328 MET cc_start: 0.5560 (OUTLIER) cc_final: 0.3821 (pp-130) REVERT: F 351 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7202 (mp0) REVERT: F 392 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7693 (mt-10) outliers start: 74 outliers final: 22 residues processed: 326 average time/residue: 0.5981 time to fit residues: 218.0906 Evaluate side-chains 313 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 273 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 504 GLU 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 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 451 LEU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 78 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 133 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 221 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 87 optimal weight: 0.0570 overall best weight: 0.6702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN C 215 ASN C 247 GLN D 273 GLN E 215 ASN E 305 HIS E 416 ASN F 493 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.155121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.113442 restraints weight = 19175.505| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.67 r_work: 0.3269 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.3267 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= 0.138 Angle : 0.545 10.157 25716 Z= 0.283 Chirality : 0.041 0.160 2934 Planarity : 0.005 0.053 3198 Dihedral : 4.533 45.378 2530 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.11 % Allowed : 12.45 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.18), residues: 2232 helix: 1.70 (0.14), residues: 1374 sheet: 2.23 (0.39), residues: 180 loop : 0.35 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 175 TYR 0.018 0.002 TYR B 216 PHE 0.031 0.002 PHE F 196 TRP 0.023 0.002 TRP C 458 HIS 0.005 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00311 (19002) covalent geometry : angle 0.54546 (25704) SS BOND : bond 0.00048 ( 6) SS BOND : angle 0.51351 ( 12) hydrogen bonds : bond 0.03604 ( 1157) hydrogen bonds : angle 4.40785 ( 3342) *********************** 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 346 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 284 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 181 ARG cc_start: 0.7919 (mmm-85) cc_final: 0.7359 (mtt-85) REVERT: A 186 ARG cc_start: 0.7352 (mtt-85) cc_final: 0.7061 (mtp180) REVERT: A 194 PHE cc_start: 0.7881 (t80) cc_final: 0.7513 (t80) REVERT: A 213 ASP cc_start: 0.6360 (t0) cc_final: 0.6057 (t0) REVERT: A 328 MET cc_start: 0.5262 (OUTLIER) cc_final: 0.4568 (pp-130) REVERT: A 341 ASN cc_start: 0.7004 (p0) cc_final: 0.6115 (t0) REVERT: A 347 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 373 GLN cc_start: 0.8454 (tt0) cc_final: 0.8050 (tt0) REVERT: A 451 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 504 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7604 (tm-30) REVERT: A 516 LEU cc_start: 0.8395 (tp) cc_final: 0.8065 (tm) REVERT: B 150 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6128 (mt-10) REVERT: B 181 ARG cc_start: 0.7821 (mmm-85) cc_final: 0.7363 (mtt-85) REVERT: B 186 ARG cc_start: 0.7631 (mtt-85) cc_final: 0.7186 (mtp180) REVERT: B 194 PHE cc_start: 0.7960 (t80) cc_final: 0.7616 (t80) REVERT: B 300 PHE cc_start: 0.8062 (m-80) cc_final: 0.6836 (t80) REVERT: B 328 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4005 (pp-130) REVERT: B 341 ASN cc_start: 0.6958 (p0) cc_final: 0.6048 (t0) REVERT: C 131 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.6340 (pt) REVERT: C 215 ASN cc_start: 0.6872 (OUTLIER) cc_final: 0.6658 (t0) REVERT: C 228 ASP cc_start: 0.8398 (m-30) cc_final: 0.8180 (m-30) REVERT: C 306 MET cc_start: 0.6580 (mmp) cc_final: 0.5697 (mtm) REVERT: C 328 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.3702 (pp-130) REVERT: C 341 ASN cc_start: 0.7322 (p0) cc_final: 0.6321 (t0) REVERT: C 347 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7460 (mt-10) REVERT: C 351 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: C 506 PHE cc_start: 0.7387 (m-10) cc_final: 0.6684 (t80) REVERT: D 176 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7266 (mmm160) REVERT: D 181 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7365 (mmt-90) REVERT: D 186 ARG cc_start: 0.7470 (mtt-85) cc_final: 0.7117 (mtp180) REVERT: D 194 PHE cc_start: 0.7857 (t80) cc_final: 0.7481 (t80) REVERT: D 256 ARG cc_start: 0.9227 (OUTLIER) cc_final: 0.8924 (mtm-85) REVERT: D 306 MET cc_start: 0.7023 (mmp) cc_final: 0.6685 (mmp) REVERT: D 328 MET cc_start: 0.5471 (OUTLIER) cc_final: 0.5013 (pp-130) REVERT: D 341 ASN cc_start: 0.6902 (p0) cc_final: 0.6353 (t0) REVERT: D 347 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7583 (mt-10) REVERT: D 373 GLN cc_start: 0.8499 (tt0) cc_final: 0.8109 (tt0) REVERT: D 421 GLU cc_start: 0.8584 (tp30) cc_final: 0.8340 (tp30) REVERT: D 451 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8712 (mp) REVERT: E 150 GLU cc_start: 0.7214 (mt-10) cc_final: 0.6625 (mt-10) REVERT: E 156 MET cc_start: 0.8788 (ttt) cc_final: 0.8560 (ttt) REVERT: E 186 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7209 (mtp180) REVERT: E 194 PHE cc_start: 0.7938 (t80) cc_final: 0.7476 (t80) REVERT: E 306 MET cc_start: 0.6991 (mmp) cc_final: 0.6707 (mmp) REVERT: E 328 MET cc_start: 0.5133 (OUTLIER) cc_final: 0.4044 (pp-130) REVERT: E 341 ASN cc_start: 0.6923 (p0) cc_final: 0.6196 (t0) REVERT: E 451 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8543 (mp) REVERT: E 504 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7632 (tp30) REVERT: F 186 ARG cc_start: 0.7477 (mtt-85) cc_final: 0.7122 (mtp180) REVERT: F 213 ASP cc_start: 0.6413 (t0) cc_final: 0.6029 (t0) REVERT: F 306 MET cc_start: 0.6872 (mmp) cc_final: 0.6326 (mtm) REVERT: F 328 MET cc_start: 0.5752 (OUTLIER) cc_final: 0.3970 (pp-130) REVERT: F 341 ASN cc_start: 0.7333 (p0) cc_final: 0.6329 (t0) REVERT: F 346 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7683 (mt-10) REVERT: F 351 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7232 (mp0) REVERT: F 392 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7514 (mt-10) REVERT: F 513 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7658 (mmtm) outliers start: 62 outliers final: 20 residues processed: 318 average time/residue: 0.5933 time to fit residues: 211.5203 Evaluate side-chains 316 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 279 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 A residue 504 GLU 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 457 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 131 ILE 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 114 optimal weight: 4.9990 chunk 142 optimal weight: 0.0060 chunk 197 optimal weight: 0.7980 chunk 144 optimal weight: 0.7980 chunk 206 optimal weight: 0.6980 chunk 109 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 0.5980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN C 247 GLN E 416 ASN F 247 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.155921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.114145 restraints weight = 19072.579| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.67 r_work: 0.3279 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.3328 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= 0.129 Angle : 0.538 9.839 25716 Z= 0.278 Chirality : 0.040 0.162 2934 Planarity : 0.005 0.057 3198 Dihedral : 4.409 37.747 2530 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.06 % Allowed : 12.65 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.18), residues: 2232 helix: 1.76 (0.14), residues: 1380 sheet: 2.20 (0.39), residues: 180 loop : 0.32 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 175 TYR 0.015 0.002 TYR A 453 PHE 0.031 0.002 PHE F 196 TRP 0.021 0.002 TRP C 458 HIS 0.007 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00289 (19002) covalent geometry : angle 0.53839 (25704) SS BOND : bond 0.00067 ( 6) SS BOND : angle 0.56196 ( 12) hydrogen bonds : bond 0.03501 ( 1157) hydrogen bonds : angle 4.34158 ( 3342) *********************** 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 340 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 279 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6942 (ttp-170) REVERT: A 181 ARG cc_start: 0.7903 (mmm-85) cc_final: 0.7372 (mtt-85) REVERT: A 186 ARG cc_start: 0.7391 (mtt-85) cc_final: 0.7080 (mtp180) REVERT: A 194 PHE cc_start: 0.7876 (t80) cc_final: 0.7545 (t80) REVERT: A 213 ASP cc_start: 0.6363 (t0) cc_final: 0.6063 (t0) REVERT: A 256 ARG cc_start: 0.9220 (OUTLIER) cc_final: 0.8734 (ttp-170) REVERT: A 328 MET cc_start: 0.5213 (OUTLIER) cc_final: 0.4562 (pp-130) REVERT: A 341 ASN cc_start: 0.7036 (p0) cc_final: 0.6115 (t0) REVERT: A 347 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7596 (mt-10) REVERT: A 373 GLN cc_start: 0.8448 (tt0) cc_final: 0.8031 (tt0) REVERT: A 451 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8705 (mp) REVERT: A 516 LEU cc_start: 0.8420 (tp) cc_final: 0.8115 (tm) REVERT: B 150 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6145 (mt-10) REVERT: B 181 ARG cc_start: 0.7824 (mmm-85) cc_final: 0.7340 (mtt-85) REVERT: B 186 ARG cc_start: 0.7627 (mtt-85) cc_final: 0.7152 (mtp180) REVERT: B 194 PHE cc_start: 0.7957 (t80) cc_final: 0.7640 (t80) REVERT: B 300 PHE cc_start: 0.8029 (m-80) cc_final: 0.6764 (t80) REVERT: B 328 MET cc_start: 0.4911 (OUTLIER) cc_final: 0.4038 (pp-130) REVERT: B 341 ASN cc_start: 0.6835 (p0) cc_final: 0.6188 (t0) REVERT: C 131 ILE cc_start: 0.7145 (OUTLIER) cc_final: 0.6195 (pt) REVERT: C 228 ASP cc_start: 0.8402 (m-30) cc_final: 0.8187 (m-30) REVERT: C 306 MET cc_start: 0.6902 (mmp) cc_final: 0.6148 (mtm) REVERT: C 328 MET cc_start: 0.5459 (OUTLIER) cc_final: 0.3685 (pp-130) REVERT: C 341 ASN cc_start: 0.7551 (p0) cc_final: 0.6405 (t0) REVERT: C 347 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 351 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: C 506 PHE cc_start: 0.7464 (m-10) cc_final: 0.6753 (t80) REVERT: D 176 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7298 (mmm160) REVERT: D 181 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7334 (mmt-90) REVERT: D 186 ARG cc_start: 0.7415 (mtt-85) cc_final: 0.7110 (mtp180) REVERT: D 194 PHE cc_start: 0.7886 (t80) cc_final: 0.7517 (t80) REVERT: D 306 MET cc_start: 0.7076 (mmp) cc_final: 0.6717 (mmp) REVERT: D 328 MET cc_start: 0.5466 (OUTLIER) cc_final: 0.5003 (pp-130) REVERT: D 347 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7597 (mt-10) REVERT: D 373 GLN cc_start: 0.8490 (tt0) cc_final: 0.8114 (tt0) REVERT: D 421 GLU cc_start: 0.8588 (tp30) cc_final: 0.8367 (tp30) REVERT: D 451 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8708 (mp) REVERT: E 150 GLU cc_start: 0.7209 (mt-10) cc_final: 0.6747 (mt-10) REVERT: E 156 MET cc_start: 0.8817 (ttt) cc_final: 0.8589 (ttt) REVERT: E 186 ARG cc_start: 0.7678 (mtt-85) cc_final: 0.7199 (mtp180) REVERT: E 194 PHE cc_start: 0.7920 (t80) cc_final: 0.7509 (t80) REVERT: E 306 MET cc_start: 0.7157 (mmp) cc_final: 0.6950 (mmp) REVERT: E 328 MET cc_start: 0.5156 (OUTLIER) cc_final: 0.4069 (pp-130) REVERT: E 341 ASN cc_start: 0.7031 (p0) cc_final: 0.6203 (t0) REVERT: E 451 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8543 (mp) REVERT: E 504 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7665 (tp30) REVERT: F 131 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6240 (pt) REVERT: F 150 GLU cc_start: 0.6083 (tp30) cc_final: 0.5597 (mt-10) REVERT: F 186 ARG cc_start: 0.7484 (mtt-85) cc_final: 0.7099 (mtp180) REVERT: F 192 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.8014 (tt) REVERT: F 213 ASP cc_start: 0.6382 (t0) cc_final: 0.5958 (t0) REVERT: F 306 MET cc_start: 0.6865 (mmp) cc_final: 0.6377 (mtm) REVERT: F 328 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.3961 (pp-130) REVERT: F 341 ASN cc_start: 0.7550 (p0) cc_final: 0.6409 (t0) REVERT: F 346 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7682 (mt-10) REVERT: F 392 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7520 (mt-10) REVERT: F 513 LYS cc_start: 0.7924 (mmmt) cc_final: 0.7594 (mmtm) outliers start: 61 outliers final: 19 residues processed: 309 average time/residue: 0.6068 time to fit residues: 209.2641 Evaluate side-chains 308 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 272 time to evaluate : 0.625 ------------------------------------------------------------------------------- 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 256 ARG 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 457 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 131 ILE 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 459 LEU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 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 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 131 ILE Chi-restraints excluded: chain F residue 190 LEU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 328 MET 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 185 optimal weight: 20.0000 chunk 158 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 205 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 122 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 215 ASN C 512 HIS C 519 GLN D 253 GLN E 406 GLN E 416 ASN F 247 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.152938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.110863 restraints weight = 19015.585| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.66 r_work: 0.3237 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3368 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= 0.181 Angle : 0.592 12.909 25716 Z= 0.308 Chirality : 0.043 0.165 2934 Planarity : 0.005 0.064 3198 Dihedral : 4.604 36.910 2530 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.91 % Allowed : 13.10 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2232 helix: 1.74 (0.14), residues: 1368 sheet: 2.18 (0.39), residues: 180 loop : 0.37 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 175 TYR 0.019 0.002 TYR B 453 PHE 0.030 0.002 PHE F 196 TRP 0.032 0.003 TRP C 458 HIS 0.008 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00420 (19002) covalent geometry : angle 0.59248 (25704) SS BOND : bond 0.00072 ( 6) SS BOND : angle 0.46326 ( 12) hydrogen bonds : bond 0.04006 ( 1157) hydrogen bonds : angle 4.48364 ( 3342) *********************** 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 323 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 265 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7219 (mtp180) REVERT: A 186 ARG cc_start: 0.7420 (mtt-85) cc_final: 0.7084 (mtp180) REVERT: A 213 ASP cc_start: 0.6410 (t0) cc_final: 0.6124 (t0) REVERT: A 328 MET cc_start: 0.5300 (OUTLIER) cc_final: 0.4652 (pp-130) REVERT: A 373 GLN cc_start: 0.8537 (tt0) cc_final: 0.8130 (tt0) REVERT: A 451 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8732 (mp) REVERT: A 516 LEU cc_start: 0.8424 (tp) cc_final: 0.8059 (tm) REVERT: B 150 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6109 (mt-10) REVERT: B 181 ARG cc_start: 0.7869 (mmm-85) cc_final: 0.7355 (mtt-85) REVERT: B 194 PHE cc_start: 0.7967 (t80) cc_final: 0.7544 (t80) REVERT: B 215 ASN cc_start: 0.7070 (OUTLIER) cc_final: 0.6777 (t0) REVERT: B 300 PHE cc_start: 0.8035 (m-80) cc_final: 0.6766 (t80) REVERT: B 328 MET cc_start: 0.5009 (OUTLIER) cc_final: 0.4102 (pp-130) REVERT: B 341 ASN cc_start: 0.6965 (p0) cc_final: 0.5966 (t0) REVERT: B 451 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8621 (mp) REVERT: C 131 ILE cc_start: 0.7161 (OUTLIER) cc_final: 0.6196 (pt) REVERT: C 215 ASN cc_start: 0.6868 (OUTLIER) cc_final: 0.6646 (t0) REVERT: C 228 ASP cc_start: 0.8414 (m-30) cc_final: 0.8185 (m-30) REVERT: C 306 MET cc_start: 0.6999 (mmp) cc_final: 0.6318 (mtm) REVERT: C 328 MET cc_start: 0.5481 (OUTLIER) cc_final: 0.3762 (pp-130) REVERT: C 347 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7351 (mt-10) REVERT: C 351 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: C 506 PHE cc_start: 0.7556 (m-10) cc_final: 0.6959 (t80) REVERT: D 176 ARG cc_start: 0.7601 (OUTLIER) cc_final: 0.7341 (mmm160) REVERT: D 186 ARG cc_start: 0.7436 (mtt-85) cc_final: 0.7121 (mtp180) REVERT: D 306 MET cc_start: 0.7112 (mmp) cc_final: 0.6743 (mmp) REVERT: D 328 MET cc_start: 0.5511 (OUTLIER) cc_final: 0.5104 (pp-130) REVERT: D 373 GLN cc_start: 0.8535 (tt0) cc_final: 0.8112 (tt0) REVERT: D 421 GLU cc_start: 0.8580 (tp30) cc_final: 0.8351 (tp30) REVERT: D 451 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8713 (mp) REVERT: E 150 GLU cc_start: 0.7183 (mt-10) cc_final: 0.6592 (mt-10) REVERT: E 156 MET cc_start: 0.8807 (ttt) cc_final: 0.8561 (ttt) REVERT: E 194 PHE cc_start: 0.7941 (t80) cc_final: 0.7487 (t80) REVERT: E 306 MET cc_start: 0.7089 (mmp) cc_final: 0.6827 (mmp) REVERT: E 328 MET cc_start: 0.5187 (OUTLIER) cc_final: 0.4097 (pp-130) REVERT: E 341 ASN cc_start: 0.6924 (p0) cc_final: 0.6052 (t0) REVERT: E 451 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8584 (mp) REVERT: E 504 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7736 (tp30) REVERT: F 192 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7996 (tp) REVERT: F 213 ASP cc_start: 0.6399 (t0) cc_final: 0.5964 (t0) REVERT: F 306 MET cc_start: 0.6922 (mmp) cc_final: 0.6350 (mtm) REVERT: F 328 MET cc_start: 0.5714 (OUTLIER) cc_final: 0.3998 (pp-130) REVERT: F 351 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7228 (mp0) outliers start: 58 outliers final: 21 residues processed: 293 average time/residue: 0.5986 time to fit residues: 196.3792 Evaluate side-chains 302 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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 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 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 451 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 131 ILE 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 459 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 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 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 192 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 110 optimal weight: 3.9990 chunk 79 optimal weight: 0.0770 chunk 149 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 136 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 chunk 157 optimal weight: 0.8980 chunk 114 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 ASN C 247 GLN C 493 ASN D 253 GLN E 416 ASN F 247 GLN F 493 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.153403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.111076 restraints weight = 18929.191| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.67 r_work: 0.3241 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 19008 Z= 0.188 Angle : 0.885 59.200 25716 Z= 0.514 Chirality : 0.043 0.424 2934 Planarity : 0.005 0.058 3198 Dihedral : 4.601 36.799 2530 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.36 % Allowed : 13.76 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2232 helix: 1.74 (0.14), residues: 1368 sheet: 2.17 (0.39), residues: 180 loop : 0.37 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 175 TYR 0.018 0.002 TYR B 453 PHE 0.029 0.002 PHE F 196 TRP 0.028 0.002 TRP C 458 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00409 (19002) covalent geometry : angle 0.88552 (25704) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.48600 ( 12) hydrogen bonds : bond 0.03967 ( 1157) hydrogen bonds : angle 4.48212 ( 3342) ********************** 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 310 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ARG cc_start: 0.7506 (OUTLIER) cc_final: 0.7216 (mtp180) REVERT: A 186 ARG cc_start: 0.7400 (mtt-85) cc_final: 0.7071 (mtp180) REVERT: A 213 ASP cc_start: 0.6405 (t0) cc_final: 0.6118 (t0) REVERT: A 328 MET cc_start: 0.5303 (OUTLIER) cc_final: 0.4654 (pp-130) REVERT: A 373 GLN cc_start: 0.8533 (tt0) cc_final: 0.8127 (tt0) REVERT: A 451 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8729 (mp) REVERT: A 516 LEU cc_start: 0.8412 (tp) cc_final: 0.8093 (tm) REVERT: B 150 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6110 (mt-10) REVERT: B 181 ARG cc_start: 0.7866 (mmm-85) cc_final: 0.7349 (mtt-85) REVERT: B 194 PHE cc_start: 0.7961 (t80) cc_final: 0.7540 (t80) REVERT: B 300 PHE cc_start: 0.8033 (m-80) cc_final: 0.6751 (t80) REVERT: B 328 MET cc_start: 0.5008 (OUTLIER) cc_final: 0.4101 (pp-130) REVERT: B 341 ASN cc_start: 0.6956 (p0) cc_final: 0.5963 (t0) REVERT: B 451 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 131 ILE cc_start: 0.7148 (OUTLIER) cc_final: 0.6188 (pt) REVERT: C 228 ASP cc_start: 0.8410 (m-30) cc_final: 0.8163 (m-30) REVERT: C 306 MET cc_start: 0.7004 (mmp) cc_final: 0.6326 (mtm) REVERT: C 328 MET cc_start: 0.5486 (OUTLIER) cc_final: 0.3761 (pp-130) REVERT: C 347 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7338 (mt-10) REVERT: C 351 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: C 506 PHE cc_start: 0.7553 (m-10) cc_final: 0.6951 (t80) REVERT: D 176 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.7444 (mmm160) REVERT: D 186 ARG cc_start: 0.7421 (mtt-85) cc_final: 0.7107 (mtp180) REVERT: D 306 MET cc_start: 0.7112 (mmp) cc_final: 0.6751 (mmp) REVERT: D 328 MET cc_start: 0.5516 (OUTLIER) cc_final: 0.5107 (pp-130) REVERT: D 373 GLN cc_start: 0.8532 (tt0) cc_final: 0.8110 (tt0) REVERT: D 421 GLU cc_start: 0.8573 (tp30) cc_final: 0.8359 (tp30) REVERT: D 451 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8715 (mp) REVERT: E 150 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6604 (mt-10) REVERT: E 156 MET cc_start: 0.8796 (ttt) cc_final: 0.8567 (ttt) REVERT: E 194 PHE cc_start: 0.7937 (t80) cc_final: 0.7483 (t80) REVERT: E 306 MET cc_start: 0.7084 (mmp) cc_final: 0.6822 (mmp) REVERT: E 328 MET cc_start: 0.5194 (OUTLIER) cc_final: 0.4102 (pp-130) REVERT: E 341 ASN cc_start: 0.6913 (p0) cc_final: 0.6047 (t0) REVERT: E 451 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8585 (mp) REVERT: E 504 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7738 (tp30) REVERT: F 192 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7999 (tp) REVERT: F 213 ASP cc_start: 0.6400 (t0) cc_final: 0.5967 (t0) REVERT: F 306 MET cc_start: 0.6921 (mmp) cc_final: 0.6349 (mtm) REVERT: F 328 MET cc_start: 0.5717 (OUTLIER) cc_final: 0.3996 (pp-130) REVERT: F 351 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7228 (mp0) outliers start: 47 outliers final: 23 residues processed: 288 average time/residue: 0.5714 time to fit residues: 184.4663 Evaluate side-chains 301 residues out of total 1992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 261 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 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 451 LEU Chi-restraints excluded: chain B residue 457 ARG Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 131 ILE 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 459 LEU Chi-restraints excluded: chain C residue 504 GLU Chi-restraints excluded: chain D residue 131 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 176 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 131 ILE 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 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 192 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 127 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 182 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 chunk 153 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 chunk 97 optimal weight: 0.4980 chunk 133 optimal weight: 1.9990 chunk 39 optimal weight: 0.2980 chunk 206 optimal weight: 0.5980 chunk 165 optimal weight: 0.0980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 ASN D 253 GLN E 416 ASN F 247 GLN F 493 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.153183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.111072 restraints weight = 19082.932| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.66 r_work: 0.3238 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 19008 Z= 0.188 Angle : 0.885 59.200 25716 Z= 0.514 Chirality : 0.043 0.424 2934 Planarity : 0.005 0.058 3198 Dihedral : 4.601 36.799 2530 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.01 % Allowed : 14.06 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.18), residues: 2232 helix: 1.74 (0.14), residues: 1368 sheet: 2.17 (0.39), residues: 180 loop : 0.37 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 175 TYR 0.018 0.002 TYR B 453 PHE 0.029 0.002 PHE F 196 TRP 0.028 0.002 TRP C 458 HIS 0.006 0.001 HIS A 305 Details of bonding type rmsd covalent geometry : bond 0.00409 (19002) covalent geometry : angle 0.88552 (25704) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.48600 ( 12) hydrogen bonds : bond 0.03967 ( 1157) hydrogen bonds : angle 4.48212 ( 3342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8365.46 seconds wall clock time: 142 minutes 38.97 seconds (8558.97 seconds total)