Starting phenix.real_space_refine on Wed Jan 22 11:42:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk8_61547/01_2025/9jk8_61547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk8_61547/01_2025/9jk8_61547.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jk8_61547/01_2025/9jk8_61547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk8_61547/01_2025/9jk8_61547.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk8_61547/01_2025/9jk8_61547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk8_61547/01_2025/9jk8_61547.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 12120 2.51 5 N 3192 2.21 5 O 3120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 18504 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3084 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 13, 'TRANS': 362} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.35, per 1000 atoms: 0.40 Number of scatterers: 18504 At special positions: 0 Unit cell: (102.72, 90.95, 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 72 16.00 O 3120 8.00 N 3192 7.00 C 12120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.75 Conformation dependent library (CDL) restraints added in 2.8 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 14 sheets defined 63.0% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 115 through 138 Proline residue: A 127 - end of helix removed outlier: 3.557A pdb=" N LEU A 133 " --> pdb=" O ALA A 129 " (cutoff:3.500A) Proline residue: A 134 - end of helix Processing helix chain 'A' and resid 146 through 172 removed outlier: 4.124A pdb=" N GLU A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.881A 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 242 removed outlier: 3.897A 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 292 through 308 removed outlier: 4.458A pdb=" N ALA A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS A 299 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 339 Processing helix chain 'A' and resid 341 through 371 removed outlier: 3.782A 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: 4.709A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.597A 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 removed outlier: 3.557A pdb=" N LEU B 133 " --> pdb=" O ALA B 129 " (cutoff:3.500A) Proline residue: B 134 - end of helix Processing helix chain 'B' and resid 146 through 172 removed outlier: 4.124A pdb=" N GLU B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 3.881A 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 242 removed outlier: 3.897A 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 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 308 removed outlier: 3.558A pdb=" N LYS B 299 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 341 through 371 removed outlier: 3.783A 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: 4.709A pdb=" N ARG B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.597A 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 removed outlier: 3.557A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 146 through 172 removed outlier: 4.123A pdb=" N GLU C 150 " --> pdb=" O GLY C 146 " (cutoff:3.500A) removed outlier: 3.881A 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 242 removed outlier: 3.897A 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 292 through 308 removed outlier: 4.459A pdb=" N ALA C 297 " --> pdb=" O ASN C 293 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 299 " --> pdb=" O LEU C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 330 through 339 Processing helix chain 'C' and resid 341 through 371 removed outlier: 3.782A 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: 4.709A pdb=" N ARG C 443 " --> pdb=" O ALA C 439 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.597A 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 removed outlier: 3.557A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 146 through 172 removed outlier: 4.124A pdb=" N GLU D 150 " --> pdb=" O GLY D 146 " (cutoff:3.500A) removed outlier: 3.881A 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 242 removed outlier: 3.897A 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 292 through 308 removed outlier: 4.458A pdb=" N ALA D 297 " --> pdb=" O ASN D 293 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS D 299 " --> pdb=" O LEU D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 339 Processing helix chain 'D' and resid 341 through 371 removed outlier: 3.782A 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: 4.710A pdb=" N ARG D 443 " --> pdb=" O ALA D 439 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 3.838A 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: 3.596A 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 removed outlier: 3.558A pdb=" N LEU E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) Proline residue: E 134 - end of helix Processing helix chain 'E' and resid 146 through 172 removed outlier: 4.123A pdb=" N GLU E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.881A 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 242 removed outlier: 3.898A 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 292 through 308 removed outlier: 4.458A pdb=" N ALA E 297 " --> pdb=" O ASN E 293 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS E 299 " --> pdb=" O LEU E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 330 through 339 Processing helix chain 'E' and resid 341 through 371 removed outlier: 3.781A 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: 4.710A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N TYR E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.597A 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 removed outlier: 3.557A pdb=" N LEU F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Proline residue: F 134 - end of helix Processing helix chain 'F' and resid 146 through 172 removed outlier: 4.123A pdb=" N GLU F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) removed outlier: 3.881A 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 242 removed outlier: 3.896A 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 292 through 308 removed outlier: 4.458A pdb=" N ALA F 297 " --> pdb=" O ASN F 293 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS F 299 " --> pdb=" O LEU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 339 Processing helix chain 'F' and resid 341 through 371 removed outlier: 3.783A 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: 4.708A pdb=" N ARG F 443 " --> pdb=" O ALA F 439 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N TYR F 444 " --> pdb=" O PHE F 440 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.597A 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 Processing sheet with id=AA2, first strand: chain 'A' and resid 373 through 375 Processing sheet with id=AA3, first strand: chain 'A' and resid 500 through 501 removed outlier: 6.221A pdb=" N ILE A 500 " --> pdb=" O ASP C 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.581A pdb=" N GLN B 373 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 515 " --> pdb=" O GLN B 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 177 through 178 Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 267 Processing sheet with id=AA7, first strand: chain 'C' and resid 373 through 375 Processing sheet with id=AA8, first strand: chain 'C' and resid 262 through 267 Processing sheet with id=AA9, first strand: chain 'D' and resid 177 through 178 removed outlier: 6.285A pdb=" N ASP D 178 " --> pdb=" O LEU E 502 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N GLU E 504 " --> pdb=" O ASP D 178 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 373 through 375 Processing sheet with id=AB2, first strand: chain 'F' and resid 177 through 178 removed outlier: 6.299A pdb=" N ILE D 501 " --> pdb=" O TRP F 463 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N LEU F 465 " --> pdb=" O ILE D 501 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N SER D 503 " --> pdb=" O LEU F 465 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N SER F 467 " --> pdb=" O SER D 503 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 373 through 375 Processing sheet with id=AB4, first strand: chain 'E' and resid 177 through 178 Processing sheet with id=AB5, first strand: chain 'F' and resid 373 through 375 removed outlier: 3.512A pdb=" N VAL E 515 " --> pdb=" O GLN F 373 " (cutoff:3.500A) 1146 hydrogen bonds defined for protein. 3318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.06 Time building geometry restraints manager: 5.15 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: 5839 1.34 - 1.46: 4093 1.46 - 1.58: 8872 1.58 - 1.70: 0 1.70 - 1.82: 120 Bond restraints: 18924 Sorted by residual: bond pdb=" CG1 ILE C 507 " pdb=" CD1 ILE C 507 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.81e+00 bond pdb=" CG1 ILE A 507 " pdb=" CD1 ILE A 507 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.76e+00 bond pdb=" CG1 ILE E 507 " pdb=" CD1 ILE E 507 " ideal model delta sigma weight residual 1.513 1.404 0.109 3.90e-02 6.57e+02 7.74e+00 bond pdb=" CG1 ILE B 507 " pdb=" CD1 ILE B 507 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.72e+00 bond pdb=" CG1 ILE F 507 " pdb=" CD1 ILE F 507 " ideal model delta sigma weight residual 1.513 1.405 0.108 3.90e-02 6.57e+02 7.71e+00 ... (remaining 18919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 24822 2.04 - 4.08: 607 4.08 - 6.12: 119 6.12 - 8.16: 42 8.16 - 10.21: 12 Bond angle restraints: 25602 Sorted by residual: angle pdb=" N LYS E 484 " pdb=" CA LYS E 484 " pdb=" C LYS E 484 " ideal model delta sigma weight residual 108.96 116.13 -7.17 1.59e+00 3.96e-01 2.04e+01 angle pdb=" N LYS D 484 " pdb=" CA LYS D 484 " pdb=" C LYS D 484 " ideal model delta sigma weight residual 108.96 116.13 -7.17 1.59e+00 3.96e-01 2.03e+01 angle pdb=" N LYS C 484 " pdb=" CA LYS C 484 " pdb=" C LYS C 484 " ideal model delta sigma weight residual 108.96 116.12 -7.16 1.59e+00 3.96e-01 2.03e+01 angle pdb=" N LYS F 484 " pdb=" CA LYS F 484 " pdb=" C LYS F 484 " ideal model delta sigma weight residual 108.96 116.10 -7.14 1.59e+00 3.96e-01 2.02e+01 angle pdb=" N LYS A 484 " pdb=" CA LYS A 484 " pdb=" C LYS A 484 " ideal model delta sigma weight residual 108.96 116.09 -7.13 1.59e+00 3.96e-01 2.01e+01 ... (remaining 25597 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.62: 10194 11.62 - 23.24: 852 23.24 - 34.85: 211 34.85 - 46.47: 73 46.47 - 58.09: 7 Dihedral angle restraints: 11337 sinusoidal: 4653 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS A 145 " pdb=" SG CYS A 145 " pdb=" SG CYS A 149 " pdb=" CB CYS A 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.20 51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA GLU B 504 " pdb=" C GLU B 504 " pdb=" N GLU B 505 " pdb=" CA GLU B 505 " ideal model delta harmonic sigma weight residual 180.00 154.82 25.18 0 5.00e+00 4.00e-02 2.54e+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 180.00 154.84 25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 11334 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2523 0.068 - 0.137: 359 0.137 - 0.205: 34 0.205 - 0.273: 0 0.273 - 0.342: 6 Chirality restraints: 2922 Sorted by residual: chirality pdb=" CB ILE B 238 " pdb=" CA ILE B 238 " pdb=" CG1 ILE B 238 " pdb=" CG2 ILE B 238 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CB ILE E 238 " pdb=" CA ILE E 238 " pdb=" CG1 ILE E 238 " pdb=" CG2 ILE E 238 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB ILE A 238 " pdb=" CA ILE A 238 " pdb=" CG1 ILE A 238 " pdb=" CG2 ILE A 238 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.88e+00 ... (remaining 2919 not shown) Planarity restraints: 3186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 221 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" CD GLN B 221 " -0.073 2.00e-02 2.50e+03 pdb=" OE1 GLN B 221 " 0.028 2.00e-02 2.50e+03 pdb=" NE2 GLN B 221 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 221 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" CD GLN F 221 " 0.073 2.00e-02 2.50e+03 pdb=" OE1 GLN F 221 " -0.027 2.00e-02 2.50e+03 pdb=" NE2 GLN F 221 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 221 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.78e+01 pdb=" CD GLN D 221 " -0.073 2.00e-02 2.50e+03 pdb=" OE1 GLN D 221 " 0.027 2.00e-02 2.50e+03 pdb=" NE2 GLN D 221 " 0.025 2.00e-02 2.50e+03 ... (remaining 3183 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 156 2.60 - 3.18: 15802 3.18 - 3.75: 30113 3.75 - 4.33: 41844 4.33 - 4.90: 68822 Nonbonded interactions: 156737 Sorted by model distance: nonbonded pdb=" SG CYS B 145 " pdb=" SG CYS B 149 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS E 145 " pdb=" SG CYS E 149 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C 145 " pdb=" SG CYS C 149 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D 145 " pdb=" SG CYS D 149 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS F 145 " pdb=" SG CYS F 149 " model vdw 2.029 3.760 ... (remaining 156732 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: 0.15 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 37.560 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 18924 Z= 0.307 Angle : 0.822 10.206 25602 Z= 0.435 Chirality : 0.050 0.342 2922 Planarity : 0.007 0.050 3186 Dihedral : 9.727 58.089 6978 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.16), residues: 2220 helix: -0.52 (0.13), residues: 1314 sheet: -1.13 (0.34), residues: 186 loop : -1.19 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP E 168 HIS 0.003 0.001 HIS F 234 PHE 0.021 0.002 PHE D 369 TYR 0.016 0.002 TYR D 283 ARG 0.010 0.001 ARG E 181 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 2.021 Fit side-chains revert: symmetry clash REVERT: A 124 PHE cc_start: 0.7474 (t80) cc_final: 0.7265 (t80) REVERT: A 172 PHE cc_start: 0.7975 (t80) cc_final: 0.7592 (t80) REVERT: A 174 LYS cc_start: 0.7884 (ptpp) cc_final: 0.7326 (mmtm) REVERT: A 207 ARG cc_start: 0.7412 (mmm-85) cc_final: 0.7073 (mmm-85) REVERT: A 219 ILE cc_start: 0.8083 (mt) cc_final: 0.7882 (mm) REVERT: A 334 ARG cc_start: 0.6977 (tpp80) cc_final: 0.6663 (tpp-160) REVERT: A 367 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7666 (mm-30) REVERT: A 373 GLN cc_start: 0.7476 (tt0) cc_final: 0.7136 (tp40) REVERT: A 388 MET cc_start: 0.8289 (ptt) cc_final: 0.8078 (ptt) REVERT: A 446 SER cc_start: 0.8430 (m) cc_final: 0.8114 (p) REVERT: B 150 GLU cc_start: 0.6993 (mt-10) cc_final: 0.6724 (mt-10) REVERT: B 207 ARG cc_start: 0.7306 (mmm-85) cc_final: 0.6717 (mmm-85) REVERT: B 242 GLU cc_start: 0.7669 (pm20) cc_final: 0.7453 (pm20) REVERT: B 300 PHE cc_start: 0.7983 (m-80) cc_final: 0.7475 (m-10) REVERT: B 353 ARG cc_start: 0.8550 (mtm-85) cc_final: 0.8326 (mtm-85) REVERT: B 367 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7152 (mm-30) REVERT: B 373 GLN cc_start: 0.7634 (tt0) cc_final: 0.7261 (tp40) REVERT: C 172 PHE cc_start: 0.7849 (t80) cc_final: 0.7625 (t80) REVERT: C 207 ARG cc_start: 0.7058 (mmm-85) cc_final: 0.6658 (mpt-90) REVERT: C 334 ARG cc_start: 0.6880 (tpp80) cc_final: 0.6634 (mtp-110) REVERT: C 351 GLU cc_start: 0.7814 (tt0) cc_final: 0.7542 (mt-10) REVERT: C 373 GLN cc_start: 0.7144 (tt0) cc_final: 0.6787 (tt0) REVERT: D 150 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6606 (mt-10) REVERT: D 176 ARG cc_start: 0.6807 (mtp180) cc_final: 0.6541 (mmm160) REVERT: D 207 ARG cc_start: 0.6875 (mmm-85) cc_final: 0.6493 (mmm-85) REVERT: D 300 PHE cc_start: 0.7930 (m-80) cc_final: 0.7668 (m-80) REVERT: D 334 ARG cc_start: 0.6830 (tpp80) cc_final: 0.6411 (tpp-160) REVERT: D 373 GLN cc_start: 0.7738 (tt0) cc_final: 0.7402 (tt0) REVERT: E 124 PHE cc_start: 0.6936 (t80) cc_final: 0.6702 (t80) REVERT: E 130 PHE cc_start: 0.7082 (m-10) cc_final: 0.6790 (m-10) REVERT: E 172 PHE cc_start: 0.7746 (t80) cc_final: 0.6380 (m-10) REVERT: E 207 ARG cc_start: 0.7006 (mmm-85) cc_final: 0.6533 (mtt90) REVERT: E 334 ARG cc_start: 0.7125 (tpp80) cc_final: 0.6797 (mtp-110) REVERT: E 373 GLN cc_start: 0.7287 (tt0) cc_final: 0.6922 (tp40) REVERT: F 174 LYS cc_start: 0.7822 (ptpp) cc_final: 0.7232 (mmtm) REVERT: F 207 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6877 (mmm-85) REVERT: F 334 ARG cc_start: 0.6835 (tpp80) cc_final: 0.6603 (mtp-110) REVERT: F 346 GLU cc_start: 0.8187 (tt0) cc_final: 0.7911 (tt0) REVERT: F 373 GLN cc_start: 0.7705 (tt0) cc_final: 0.7241 (tt0) REVERT: F 389 ASP cc_start: 0.7250 (p0) cc_final: 0.6965 (p0) outliers start: 0 outliers final: 0 residues processed: 413 average time/residue: 1.7631 time to fit residues: 802.1777 Evaluate side-chains 289 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 187 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 93 optimal weight: 0.0170 chunk 57 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 chunk 174 optimal weight: 1.9990 chunk 67 optimal weight: 0.3980 chunk 105 optimal weight: 0.0670 chunk 129 optimal weight: 1.9990 chunk 201 optimal weight: 0.6980 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN A 341 ASN A 371 HIS A 416 ASN A 512 HIS B 221 GLN B 234 HIS B 247 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 425 GLN B 512 HIS C 234 HIS ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 406 GLN C 416 ASN C 425 GLN C 512 HIS D 221 GLN D 234 HIS D 406 GLN D 425 GLN D 473 ASN D 512 HIS ** E 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 341 ASN E 473 ASN E 512 HIS ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN F 425 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.162143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.121819 restraints weight = 20257.062| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.80 r_work: 0.3305 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18924 Z= 0.204 Angle : 0.574 9.999 25602 Z= 0.301 Chirality : 0.042 0.169 2922 Planarity : 0.005 0.040 3186 Dihedral : 4.630 23.703 2514 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.52 % Allowed : 9.01 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.17), residues: 2220 helix: 0.68 (0.13), residues: 1368 sheet: -0.30 (0.35), residues: 192 loop : -1.06 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 138 HIS 0.005 0.001 HIS A 234 PHE 0.027 0.002 PHE D 196 TYR 0.014 0.002 TYR D 453 ARG 0.005 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 332 time to evaluate : 2.108 Fit side-chains REVERT: A 172 PHE cc_start: 0.7674 (t80) cc_final: 0.7299 (t80) REVERT: A 174 LYS cc_start: 0.7948 (ptpp) cc_final: 0.7358 (mmtm) REVERT: A 207 ARG cc_start: 0.7314 (mmm-85) cc_final: 0.6850 (mmm-85) REVERT: A 334 ARG cc_start: 0.6895 (tpp80) cc_final: 0.6481 (tpp-160) REVERT: A 373 GLN cc_start: 0.7481 (tt0) cc_final: 0.7028 (tt0) REVERT: A 420 MET cc_start: 0.8255 (OUTLIER) cc_final: 0.7687 (ttm) REVERT: A 446 SER cc_start: 0.8460 (m) cc_final: 0.8143 (p) REVERT: B 172 PHE cc_start: 0.7546 (t80) cc_final: 0.7127 (t80) REVERT: B 179 MET cc_start: 0.8928 (mtm) cc_final: 0.8662 (mtm) REVERT: B 207 ARG cc_start: 0.7335 (mmm-85) cc_final: 0.6618 (mmm-85) REVERT: B 267 LEU cc_start: 0.8941 (mt) cc_final: 0.8736 (mp) REVERT: B 285 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7603 (ttpp) REVERT: B 300 PHE cc_start: 0.8283 (m-80) cc_final: 0.7565 (m-10) REVERT: B 334 ARG cc_start: 0.6904 (mtp-110) cc_final: 0.6546 (tpp-160) REVERT: B 373 GLN cc_start: 0.7871 (tt0) cc_final: 0.7421 (tp40) REVERT: B 413 ARG cc_start: 0.8595 (mmt90) cc_final: 0.8355 (mmt90) REVERT: C 172 PHE cc_start: 0.7794 (t80) cc_final: 0.7508 (t80) REVERT: C 207 ARG cc_start: 0.7337 (mmm-85) cc_final: 0.6643 (mmm-85) REVERT: C 249 MET cc_start: 0.8818 (tpt) cc_final: 0.8555 (mmm) REVERT: C 300 PHE cc_start: 0.8121 (m-80) cc_final: 0.7769 (m-80) REVERT: C 346 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7567 (tt0) REVERT: C 351 GLU cc_start: 0.7992 (tt0) cc_final: 0.7631 (mt-10) REVERT: C 373 GLN cc_start: 0.7183 (tt0) cc_final: 0.6875 (tt0) REVERT: C 420 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8015 (tpp) REVERT: C 446 SER cc_start: 0.8369 (m) cc_final: 0.8154 (p) REVERT: C 456 ASP cc_start: 0.8094 (p0) cc_final: 0.7861 (p0) REVERT: C 516 LEU cc_start: 0.8616 (tp) cc_final: 0.8410 (tm) REVERT: D 124 PHE cc_start: 0.7529 (t80) cc_final: 0.7275 (t80) REVERT: D 156 MET cc_start: 0.7527 (ttt) cc_final: 0.7311 (ttt) REVERT: D 174 LYS cc_start: 0.7969 (ptpp) cc_final: 0.7052 (mmtt) REVERT: D 207 ARG cc_start: 0.6929 (mmm-85) cc_final: 0.6666 (mmm-85) REVERT: D 263 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7566 (mtp180) REVERT: D 267 LEU cc_start: 0.8808 (mt) cc_final: 0.8581 (mp) REVERT: D 285 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7676 (ttpp) REVERT: D 300 PHE cc_start: 0.8075 (m-80) cc_final: 0.7648 (m-80) REVERT: D 334 ARG cc_start: 0.7202 (tpp80) cc_final: 0.6692 (tpp-160) REVERT: D 373 GLN cc_start: 0.7532 (tt0) cc_final: 0.7181 (tt0) REVERT: E 172 PHE cc_start: 0.7536 (t80) cc_final: 0.7195 (t80) REVERT: E 207 ARG cc_start: 0.7093 (mmm-85) cc_final: 0.6765 (mmm-85) REVERT: E 247 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8069 (tt0) REVERT: E 334 ARG cc_start: 0.7162 (tpp80) cc_final: 0.6635 (tpp-160) REVERT: E 346 GLU cc_start: 0.8036 (tt0) cc_final: 0.7627 (tm-30) REVERT: E 373 GLN cc_start: 0.7466 (tt0) cc_final: 0.6975 (tt0) REVERT: E 420 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7778 (ttm) REVERT: E 456 ASP cc_start: 0.8078 (p0) cc_final: 0.7861 (p0) REVERT: F 174 LYS cc_start: 0.7929 (ptpp) cc_final: 0.7360 (mmtm) REVERT: F 207 ARG cc_start: 0.6953 (mmm-85) cc_final: 0.6559 (mmm-85) REVERT: F 300 PHE cc_start: 0.8248 (m-80) cc_final: 0.7519 (m-10) REVERT: F 346 GLU cc_start: 0.8078 (tt0) cc_final: 0.7851 (tt0) REVERT: F 373 GLN cc_start: 0.7774 (tt0) cc_final: 0.7275 (tp40) REVERT: F 389 ASP cc_start: 0.7191 (p0) cc_final: 0.6976 (p0) outliers start: 50 outliers final: 18 residues processed: 360 average time/residue: 1.5580 time to fit residues: 622.5809 Evaluate side-chains 305 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 186 ARG Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 64 optimal weight: 0.3980 chunk 201 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 133 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 106 optimal weight: 0.0980 chunk 208 optimal weight: 0.8980 chunk 191 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 ASN A 416 ASN A 493 ASN B 247 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 425 GLN C 247 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN D 221 GLN D 293 ASN D 350 HIS D 416 ASN E 234 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 234 HIS F 247 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN F 425 GLN F 512 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.158787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.118259 restraints weight = 20371.759| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 1.78 r_work: 0.3260 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18924 Z= 0.205 Angle : 0.559 9.996 25602 Z= 0.288 Chirality : 0.041 0.163 2922 Planarity : 0.005 0.038 3186 Dihedral : 4.423 22.182 2514 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.97 % Allowed : 13.34 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2220 helix: 1.29 (0.14), residues: 1380 sheet: 0.11 (0.39), residues: 180 loop : -0.58 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 458 HIS 0.005 0.001 HIS F 234 PHE 0.024 0.002 PHE C 196 TYR 0.014 0.002 TYR F 453 ARG 0.004 0.000 ARG C 334 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 2.202 Fit side-chains REVERT: A 172 PHE cc_start: 0.7648 (t80) cc_final: 0.7329 (t80) REVERT: A 174 LYS cc_start: 0.7991 (ptpp) cc_final: 0.7375 (mmtm) REVERT: A 196 PHE cc_start: 0.7159 (t80) cc_final: 0.6915 (t80) REVERT: A 207 ARG cc_start: 0.7214 (mmm-85) cc_final: 0.6714 (mmm-85) REVERT: A 334 ARG cc_start: 0.7050 (tpp80) cc_final: 0.6696 (tpp-160) REVERT: A 367 GLU cc_start: 0.7941 (mt-10) cc_final: 0.7311 (mm-30) REVERT: A 373 GLN cc_start: 0.7583 (tt0) cc_final: 0.7118 (tt0) REVERT: A 420 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7836 (ttm) REVERT: B 174 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7674 (mmtt) REVERT: B 207 ARG cc_start: 0.7332 (mmm-85) cc_final: 0.6520 (mmm-85) REVERT: B 285 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7640 (ttpp) REVERT: B 334 ARG cc_start: 0.6979 (mtp-110) cc_final: 0.6604 (tpp-160) REVERT: B 373 GLN cc_start: 0.7934 (tt0) cc_final: 0.7430 (tp40) REVERT: B 413 ARG cc_start: 0.8535 (mmt90) cc_final: 0.8235 (mmt90) REVERT: C 172 PHE cc_start: 0.7647 (t80) cc_final: 0.7355 (t80) REVERT: C 207 ARG cc_start: 0.7288 (mmm-85) cc_final: 0.6507 (mmm-85) REVERT: C 267 LEU cc_start: 0.8842 (mt) cc_final: 0.8630 (mp) REVERT: C 300 PHE cc_start: 0.8273 (m-80) cc_final: 0.7879 (m-10) REVERT: C 346 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7572 (tt0) REVERT: C 351 GLU cc_start: 0.7974 (tt0) cc_final: 0.7742 (tt0) REVERT: C 373 GLN cc_start: 0.7419 (tt0) cc_final: 0.7087 (tt0) REVERT: C 516 LEU cc_start: 0.8633 (tp) cc_final: 0.8423 (tm) REVERT: D 124 PHE cc_start: 0.7450 (t80) cc_final: 0.7236 (t80) REVERT: D 174 LYS cc_start: 0.8186 (ptpp) cc_final: 0.7359 (mmtt) REVERT: D 207 ARG cc_start: 0.6987 (mmm-85) cc_final: 0.6606 (mmm-85) REVERT: D 263 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7658 (mtp180) REVERT: D 267 LEU cc_start: 0.8804 (mt) cc_final: 0.8587 (mp) REVERT: D 285 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7652 (ttpp) REVERT: D 300 PHE cc_start: 0.8116 (m-80) cc_final: 0.7685 (m-80) REVERT: D 334 ARG cc_start: 0.7202 (tpp80) cc_final: 0.6811 (tpp-160) REVERT: D 373 GLN cc_start: 0.7549 (tt0) cc_final: 0.7147 (tt0) REVERT: D 455 LYS cc_start: 0.8083 (mttp) cc_final: 0.7875 (mmtt) REVERT: E 172 PHE cc_start: 0.7639 (t80) cc_final: 0.7284 (t80) REVERT: E 207 ARG cc_start: 0.7145 (mmm-85) cc_final: 0.6697 (mmm-85) REVERT: E 215 ASN cc_start: 0.7374 (p0) cc_final: 0.7072 (t0) REVERT: E 273 GLN cc_start: 0.8726 (mt0) cc_final: 0.8076 (mt0) REVERT: E 334 ARG cc_start: 0.7143 (tpp80) cc_final: 0.6885 (mtp-110) REVERT: E 346 GLU cc_start: 0.8081 (tt0) cc_final: 0.7685 (tm-30) REVERT: E 367 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7321 (mm-30) REVERT: E 373 GLN cc_start: 0.7761 (tt0) cc_final: 0.7205 (tt0) REVERT: E 420 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7817 (ttm) REVERT: F 119 LEU cc_start: 0.7079 (OUTLIER) cc_final: 0.6049 (tm) REVERT: F 174 LYS cc_start: 0.8075 (ptpp) cc_final: 0.7531 (mmtm) REVERT: F 207 ARG cc_start: 0.6991 (mmm-85) cc_final: 0.6472 (mmm-85) REVERT: F 304 LYS cc_start: 0.7703 (tttt) cc_final: 0.7089 (mptt) REVERT: F 334 ARG cc_start: 0.6984 (mmm160) cc_final: 0.6558 (tpp-160) REVERT: F 373 GLN cc_start: 0.7899 (tt0) cc_final: 0.7382 (tt0) REVERT: F 389 ASP cc_start: 0.7346 (p0) cc_final: 0.7108 (p0) outliers start: 59 outliers final: 21 residues processed: 339 average time/residue: 1.5582 time to fit residues: 587.1865 Evaluate side-chains 308 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 280 time to evaluate : 2.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 186 ARG Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 371 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 34 optimal weight: 0.0050 chunk 138 optimal weight: 2.9990 chunk 190 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN A 493 ASN B 247 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS D 247 GLN D 406 GLN ** E 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 425 GLN E 493 ASN F 425 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.115768 restraints weight = 20244.255| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 1.77 r_work: 0.3227 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18924 Z= 0.228 Angle : 0.562 10.416 25602 Z= 0.287 Chirality : 0.041 0.156 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.392 22.193 2514 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.22 % Allowed : 13.75 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.18), residues: 2220 helix: 1.46 (0.14), residues: 1380 sheet: 0.43 (0.39), residues: 186 loop : -0.49 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 458 HIS 0.005 0.001 HIS F 234 PHE 0.026 0.002 PHE E 196 TYR 0.014 0.002 TYR B 453 ARG 0.006 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 2.024 Fit side-chains REVERT: A 172 PHE cc_start: 0.7620 (t80) cc_final: 0.7284 (t80) REVERT: A 174 LYS cc_start: 0.8092 (ptpp) cc_final: 0.7306 (mmtm) REVERT: A 207 ARG cc_start: 0.7329 (mmm-85) cc_final: 0.6706 (mmm-85) REVERT: A 334 ARG cc_start: 0.7142 (tpp80) cc_final: 0.6793 (tpp-160) REVERT: A 346 GLU cc_start: 0.8097 (tt0) cc_final: 0.7703 (tm-30) REVERT: A 367 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7325 (mm-30) REVERT: A 373 GLN cc_start: 0.7600 (tt0) cc_final: 0.7164 (tt0) REVERT: A 389 ASP cc_start: 0.7263 (p0) cc_final: 0.7027 (p0) REVERT: A 420 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7976 (ttm) REVERT: B 174 LYS cc_start: 0.8627 (ptpt) cc_final: 0.7683 (mmtt) REVERT: B 207 ARG cc_start: 0.7361 (mmm-85) cc_final: 0.6854 (mmm-85) REVERT: B 285 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7815 (ttpp) REVERT: B 334 ARG cc_start: 0.7095 (mtp-110) cc_final: 0.6684 (tpp-160) REVERT: B 373 GLN cc_start: 0.8001 (tt0) cc_final: 0.7540 (tt0) REVERT: B 438 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8365 (tptt) REVERT: C 124 PHE cc_start: 0.7545 (t80) cc_final: 0.7344 (t80) REVERT: C 172 PHE cc_start: 0.7680 (t80) cc_final: 0.7353 (t80) REVERT: C 207 ARG cc_start: 0.7271 (mmm-85) cc_final: 0.6643 (mmm-85) REVERT: C 273 GLN cc_start: 0.8648 (mt0) cc_final: 0.8286 (mt0) REVERT: C 300 PHE cc_start: 0.8070 (m-80) cc_final: 0.7684 (m-10) REVERT: C 346 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7555 (tt0) REVERT: C 351 GLU cc_start: 0.7975 (tt0) cc_final: 0.7744 (tt0) REVERT: C 373 GLN cc_start: 0.7458 (tt0) cc_final: 0.7156 (tt0) REVERT: C 420 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7878 (tpp) REVERT: D 174 LYS cc_start: 0.8254 (ptpp) cc_final: 0.7409 (mmtt) REVERT: D 207 ARG cc_start: 0.7044 (mmm-85) cc_final: 0.6615 (mmm-85) REVERT: D 247 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8261 (tt0) REVERT: D 285 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7878 (ttpp) REVERT: D 300 PHE cc_start: 0.8185 (m-80) cc_final: 0.7767 (m-10) REVERT: D 334 ARG cc_start: 0.7043 (tpp80) cc_final: 0.6615 (tpp-160) REVERT: D 373 GLN cc_start: 0.7681 (tt0) cc_final: 0.7310 (tt0) REVERT: E 172 PHE cc_start: 0.7528 (t80) cc_final: 0.7116 (t80) REVERT: E 207 ARG cc_start: 0.7299 (mmm-85) cc_final: 0.6802 (mmm-85) REVERT: E 215 ASN cc_start: 0.7210 (p0) cc_final: 0.6978 (t0) REVERT: E 247 GLN cc_start: 0.8374 (tp40) cc_final: 0.7940 (tt0) REVERT: E 249 MET cc_start: 0.9199 (mmt) cc_final: 0.8989 (mmt) REVERT: E 334 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6884 (mtp-110) REVERT: E 346 GLU cc_start: 0.8099 (tt0) cc_final: 0.7713 (tm-30) REVERT: E 367 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7293 (mm-30) REVERT: E 373 GLN cc_start: 0.7871 (tt0) cc_final: 0.7340 (tt0) REVERT: E 420 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7850 (ttm) REVERT: F 158 PHE cc_start: 0.8441 (m-80) cc_final: 0.8173 (m-10) REVERT: F 174 LYS cc_start: 0.8138 (ptpp) cc_final: 0.7551 (mmtm) REVERT: F 207 ARG cc_start: 0.6988 (mmm-85) cc_final: 0.6438 (mmm-85) REVERT: F 334 ARG cc_start: 0.7053 (mmm160) cc_final: 0.6651 (tpp-160) REVERT: F 373 GLN cc_start: 0.7853 (tt0) cc_final: 0.7343 (tt0) REVERT: F 389 ASP cc_start: 0.7446 (p0) cc_final: 0.7186 (p0) outliers start: 64 outliers final: 24 residues processed: 327 average time/residue: 1.5225 time to fit residues: 553.3377 Evaluate side-chains 298 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 267 time to evaluate : 2.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 371 HIS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 208 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 193 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 2.9990 chunk 134 optimal weight: 0.7980 chunk 61 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 416 ASN A 493 ASN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 425 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114563 restraints weight = 20371.013| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.77 r_work: 0.3215 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18924 Z= 0.244 Angle : 0.575 10.334 25602 Z= 0.291 Chirality : 0.041 0.162 2922 Planarity : 0.005 0.038 3186 Dihedral : 4.403 22.043 2514 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.63 % Allowed : 14.95 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.18), residues: 2220 helix: 1.50 (0.14), residues: 1380 sheet: 0.52 (0.40), residues: 180 loop : -0.22 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 458 HIS 0.007 0.001 HIS E 371 PHE 0.027 0.002 PHE C 429 TYR 0.013 0.002 TYR B 453 ARG 0.006 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 275 time to evaluate : 2.115 Fit side-chains REVERT: A 172 PHE cc_start: 0.7680 (t80) cc_final: 0.7355 (t80) REVERT: A 174 LYS cc_start: 0.8161 (ptpp) cc_final: 0.7330 (mmtm) REVERT: A 181 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7516 (mtt180) REVERT: A 207 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6677 (mmm-85) REVERT: A 249 MET cc_start: 0.9022 (mmm) cc_final: 0.8743 (mmt) REVERT: A 334 ARG cc_start: 0.7229 (tpp80) cc_final: 0.6878 (tpp-160) REVERT: A 346 GLU cc_start: 0.8110 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 367 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7298 (mm-30) REVERT: A 373 GLN cc_start: 0.7757 (tt0) cc_final: 0.7323 (tt0) REVERT: A 389 ASP cc_start: 0.7355 (p0) cc_final: 0.7098 (p0) REVERT: A 420 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7957 (ttm) REVERT: B 172 PHE cc_start: 0.7620 (t80) cc_final: 0.7197 (t80) REVERT: B 174 LYS cc_start: 0.8670 (ptpt) cc_final: 0.7726 (mmtt) REVERT: B 207 ARG cc_start: 0.7258 (mmm-85) cc_final: 0.6739 (mmm-85) REVERT: B 285 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7862 (ttpp) REVERT: B 373 GLN cc_start: 0.8057 (tt0) cc_final: 0.7596 (tt0) REVERT: B 438 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8377 (tptt) REVERT: C 172 PHE cc_start: 0.7764 (t80) cc_final: 0.7454 (t80) REVERT: C 207 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.6708 (mmm-85) REVERT: C 263 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8502 (mmm160) REVERT: C 300 PHE cc_start: 0.8110 (m-80) cc_final: 0.7741 (m-10) REVERT: C 346 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7548 (tt0) REVERT: C 351 GLU cc_start: 0.8003 (tt0) cc_final: 0.7758 (tt0) REVERT: C 367 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7228 (mm-30) REVERT: C 373 GLN cc_start: 0.7533 (tt0) cc_final: 0.7221 (tt0) REVERT: C 420 MET cc_start: 0.8509 (tmm) cc_final: 0.7906 (tpp) REVERT: C 493 ASN cc_start: 0.8512 (p0) cc_final: 0.8162 (p0) REVERT: D 174 LYS cc_start: 0.8275 (ptpp) cc_final: 0.7417 (mmtt) REVERT: D 207 ARG cc_start: 0.7121 (mmm-85) cc_final: 0.6665 (mmm-85) REVERT: D 247 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: D 285 LYS cc_start: 0.8223 (OUTLIER) cc_final: 0.7901 (ttpp) REVERT: D 300 PHE cc_start: 0.8190 (m-80) cc_final: 0.7945 (m-80) REVERT: D 334 ARG cc_start: 0.7054 (tpp80) cc_final: 0.6506 (tpp-160) REVERT: D 373 GLN cc_start: 0.7708 (tt0) cc_final: 0.7362 (tt0) REVERT: D 487 ASP cc_start: 0.7837 (m-30) cc_final: 0.7620 (m-30) REVERT: D 493 ASN cc_start: 0.8525 (p0) cc_final: 0.8194 (p0) REVERT: E 172 PHE cc_start: 0.7592 (t80) cc_final: 0.7208 (t80) REVERT: E 207 ARG cc_start: 0.7380 (mmm-85) cc_final: 0.6869 (mmm-85) REVERT: E 215 ASN cc_start: 0.7259 (p0) cc_final: 0.7008 (t0) REVERT: E 247 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8055 (tt0) REVERT: E 334 ARG cc_start: 0.7173 (tpp80) cc_final: 0.6912 (mtp-110) REVERT: E 346 GLU cc_start: 0.8118 (tt0) cc_final: 0.7735 (tm-30) REVERT: E 367 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7227 (mm-30) REVERT: E 373 GLN cc_start: 0.7760 (tt0) cc_final: 0.7364 (tt0) REVERT: E 420 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7872 (ttm) REVERT: F 158 PHE cc_start: 0.8426 (m-80) cc_final: 0.8172 (m-10) REVERT: F 174 LYS cc_start: 0.8327 (ptpp) cc_final: 0.7606 (mmtm) REVERT: F 207 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6566 (mmm-85) REVERT: F 334 ARG cc_start: 0.7058 (mmm160) cc_final: 0.6641 (tpp-160) REVERT: F 373 GLN cc_start: 0.7851 (tt0) cc_final: 0.7635 (tt0) REVERT: F 389 ASP cc_start: 0.7496 (p0) cc_final: 0.7241 (p0) REVERT: F 413 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.8279 (mmt90) outliers start: 72 outliers final: 32 residues processed: 316 average time/residue: 1.4307 time to fit residues: 503.9900 Evaluate side-chains 303 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 262 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 371 HIS Chi-restraints excluded: chain F residue 413 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 43 optimal weight: 0.6980 chunk 145 optimal weight: 0.5980 chunk 162 optimal weight: 0.0980 chunk 140 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 chunk 185 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 198 optimal weight: 0.3980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 493 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 519 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN D 215 ASN D 247 GLN E 215 ASN E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 425 GLN F 493 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.156497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.115596 restraints weight = 20539.891| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.82 r_work: 0.3225 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 18924 Z= 0.203 Angle : 0.561 9.971 25602 Z= 0.283 Chirality : 0.040 0.179 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.281 21.857 2514 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.58 % Allowed : 15.66 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.18), residues: 2220 helix: 1.60 (0.14), residues: 1380 sheet: 0.67 (0.39), residues: 186 loop : -0.12 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 138 HIS 0.005 0.001 HIS C 269 PHE 0.024 0.002 PHE E 196 TYR 0.012 0.002 TYR E 453 ARG 0.009 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 280 time to evaluate : 2.173 Fit side-chains REVERT: A 172 PHE cc_start: 0.7577 (t80) cc_final: 0.7178 (t80) REVERT: A 174 LYS cc_start: 0.8131 (ptpp) cc_final: 0.7272 (mmtm) REVERT: A 181 ARG cc_start: 0.8247 (mmm-85) cc_final: 0.7810 (mmt90) REVERT: A 207 ARG cc_start: 0.7279 (mmm-85) cc_final: 0.6606 (mmm-85) REVERT: A 249 MET cc_start: 0.9028 (mmm) cc_final: 0.8761 (mmt) REVERT: A 334 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6853 (tpp-160) REVERT: A 346 GLU cc_start: 0.8119 (tt0) cc_final: 0.7719 (tm-30) REVERT: A 367 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7258 (mm-30) REVERT: A 373 GLN cc_start: 0.7781 (tt0) cc_final: 0.7342 (tt0) REVERT: A 389 ASP cc_start: 0.7318 (p0) cc_final: 0.7060 (p0) REVERT: A 420 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7910 (ttm) REVERT: B 174 LYS cc_start: 0.8686 (ptpt) cc_final: 0.7794 (mmtt) REVERT: B 207 ARG cc_start: 0.7243 (mmm-85) cc_final: 0.6705 (mmm-85) REVERT: B 285 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7641 (ttpp) REVERT: B 334 ARG cc_start: 0.7150 (tpp80) cc_final: 0.6673 (tpp-160) REVERT: B 373 GLN cc_start: 0.7992 (tt0) cc_final: 0.7524 (tt0) REVERT: B 438 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8272 (tptp) REVERT: C 172 PHE cc_start: 0.7657 (t80) cc_final: 0.7331 (t80) REVERT: C 207 ARG cc_start: 0.7360 (mmm-85) cc_final: 0.6674 (mmm-85) REVERT: C 300 PHE cc_start: 0.8010 (m-80) cc_final: 0.7635 (m-10) REVERT: C 346 GLU cc_start: 0.7972 (mm-30) cc_final: 0.7551 (tt0) REVERT: C 351 GLU cc_start: 0.7977 (tt0) cc_final: 0.7732 (tt0) REVERT: C 373 GLN cc_start: 0.7505 (tt0) cc_final: 0.7211 (tt0) REVERT: C 420 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7872 (tpp) REVERT: D 124 PHE cc_start: 0.7419 (t80) cc_final: 0.7185 (t80) REVERT: D 174 LYS cc_start: 0.8283 (ptpp) cc_final: 0.7445 (mmtt) REVERT: D 207 ARG cc_start: 0.7103 (mmm-85) cc_final: 0.6632 (mmm-85) REVERT: D 247 GLN cc_start: 0.8609 (OUTLIER) cc_final: 0.8297 (tt0) REVERT: D 285 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7740 (ttpp) REVERT: D 300 PHE cc_start: 0.8176 (m-80) cc_final: 0.7930 (m-80) REVERT: D 334 ARG cc_start: 0.7004 (tpp80) cc_final: 0.6474 (tpp-160) REVERT: D 373 GLN cc_start: 0.7691 (tt0) cc_final: 0.7351 (tt0) REVERT: D 455 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7861 (mmtt) REVERT: D 487 ASP cc_start: 0.7812 (m-30) cc_final: 0.7564 (m-30) REVERT: E 145 CYS cc_start: 0.4287 (OUTLIER) cc_final: 0.4085 (p) REVERT: E 172 PHE cc_start: 0.7540 (t80) cc_final: 0.7147 (t80) REVERT: E 207 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6821 (mmm-85) REVERT: E 215 ASN cc_start: 0.7221 (OUTLIER) cc_final: 0.6983 (t0) REVERT: E 247 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: E 334 ARG cc_start: 0.7125 (tpp80) cc_final: 0.6844 (mtp-110) REVERT: E 346 GLU cc_start: 0.8114 (tt0) cc_final: 0.7726 (tm-30) REVERT: E 367 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7346 (mm-30) REVERT: E 373 GLN cc_start: 0.7758 (tt0) cc_final: 0.7311 (tt0) REVERT: E 389 ASP cc_start: 0.7422 (p0) cc_final: 0.7186 (p0) REVERT: E 420 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7802 (ttm) REVERT: F 158 PHE cc_start: 0.8403 (m-80) cc_final: 0.8112 (m-10) REVERT: F 174 LYS cc_start: 0.8313 (ptpp) cc_final: 0.7591 (mmtm) REVERT: F 181 ARG cc_start: 0.8087 (mmm-85) cc_final: 0.7617 (mmt90) REVERT: F 207 ARG cc_start: 0.7099 (mmm-85) cc_final: 0.6558 (mmm-85) REVERT: F 373 GLN cc_start: 0.7832 (tt0) cc_final: 0.7433 (tt0) REVERT: F 389 ASP cc_start: 0.7337 (p0) cc_final: 0.7105 (p0) outliers start: 71 outliers final: 26 residues processed: 324 average time/residue: 1.3645 time to fit residues: 495.1999 Evaluate side-chains 303 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 266 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 215 ASN Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 371 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 178 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 493 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN C 416 ASN C 519 GLN D 215 ASN D 247 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 215 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.153453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112646 restraints weight = 20349.991| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.77 r_work: 0.3186 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18924 Z= 0.269 Angle : 0.599 10.491 25602 Z= 0.301 Chirality : 0.042 0.184 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.417 22.391 2514 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.63 % Allowed : 16.26 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.18), residues: 2220 helix: 1.57 (0.14), residues: 1380 sheet: 0.57 (0.38), residues: 186 loop : -0.05 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP E 138 HIS 0.005 0.001 HIS C 269 PHE 0.025 0.002 PHE E 196 TYR 0.015 0.002 TYR C 200 ARG 0.009 0.001 ARG F 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 2.116 Fit side-chains REVERT: A 172 PHE cc_start: 0.7649 (t80) cc_final: 0.7273 (t80) REVERT: A 174 LYS cc_start: 0.8187 (ptpp) cc_final: 0.7350 (mmtm) REVERT: A 207 ARG cc_start: 0.7136 (mmm-85) cc_final: 0.6452 (mmm-85) REVERT: A 249 MET cc_start: 0.9060 (mmm) cc_final: 0.8802 (mmt) REVERT: A 334 ARG cc_start: 0.7188 (tpp80) cc_final: 0.6927 (mtp-110) REVERT: A 346 GLU cc_start: 0.8142 (tt0) cc_final: 0.7743 (tm-30) REVERT: A 367 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7279 (mm-30) REVERT: A 373 GLN cc_start: 0.7773 (tt0) cc_final: 0.7383 (tt0) REVERT: A 389 ASP cc_start: 0.7408 (p0) cc_final: 0.7173 (p0) REVERT: A 420 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.7898 (ttm) REVERT: B 174 LYS cc_start: 0.8732 (ptpt) cc_final: 0.7851 (mmtt) REVERT: B 207 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6704 (mmm-85) REVERT: B 285 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7978 (ttmm) REVERT: B 334 ARG cc_start: 0.7225 (tpp80) cc_final: 0.6601 (tpp-160) REVERT: B 373 GLN cc_start: 0.8043 (tt0) cc_final: 0.7566 (tt0) REVERT: B 438 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8385 (tptt) REVERT: C 172 PHE cc_start: 0.7751 (t80) cc_final: 0.7442 (t80) REVERT: C 174 LYS cc_start: 0.8333 (ptpp) cc_final: 0.7585 (mmtt) REVERT: C 207 ARG cc_start: 0.7199 (mmm-85) cc_final: 0.6551 (mmm-85) REVERT: C 300 PHE cc_start: 0.8010 (m-80) cc_final: 0.7789 (m-80) REVERT: C 346 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7535 (tt0) REVERT: C 351 GLU cc_start: 0.8035 (tt0) cc_final: 0.7778 (tt0) REVERT: C 367 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7228 (mm-30) REVERT: C 373 GLN cc_start: 0.7608 (tt0) cc_final: 0.7291 (tt0) REVERT: C 420 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7839 (tpp) REVERT: C 493 ASN cc_start: 0.8566 (p0) cc_final: 0.8196 (p0) REVERT: D 124 PHE cc_start: 0.7466 (t80) cc_final: 0.7221 (t80) REVERT: D 174 LYS cc_start: 0.8327 (ptpp) cc_final: 0.7487 (mmtt) REVERT: D 207 ARG cc_start: 0.7186 (mmm-85) cc_final: 0.6680 (mmm-85) REVERT: D 247 GLN cc_start: 0.8456 (OUTLIER) cc_final: 0.8236 (tt0) REVERT: D 285 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7937 (ttpp) REVERT: D 300 PHE cc_start: 0.8161 (m-80) cc_final: 0.7932 (m-80) REVERT: D 334 ARG cc_start: 0.7023 (tpp80) cc_final: 0.6469 (tpp-160) REVERT: D 373 GLN cc_start: 0.7829 (tt0) cc_final: 0.7546 (tt0) REVERT: D 487 ASP cc_start: 0.7909 (m-30) cc_final: 0.7697 (m-30) REVERT: D 493 ASN cc_start: 0.8568 (p0) cc_final: 0.8183 (p0) REVERT: E 145 CYS cc_start: 0.4494 (OUTLIER) cc_final: 0.4256 (p) REVERT: E 172 PHE cc_start: 0.7652 (t80) cc_final: 0.7288 (t80) REVERT: E 174 LYS cc_start: 0.8197 (ptpp) cc_final: 0.7278 (mmtm) REVERT: E 207 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.6849 (mmm-85) REVERT: E 228 ASP cc_start: 0.7821 (m-30) cc_final: 0.7365 (m-30) REVERT: E 334 ARG cc_start: 0.7133 (tpp80) cc_final: 0.6857 (mtp-110) REVERT: E 346 GLU cc_start: 0.8148 (tt0) cc_final: 0.7765 (tm-30) REVERT: E 367 GLU cc_start: 0.7928 (mt-10) cc_final: 0.7353 (mm-30) REVERT: E 373 GLN cc_start: 0.7772 (tt0) cc_final: 0.7405 (tt0) REVERT: E 389 ASP cc_start: 0.7465 (p0) cc_final: 0.7199 (p0) REVERT: E 420 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.7865 (ttm) REVERT: F 158 PHE cc_start: 0.8375 (m-80) cc_final: 0.8104 (m-10) REVERT: F 174 LYS cc_start: 0.8410 (ptpp) cc_final: 0.7659 (mmtm) REVERT: F 207 ARG cc_start: 0.7104 (mmm-85) cc_final: 0.6548 (mmm-85) REVERT: F 215 ASN cc_start: 0.7141 (OUTLIER) cc_final: 0.6921 (t0) REVERT: F 334 ARG cc_start: 0.7090 (tpp80) cc_final: 0.6618 (tpp-160) REVERT: F 373 GLN cc_start: 0.7920 (tt0) cc_final: 0.7702 (tt0) REVERT: F 389 ASP cc_start: 0.7569 (p0) cc_final: 0.7297 (p0) outliers start: 72 outliers final: 29 residues processed: 323 average time/residue: 1.3448 time to fit residues: 486.9998 Evaluate side-chains 307 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 269 time to evaluate : 2.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 371 HIS Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 215 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 195 optimal weight: 0.4980 chunk 136 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 chunk 216 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 142 optimal weight: 0.6980 chunk 201 optimal weight: 0.7980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN C 416 ASN D 215 ASN D 519 GLN E 215 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 215 ASN F 425 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.155628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114898 restraints weight = 20317.438| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.78 r_work: 0.3217 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18924 Z= 0.204 Angle : 0.574 10.796 25602 Z= 0.286 Chirality : 0.040 0.186 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.295 21.963 2514 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.77 % Allowed : 17.22 % Favored : 80.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.18), residues: 2220 helix: 1.69 (0.14), residues: 1374 sheet: 0.56 (0.39), residues: 186 loop : -0.07 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 138 HIS 0.009 0.001 HIS E 371 PHE 0.033 0.002 PHE D 196 TYR 0.012 0.002 TYR C 453 ARG 0.009 0.000 ARG F 334 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 271 time to evaluate : 2.102 Fit side-chains REVERT: A 172 PHE cc_start: 0.7547 (t80) cc_final: 0.7154 (t80) REVERT: A 174 LYS cc_start: 0.8130 (ptpp) cc_final: 0.7332 (mmtm) REVERT: A 176 ARG cc_start: 0.7586 (mtp180) cc_final: 0.7357 (mmm160) REVERT: A 181 ARG cc_start: 0.8358 (mmm-85) cc_final: 0.7987 (mmt90) REVERT: A 207 ARG cc_start: 0.7083 (mmm-85) cc_final: 0.6414 (mmm-85) REVERT: A 249 MET cc_start: 0.9019 (mmm) cc_final: 0.8760 (mmt) REVERT: A 334 ARG cc_start: 0.7195 (tpp80) cc_final: 0.6897 (mtp-110) REVERT: A 346 GLU cc_start: 0.8124 (tt0) cc_final: 0.7718 (tm-30) REVERT: A 367 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7247 (mm-30) REVERT: A 373 GLN cc_start: 0.7762 (tt0) cc_final: 0.7378 (tt0) REVERT: A 389 ASP cc_start: 0.7366 (p0) cc_final: 0.7100 (p0) REVERT: A 420 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7950 (ttm) REVERT: B 174 LYS cc_start: 0.8729 (ptpt) cc_final: 0.7873 (mmtt) REVERT: B 207 ARG cc_start: 0.7224 (mmm-85) cc_final: 0.6664 (mmm-85) REVERT: B 285 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7745 (ttmm) REVERT: B 334 ARG cc_start: 0.7239 (tpp80) cc_final: 0.6641 (tpp-160) REVERT: B 373 GLN cc_start: 0.8056 (tt0) cc_final: 0.7611 (tt0) REVERT: B 389 ASP cc_start: 0.7230 (p0) cc_final: 0.6987 (p0) REVERT: B 438 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8293 (tptp) REVERT: C 172 PHE cc_start: 0.7605 (t80) cc_final: 0.7297 (t80) REVERT: C 174 LYS cc_start: 0.8312 (ptpp) cc_final: 0.7585 (mmtt) REVERT: C 207 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6533 (mmm-85) REVERT: C 300 PHE cc_start: 0.8013 (m-80) cc_final: 0.7776 (m-80) REVERT: C 346 GLU cc_start: 0.7961 (mm-30) cc_final: 0.7541 (tt0) REVERT: C 351 GLU cc_start: 0.8015 (tt0) cc_final: 0.7764 (tt0) REVERT: C 373 GLN cc_start: 0.7629 (tt0) cc_final: 0.7308 (tt0) REVERT: C 420 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7889 (tpp) REVERT: D 124 PHE cc_start: 0.7380 (t80) cc_final: 0.7037 (t80) REVERT: D 174 LYS cc_start: 0.8319 (ptpp) cc_final: 0.7489 (mmtt) REVERT: D 207 ARG cc_start: 0.7115 (mmm-85) cc_final: 0.6635 (mmm-85) REVERT: D 247 GLN cc_start: 0.8546 (tp-100) cc_final: 0.8322 (tt0) REVERT: D 300 PHE cc_start: 0.8149 (m-80) cc_final: 0.7734 (m-10) REVERT: D 334 ARG cc_start: 0.7012 (tpp80) cc_final: 0.6456 (tpp-160) REVERT: D 373 GLN cc_start: 0.7756 (tt0) cc_final: 0.7466 (tt0) REVERT: D 487 ASP cc_start: 0.7854 (m-30) cc_final: 0.7614 (m-30) REVERT: E 145 CYS cc_start: 0.4492 (OUTLIER) cc_final: 0.4267 (p) REVERT: E 172 PHE cc_start: 0.7563 (t80) cc_final: 0.7193 (t80) REVERT: E 174 LYS cc_start: 0.8147 (ptpp) cc_final: 0.7277 (mmtm) REVERT: E 207 ARG cc_start: 0.7363 (mmm-85) cc_final: 0.6815 (mmm-85) REVERT: E 228 ASP cc_start: 0.7919 (m-30) cc_final: 0.7449 (m-30) REVERT: E 334 ARG cc_start: 0.7082 (tpp80) cc_final: 0.6864 (mtp-110) REVERT: E 346 GLU cc_start: 0.8129 (tt0) cc_final: 0.7744 (tm-30) REVERT: E 367 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7307 (mm-30) REVERT: E 373 GLN cc_start: 0.7768 (tt0) cc_final: 0.7360 (tt0) REVERT: E 389 ASP cc_start: 0.7453 (p0) cc_final: 0.7248 (p0) REVERT: E 420 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7750 (ttm) REVERT: F 158 PHE cc_start: 0.8365 (m-80) cc_final: 0.8079 (m-10) REVERT: F 174 LYS cc_start: 0.8406 (ptpp) cc_final: 0.7665 (mmtm) REVERT: F 178 ASP cc_start: 0.8524 (m-30) cc_final: 0.8159 (m-30) REVERT: F 207 ARG cc_start: 0.7036 (mmm-85) cc_final: 0.6472 (mmm-85) REVERT: F 334 ARG cc_start: 0.7102 (tpp80) cc_final: 0.6595 (tpp-160) REVERT: F 373 GLN cc_start: 0.7891 (tt0) cc_final: 0.7679 (tt0) REVERT: F 389 ASP cc_start: 0.7502 (p0) cc_final: 0.7266 (p0) outliers start: 55 outliers final: 24 residues processed: 306 average time/residue: 1.4168 time to fit residues: 484.1549 Evaluate side-chains 294 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 264 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain F residue 164 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 186 optimal weight: 0.7980 chunk 218 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.1980 chunk 2 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN D 519 GLN E 215 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 215 ASN F 425 GLN F 519 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.156988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116836 restraints weight = 21297.733| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.84 r_work: 0.3281 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18924 Z= 0.244 Angle : 0.591 10.864 25602 Z= 0.295 Chirality : 0.041 0.189 2922 Planarity : 0.005 0.036 3186 Dihedral : 4.373 22.595 2514 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.32 % Allowed : 17.37 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.18), residues: 2220 helix: 1.67 (0.14), residues: 1374 sheet: 0.44 (0.38), residues: 186 loop : -0.03 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP F 138 HIS 0.004 0.001 HIS C 269 PHE 0.030 0.002 PHE D 196 TYR 0.013 0.002 TYR B 453 ARG 0.008 0.000 ARG F 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 272 time to evaluate : 1.997 Fit side-chains REVERT: A 172 PHE cc_start: 0.7575 (t80) cc_final: 0.7187 (t80) REVERT: A 174 LYS cc_start: 0.8192 (ptpp) cc_final: 0.7366 (mmtm) REVERT: A 181 ARG cc_start: 0.8410 (mmm-85) cc_final: 0.8043 (mmt90) REVERT: A 207 ARG cc_start: 0.7148 (mmm-85) cc_final: 0.6481 (mmm-85) REVERT: A 249 MET cc_start: 0.9074 (mmm) cc_final: 0.8831 (mmt) REVERT: A 334 ARG cc_start: 0.7156 (tpp80) cc_final: 0.6877 (mtp-110) REVERT: A 346 GLU cc_start: 0.8186 (tt0) cc_final: 0.7797 (tm-30) REVERT: A 367 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7350 (mm-30) REVERT: A 373 GLN cc_start: 0.7855 (tt0) cc_final: 0.7527 (tt0) REVERT: A 389 ASP cc_start: 0.7498 (p0) cc_final: 0.7198 (p0) REVERT: A 420 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7848 (ttm) REVERT: B 174 LYS cc_start: 0.8722 (ptpt) cc_final: 0.7889 (mmtt) REVERT: B 207 ARG cc_start: 0.7270 (mmm-85) cc_final: 0.6557 (mmm-85) REVERT: B 285 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7918 (ttmm) REVERT: B 373 GLN cc_start: 0.8081 (tt0) cc_final: 0.7732 (tt0) REVERT: B 389 ASP cc_start: 0.7408 (p0) cc_final: 0.6550 (p0) REVERT: B 438 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8345 (tptt) REVERT: B 462 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7731 (pm20) REVERT: C 172 PHE cc_start: 0.7623 (t80) cc_final: 0.7317 (t80) REVERT: C 174 LYS cc_start: 0.8370 (ptpp) cc_final: 0.7642 (mmtt) REVERT: C 207 ARG cc_start: 0.7214 (mmm-85) cc_final: 0.6617 (mmm-85) REVERT: C 300 PHE cc_start: 0.8036 (m-80) cc_final: 0.7823 (m-80) REVERT: C 346 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7591 (tt0) REVERT: C 351 GLU cc_start: 0.8012 (tt0) cc_final: 0.7782 (tt0) REVERT: C 367 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7314 (mm-30) REVERT: C 373 GLN cc_start: 0.7841 (tt0) cc_final: 0.7580 (tt0) REVERT: C 420 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7909 (tpp) REVERT: C 493 ASN cc_start: 0.8443 (p0) cc_final: 0.8068 (p0) REVERT: D 174 LYS cc_start: 0.8379 (ptpp) cc_final: 0.7525 (mmtt) REVERT: D 207 ARG cc_start: 0.7216 (mmm-85) cc_final: 0.6686 (mmm-85) REVERT: D 300 PHE cc_start: 0.8182 (m-80) cc_final: 0.7961 (m-80) REVERT: D 334 ARG cc_start: 0.7112 (tpp80) cc_final: 0.6516 (tpp-160) REVERT: D 373 GLN cc_start: 0.7967 (tt0) cc_final: 0.7718 (tt0) REVERT: D 493 ASN cc_start: 0.8497 (p0) cc_final: 0.8148 (p0) REVERT: E 145 CYS cc_start: 0.4534 (OUTLIER) cc_final: 0.4295 (p) REVERT: E 172 PHE cc_start: 0.7587 (t80) cc_final: 0.7227 (t80) REVERT: E 174 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7370 (mmtm) REVERT: E 207 ARG cc_start: 0.7433 (mmm-85) cc_final: 0.6843 (mmm-85) REVERT: E 228 ASP cc_start: 0.7833 (m-30) cc_final: 0.7363 (m-30) REVERT: E 334 ARG cc_start: 0.7091 (tpp80) cc_final: 0.6834 (mtp-110) REVERT: E 346 GLU cc_start: 0.8212 (tt0) cc_final: 0.7836 (tm-30) REVERT: E 367 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7390 (mm-30) REVERT: E 373 GLN cc_start: 0.7822 (tt0) cc_final: 0.7482 (tt0) REVERT: E 389 ASP cc_start: 0.7510 (p0) cc_final: 0.7247 (p0) REVERT: E 420 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7744 (ttm) REVERT: F 158 PHE cc_start: 0.8413 (m-80) cc_final: 0.8139 (m-10) REVERT: F 174 LYS cc_start: 0.8434 (ptpp) cc_final: 0.7683 (mmtm) REVERT: F 178 ASP cc_start: 0.8490 (m-30) cc_final: 0.8134 (m-30) REVERT: F 181 ARG cc_start: 0.8279 (mmm-85) cc_final: 0.7786 (mmt90) REVERT: F 207 ARG cc_start: 0.7071 (mmm-85) cc_final: 0.6512 (mmm-85) REVERT: F 334 ARG cc_start: 0.7168 (tpp80) cc_final: 0.6642 (tpp-160) REVERT: F 389 ASP cc_start: 0.7670 (p0) cc_final: 0.7402 (p0) outliers start: 46 outliers final: 28 residues processed: 304 average time/residue: 1.3863 time to fit residues: 469.7714 Evaluate side-chains 294 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 259 time to evaluate : 2.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 371 HIS Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain F residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 159 optimal weight: 0.5980 chunk 47 optimal weight: 0.7980 chunk 143 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 152 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN A 519 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS E 371 HIS E 493 ASN E 519 GLN F 519 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.153683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.113237 restraints weight = 20353.487| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.75 r_work: 0.3184 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18924 Z= 0.260 Angle : 0.602 10.961 25602 Z= 0.301 Chirality : 0.042 0.191 2922 Planarity : 0.005 0.037 3186 Dihedral : 4.421 22.564 2514 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.27 % Allowed : 17.62 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.18), residues: 2220 helix: 1.65 (0.14), residues: 1374 sheet: 0.40 (0.38), residues: 186 loop : -0.01 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP B 138 HIS 0.007 0.001 HIS E 371 PHE 0.030 0.002 PHE D 196 TYR 0.012 0.002 TYR F 453 ARG 0.008 0.000 ARG F 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 258 time to evaluate : 2.188 Fit side-chains REVERT: A 172 PHE cc_start: 0.7557 (t80) cc_final: 0.7178 (t80) REVERT: A 174 LYS cc_start: 0.8196 (ptpp) cc_final: 0.7351 (mmtm) REVERT: A 181 ARG cc_start: 0.8421 (mmm-85) cc_final: 0.8030 (mmt90) REVERT: A 207 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6464 (mmm-85) REVERT: A 249 MET cc_start: 0.9131 (mmm) cc_final: 0.8879 (mmt) REVERT: A 334 ARG cc_start: 0.7150 (tpp80) cc_final: 0.6902 (mtp-110) REVERT: A 346 GLU cc_start: 0.8121 (tt0) cc_final: 0.7719 (tm-30) REVERT: A 367 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7284 (mm-30) REVERT: A 373 GLN cc_start: 0.7841 (tt0) cc_final: 0.7515 (tt0) REVERT: A 389 ASP cc_start: 0.7436 (p0) cc_final: 0.7126 (p0) REVERT: A 420 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.7866 (ttm) REVERT: B 174 LYS cc_start: 0.8715 (ptpt) cc_final: 0.7884 (mmtt) REVERT: B 207 ARG cc_start: 0.7269 (mmm-85) cc_final: 0.6562 (mmm-85) REVERT: B 285 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7927 (ttmm) REVERT: B 438 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8370 (tptt) REVERT: B 462 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.7757 (pm20) REVERT: C 172 PHE cc_start: 0.7596 (t80) cc_final: 0.7296 (t80) REVERT: C 174 LYS cc_start: 0.8385 (ptpp) cc_final: 0.7587 (mmtt) REVERT: C 207 ARG cc_start: 0.7215 (mmm-85) cc_final: 0.6629 (mmm-85) REVERT: C 300 PHE cc_start: 0.8003 (m-80) cc_final: 0.7771 (m-80) REVERT: C 346 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7513 (tt0) REVERT: C 351 GLU cc_start: 0.7956 (tt0) cc_final: 0.7705 (tt0) REVERT: C 367 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7239 (mm-30) REVERT: C 373 GLN cc_start: 0.7834 (tt0) cc_final: 0.7551 (tt0) REVERT: C 420 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7863 (tpp) REVERT: C 493 ASN cc_start: 0.8462 (p0) cc_final: 0.8048 (p0) REVERT: D 124 PHE cc_start: 0.7398 (t80) cc_final: 0.7171 (t80) REVERT: D 174 LYS cc_start: 0.8369 (ptpp) cc_final: 0.7494 (mmtt) REVERT: D 207 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6708 (mmm-85) REVERT: D 300 PHE cc_start: 0.8148 (m-80) cc_final: 0.7915 (m-80) REVERT: D 334 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6449 (tpp-160) REVERT: D 373 GLN cc_start: 0.7871 (tt0) cc_final: 0.7647 (tt0) REVERT: D 493 ASN cc_start: 0.8521 (p0) cc_final: 0.8156 (p0) REVERT: E 145 CYS cc_start: 0.4505 (OUTLIER) cc_final: 0.4271 (p) REVERT: E 172 PHE cc_start: 0.7620 (t80) cc_final: 0.7226 (t80) REVERT: E 174 LYS cc_start: 0.8216 (ptpp) cc_final: 0.7317 (mmtm) REVERT: E 207 ARG cc_start: 0.7385 (mmm-85) cc_final: 0.6776 (mmm-85) REVERT: E 228 ASP cc_start: 0.7833 (m-30) cc_final: 0.7291 (m-30) REVERT: E 334 ARG cc_start: 0.7058 (tpp80) cc_final: 0.6786 (mtp-110) REVERT: E 346 GLU cc_start: 0.8115 (tt0) cc_final: 0.7724 (tm-30) REVERT: E 367 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7316 (mm-30) REVERT: E 373 GLN cc_start: 0.7840 (tt0) cc_final: 0.7446 (tt0) REVERT: E 389 ASP cc_start: 0.7451 (p0) cc_final: 0.7157 (p0) REVERT: E 420 MET cc_start: 0.8339 (OUTLIER) cc_final: 0.7777 (ttm) REVERT: E 435 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8824 (mtp) REVERT: F 158 PHE cc_start: 0.8436 (m-80) cc_final: 0.8155 (m-10) REVERT: F 174 LYS cc_start: 0.8499 (ptpp) cc_final: 0.7649 (mmtm) REVERT: F 178 ASP cc_start: 0.8532 (m-30) cc_final: 0.8158 (m-30) REVERT: F 181 ARG cc_start: 0.8230 (mmm-85) cc_final: 0.7735 (mmt90) REVERT: F 207 ARG cc_start: 0.7107 (mmm-85) cc_final: 0.6524 (mmm-85) REVERT: F 334 ARG cc_start: 0.7156 (tpp80) cc_final: 0.6662 (tpp-160) REVERT: F 389 ASP cc_start: 0.7683 (p0) cc_final: 0.6930 (p0) outliers start: 45 outliers final: 27 residues processed: 290 average time/residue: 1.4401 time to fit residues: 474.6695 Evaluate side-chains 285 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 250 time to evaluate : 2.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain B residue 462 GLN Chi-restraints excluded: chain C residue 145 CYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 145 CYS Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 145 CYS Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain F residue 164 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 44 optimal weight: 0.1980 chunk 3 optimal weight: 20.0000 chunk 71 optimal weight: 0.6980 chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.2980 chunk 175 optimal weight: 0.8980 chunk 204 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 519 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.157990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.119171 restraints weight = 21165.089| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.79 r_work: 0.3284 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18924 Z= 0.216 Angle : 0.578 11.184 25602 Z= 0.288 Chirality : 0.041 0.190 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.307 22.011 2514 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.01 % Allowed : 18.23 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.18), residues: 2220 helix: 1.71 (0.14), residues: 1374 sheet: 0.47 (0.39), residues: 186 loop : 0.02 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 138 HIS 0.004 0.001 HIS B 269 PHE 0.028 0.002 PHE D 196 TYR 0.012 0.002 TYR B 453 ARG 0.008 0.000 ARG F 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15212.12 seconds wall clock time: 276 minutes 33.01 seconds (16593.01 seconds total)