Starting phenix.real_space_refine on Mon Jun 16 09:46:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk8_61547/06_2025/9jk8_61547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk8_61547/06_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_61547/06_2025/9jk8_61547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk8_61547/06_2025/9jk8_61547.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk8_61547/06_2025/9jk8_61547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk8_61547/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 18504 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3084 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 13, 'TRANS': 362} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 8.33, per 1000 atoms: 0.45 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=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 145 " - pdb=" SG CYS A 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS B 145 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS F 145 " - pdb=" SG CYS F 149 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.16 Conformation dependent library (CDL) restraints added in 2.4 seconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 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: 2.20 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: 6.62 Time building geometry restraints manager: 6.16 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: 216 34.85 - 46.47: 78 46.47 - 58.09: 12 Dihedral angle restraints: 11352 sinusoidal: 4668 harmonic: 6684 Sorted by residual: dihedral pdb=" CB CYS E 145 " pdb=" SG CYS E 145 " pdb=" SG CYS E 149 " pdb=" CB CYS E 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.17 51.83 1 1.00e+01 1.00e-02 3.67e+01 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=" CB CYS D 145 " pdb=" SG CYS D 145 " pdb=" SG CYS D 149 " pdb=" CB CYS D 149 " ideal model delta sinusoidal sigma weight residual 93.00 41.20 51.80 1 1.00e+01 1.00e-02 3.66e+01 ... (remaining 11349 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: 2.29 - 2.81: 4826 2.81 - 3.33: 18219 3.33 - 3.85: 32117 3.85 - 4.38: 37822 4.38 - 4.90: 63738 Nonbonded interactions: 156722 Sorted by model distance: nonbonded pdb=" O ALA C 447 " pdb=" OH TYR C 453 " model vdw 2.286 3.040 nonbonded pdb=" O ALA B 447 " pdb=" OH TYR B 453 " model vdw 2.286 3.040 nonbonded pdb=" O ALA E 447 " pdb=" OH TYR E 453 " model vdw 2.286 3.040 nonbonded pdb=" O ALA A 447 " pdb=" OH TYR A 453 " model vdw 2.286 3.040 nonbonded pdb=" O ALA F 447 " pdb=" OH TYR F 453 " model vdw 2.287 3.040 ... (remaining 156717 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: 5.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 42.160 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.120 ------------------------------------------------------------------------------- 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 18930 Z= 0.211 Angle : 0.822 10.206 25614 Z= 0.435 Chirality : 0.050 0.342 2922 Planarity : 0.007 0.050 3186 Dihedral : 9.727 58.089 6978 Min Nonbonded Distance : 2.286 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 Details of bonding type rmsd hydrogen bonds : bond 0.13597 ( 1146) hydrogen bonds : angle 6.63072 ( 3318) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.47913 ( 12) covalent geometry : bond 0.00472 (18924) covalent geometry : angle 0.82219 (25602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 2.176 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: 1.6239 time to fit residues: 739.9481 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 : 1.994 ------------------------------------------------------------------------------- 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 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 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.162656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122165 restraints weight = 20116.576| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.77 r_work: 0.3308 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18930 Z= 0.139 Angle : 0.572 10.492 25614 Z= 0.300 Chirality : 0.042 0.167 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.592 23.588 2514 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.57 % Allowed : 9.32 % Favored : 88.12 % 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: 0.14 (0.17), residues: 2220 helix: 0.75 (0.13), residues: 1368 sheet: -0.26 (0.35), residues: 192 loop : -1.01 (0.22), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 138 HIS 0.006 0.001 HIS A 234 PHE 0.027 0.002 PHE D 196 TYR 0.014 0.002 TYR D 453 ARG 0.006 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 1146) hydrogen bonds : angle 4.65380 ( 3318) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.51034 ( 12) covalent geometry : bond 0.00311 (18924) covalent geometry : angle 0.57170 (25602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 334 time to evaluate : 3.903 Fit side-chains REVERT: A 172 PHE cc_start: 0.7635 (t80) cc_final: 0.7290 (t80) REVERT: A 174 LYS cc_start: 0.7949 (ptpp) cc_final: 0.7660 (mmtt) REVERT: A 207 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.6775 (mmm-85) REVERT: A 334 ARG cc_start: 0.6901 (tpp80) cc_final: 0.6509 (tpp-160) REVERT: A 373 GLN cc_start: 0.7427 (tt0) cc_final: 0.6969 (tt0) REVERT: A 420 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.7668 (ttm) REVERT: A 446 SER cc_start: 0.8461 (m) cc_final: 0.8145 (p) REVERT: B 172 PHE cc_start: 0.7467 (t80) cc_final: 0.7084 (t80) REVERT: B 179 MET cc_start: 0.8902 (mtm) cc_final: 0.8695 (mtm) REVERT: B 207 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6736 (mmm-85) REVERT: B 267 LEU cc_start: 0.8938 (mt) cc_final: 0.8736 (mp) REVERT: B 285 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7587 (ttpp) REVERT: B 334 ARG cc_start: 0.6893 (mtp-110) cc_final: 0.6551 (tpp-160) REVERT: B 373 GLN cc_start: 0.7866 (tt0) cc_final: 0.7411 (tp40) REVERT: B 413 ARG cc_start: 0.8577 (mmt90) cc_final: 0.8377 (mtt90) REVERT: C 172 PHE cc_start: 0.7711 (t80) cc_final: 0.7430 (t80) REVERT: C 207 ARG cc_start: 0.7299 (mmm-85) cc_final: 0.6549 (mmm-85) REVERT: C 249 MET cc_start: 0.8803 (tpt) cc_final: 0.8559 (mmm) REVERT: C 300 PHE cc_start: 0.8231 (m-80) cc_final: 0.7879 (m-80) REVERT: C 334 ARG cc_start: 0.6795 (tpp80) cc_final: 0.6525 (mtp-110) REVERT: C 346 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7568 (tt0) REVERT: C 351 GLU cc_start: 0.7994 (tt0) cc_final: 0.7639 (mt-10) REVERT: C 373 GLN cc_start: 0.7225 (tt0) cc_final: 0.6930 (tt0) REVERT: C 420 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.8013 (tpp) REVERT: C 446 SER cc_start: 0.8359 (m) cc_final: 0.8142 (p) REVERT: C 456 ASP cc_start: 0.8156 (p0) cc_final: 0.7899 (p0) REVERT: C 516 LEU cc_start: 0.8580 (tp) cc_final: 0.8358 (tm) REVERT: D 124 PHE cc_start: 0.7512 (t80) cc_final: 0.7255 (t80) REVERT: D 174 LYS cc_start: 0.7987 (ptpp) cc_final: 0.7102 (mmtt) REVERT: D 207 ARG cc_start: 0.6947 (mmm-85) cc_final: 0.6660 (mmm-85) REVERT: D 263 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7635 (mtp180) REVERT: D 267 LEU cc_start: 0.8772 (mt) cc_final: 0.8544 (mp) REVERT: D 285 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7621 (ttpp) REVERT: D 300 PHE cc_start: 0.8053 (m-80) cc_final: 0.7632 (m-80) REVERT: D 373 GLN cc_start: 0.7526 (tt0) cc_final: 0.7150 (tt0) REVERT: E 172 PHE cc_start: 0.7493 (t80) cc_final: 0.7138 (t80) REVERT: E 207 ARG cc_start: 0.7061 (mmm-85) cc_final: 0.6631 (mmm-85) REVERT: E 247 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: E 334 ARG cc_start: 0.7105 (tpp80) cc_final: 0.6593 (tpp-160) REVERT: E 346 GLU cc_start: 0.8063 (tt0) cc_final: 0.7671 (tm-30) REVERT: E 373 GLN cc_start: 0.7482 (tt0) cc_final: 0.6999 (tt0) REVERT: E 413 ARG cc_start: 0.8305 (mpt-90) cc_final: 0.7732 (mtm180) REVERT: E 420 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7770 (ttm) REVERT: E 456 ASP cc_start: 0.8043 (p0) cc_final: 0.7826 (p0) REVERT: F 148 ILE cc_start: 0.7273 (mm) cc_final: 0.6942 (tt) REVERT: F 174 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7388 (mmtm) REVERT: F 207 ARG cc_start: 0.6956 (mmm-85) cc_final: 0.6505 (mmm-85) REVERT: F 346 GLU cc_start: 0.8065 (tt0) cc_final: 0.7846 (tt0) REVERT: F 373 GLN cc_start: 0.7765 (tt0) cc_final: 0.7274 (tp40) REVERT: F 389 ASP cc_start: 0.7206 (p0) cc_final: 0.6984 (p0) REVERT: F 413 ARG cc_start: 0.8394 (mmt90) cc_final: 0.8174 (mmt90) outliers start: 51 outliers final: 19 residues processed: 361 average time/residue: 2.1200 time to fit residues: 859.4102 Evaluate side-chains 315 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 4.198 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 154 ILE 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 C residue 493 ASN Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 154 ILE 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 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: 3.9990 chunk 201 optimal weight: 0.5980 chunk 54 optimal weight: 0.0470 chunk 133 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 106 optimal weight: 0.0770 chunk 208 optimal weight: 0.6980 chunk 191 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- 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 416 ASN B 247 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 425 GLN B 493 ASN C 247 GLN ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 GLN C 493 ASN D 221 GLN D 293 ASN 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 493 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.161106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120431 restraints weight = 20185.683| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 1.78 r_work: 0.3288 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18930 Z= 0.127 Angle : 0.549 10.466 25614 Z= 0.281 Chirality : 0.040 0.162 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.347 21.844 2514 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.47 % Allowed : 13.75 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.17), residues: 2220 helix: 1.31 (0.14), residues: 1380 sheet: 0.14 (0.38), residues: 186 loop : -0.70 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 458 HIS 0.004 0.001 HIS D 426 PHE 0.024 0.002 PHE C 196 TYR 0.013 0.002 TYR F 453 ARG 0.007 0.000 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 1146) hydrogen bonds : angle 4.35674 ( 3318) SS BOND : bond 0.00059 ( 6) SS BOND : angle 0.42488 ( 12) covalent geometry : bond 0.00287 (18924) covalent geometry : angle 0.54902 (25602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 303 time to evaluate : 2.040 Fit side-chains REVERT: A 172 PHE cc_start: 0.7621 (t80) cc_final: 0.7295 (t80) REVERT: A 174 LYS cc_start: 0.7991 (ptpp) cc_final: 0.7318 (mmtm) REVERT: A 196 PHE cc_start: 0.7114 (t80) cc_final: 0.6897 (t80) REVERT: A 207 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6713 (mmm-85) REVERT: A 334 ARG cc_start: 0.7065 (tpp80) cc_final: 0.6639 (tpp-160) REVERT: A 373 GLN cc_start: 0.7459 (tt0) cc_final: 0.7007 (tt0) REVERT: B 207 ARG cc_start: 0.7323 (mmm-85) cc_final: 0.6524 (mmm-85) REVERT: B 285 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7462 (ttpp) REVERT: B 304 LYS cc_start: 0.7659 (ttmm) cc_final: 0.7002 (mppt) REVERT: B 334 ARG cc_start: 0.6939 (mtp-110) cc_final: 0.6566 (tpp-160) REVERT: B 373 GLN cc_start: 0.7845 (tt0) cc_final: 0.7365 (tp40) REVERT: B 413 ARG cc_start: 0.8540 (mmt90) cc_final: 0.8219 (mmt90) REVERT: C 172 PHE cc_start: 0.7628 (t80) cc_final: 0.7323 (t80) REVERT: C 207 ARG cc_start: 0.7283 (mmm-85) cc_final: 0.6512 (mmm-85) REVERT: C 267 LEU cc_start: 0.8777 (mt) cc_final: 0.8571 (mp) REVERT: C 300 PHE cc_start: 0.8246 (m-80) cc_final: 0.7873 (m-10) REVERT: C 346 GLU cc_start: 0.7935 (mm-30) cc_final: 0.7564 (tt0) REVERT: C 351 GLU cc_start: 0.7967 (tt0) cc_final: 0.7752 (tt0) REVERT: C 373 GLN cc_start: 0.7362 (tt0) cc_final: 0.7040 (tt0) REVERT: C 420 MET cc_start: 0.8517 (OUTLIER) cc_final: 0.8087 (tpp) REVERT: D 124 PHE cc_start: 0.7263 (t80) cc_final: 0.7000 (t80) REVERT: D 174 LYS cc_start: 0.8056 (ptpp) cc_final: 0.7175 (mmtt) REVERT: D 207 ARG cc_start: 0.6945 (mmm-85) cc_final: 0.6576 (mmm-85) REVERT: D 263 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7657 (mtp180) REVERT: D 267 LEU cc_start: 0.8737 (mt) cc_final: 0.8513 (mp) REVERT: D 285 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7581 (ttpp) REVERT: D 300 PHE cc_start: 0.8097 (m-80) cc_final: 0.7628 (m-80) REVERT: D 334 ARG cc_start: 0.7067 (tpp80) cc_final: 0.6644 (tpp-160) REVERT: D 373 GLN cc_start: 0.7517 (tt0) cc_final: 0.7125 (tt0) REVERT: E 172 PHE cc_start: 0.7595 (t80) cc_final: 0.7228 (t80) REVERT: E 207 ARG cc_start: 0.7054 (mmm-85) cc_final: 0.6598 (mmm-85) REVERT: E 334 ARG cc_start: 0.7148 (tpp80) cc_final: 0.6647 (tpp-160) REVERT: E 346 GLU cc_start: 0.8063 (tt0) cc_final: 0.7670 (tm-30) REVERT: E 367 GLU cc_start: 0.7885 (mt-10) cc_final: 0.7303 (mm-30) REVERT: E 373 GLN cc_start: 0.7733 (tt0) cc_final: 0.7207 (tt0) REVERT: E 413 ARG cc_start: 0.8326 (mpt-90) cc_final: 0.8096 (mmt90) REVERT: E 420 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7775 (ttm) REVERT: F 119 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.5992 (tm) REVERT: F 174 LYS cc_start: 0.8034 (ptpp) cc_final: 0.7489 (mmtm) REVERT: F 207 ARG cc_start: 0.6927 (mmm-85) cc_final: 0.6441 (mmm-85) REVERT: F 304 LYS cc_start: 0.7664 (tttt) cc_final: 0.7084 (mptt) REVERT: F 334 ARG cc_start: 0.7009 (mmm160) cc_final: 0.6648 (mtp-110) REVERT: F 373 GLN cc_start: 0.7872 (tt0) cc_final: 0.7358 (tt0) REVERT: F 389 ASP cc_start: 0.7279 (p0) cc_final: 0.7055 (p0) REVERT: F 413 ARG cc_start: 0.8477 (mmt90) cc_final: 0.8222 (mmt90) outliers start: 49 outliers final: 21 residues processed: 330 average time/residue: 1.4094 time to fit residues: 516.5528 Evaluate side-chains 304 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 277 time to evaluate : 2.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU 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 C residue 420 MET Chi-restraints excluded: chain D residue 233 ILE 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 446 SER Chi-restraints excluded: chain E residue 155 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: 0.9990 chunk 138 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 84 optimal weight: 4.9990 chunk 199 optimal weight: 0.3980 chunk 213 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN B 247 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 406 GLN B 425 GLN C 247 GLN C 350 HIS C 493 ASN D 247 GLN D 350 HIS D 406 GLN E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 425 GLN E 493 ASN F 247 GLN F 406 GLN F 425 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.155487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.114024 restraints weight = 20133.826| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.78 r_work: 0.3206 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18930 Z= 0.169 Angle : 0.585 9.938 25614 Z= 0.298 Chirality : 0.042 0.153 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.487 22.357 2514 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.58 % Allowed : 13.60 % Favored : 82.83 % 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: 1.42 (0.14), residues: 1380 sheet: 0.43 (0.40), residues: 180 loop : -0.38 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 458 HIS 0.005 0.001 HIS B 426 PHE 0.023 0.002 PHE C 196 TYR 0.016 0.002 TYR F 453 ARG 0.006 0.001 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03677 ( 1146) hydrogen bonds : angle 4.32618 ( 3318) SS BOND : bond 0.00088 ( 6) SS BOND : angle 0.54895 ( 12) covalent geometry : bond 0.00397 (18924) covalent geometry : angle 0.58464 (25602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 307 time to evaluate : 2.303 Fit side-chains REVERT: A 172 PHE cc_start: 0.7681 (t80) cc_final: 0.7370 (t80) REVERT: A 174 LYS cc_start: 0.8120 (ptpp) cc_final: 0.7317 (mmtm) REVERT: A 207 ARG cc_start: 0.7345 (mmm-85) cc_final: 0.6669 (mmm-85) REVERT: A 249 MET cc_start: 0.9014 (mmm) cc_final: 0.8774 (mmt) REVERT: A 334 ARG cc_start: 0.7154 (tpp80) cc_final: 0.6647 (tpp-160) REVERT: A 346 GLU cc_start: 0.8126 (tt0) cc_final: 0.7713 (tm-30) REVERT: A 367 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7353 (mm-30) REVERT: A 373 GLN cc_start: 0.7651 (tt0) cc_final: 0.7242 (tt0) REVERT: A 389 ASP cc_start: 0.7276 (p0) cc_final: 0.7043 (p0) REVERT: A 420 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.7845 (ttm) REVERT: B 174 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7730 (mmtt) REVERT: B 207 ARG cc_start: 0.7376 (mmm-85) cc_final: 0.6505 (mmm-85) REVERT: B 285 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7890 (ttmm) REVERT: B 373 GLN cc_start: 0.8057 (tt0) cc_final: 0.7576 (tt0) REVERT: B 438 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8398 (tptt) REVERT: C 172 PHE cc_start: 0.7758 (t80) cc_final: 0.7477 (t80) REVERT: C 207 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6503 (mmm-85) REVERT: C 300 PHE cc_start: 0.8112 (m-80) cc_final: 0.7864 (m-80) REVERT: C 346 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7536 (tt0) REVERT: C 351 GLU cc_start: 0.8011 (tt0) cc_final: 0.7765 (tt0) REVERT: C 367 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7211 (mm-30) REVERT: C 373 GLN cc_start: 0.7530 (tt0) cc_final: 0.7217 (tt0) REVERT: D 174 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7451 (mmtt) REVERT: D 207 ARG cc_start: 0.7021 (mmm-85) cc_final: 0.6582 (mmm-85) REVERT: D 247 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8166 (tt0) REVERT: D 285 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7944 (ttpp) REVERT: D 300 PHE cc_start: 0.8182 (m-80) cc_final: 0.7942 (m-80) REVERT: D 334 ARG cc_start: 0.6888 (tpp80) cc_final: 0.6491 (tpp-160) REVERT: D 373 GLN cc_start: 0.7726 (tt0) cc_final: 0.7373 (tt0) REVERT: D 493 ASN cc_start: 0.8491 (p0) cc_final: 0.8118 (p0) REVERT: E 172 PHE cc_start: 0.7652 (t80) cc_final: 0.7274 (t80) REVERT: E 207 ARG cc_start: 0.7358 (mmm-85) cc_final: 0.6812 (mmm-85) REVERT: E 215 ASN cc_start: 0.7212 (p0) cc_final: 0.6975 (t0) REVERT: E 247 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: E 334 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6883 (mtp-110) REVERT: E 346 GLU cc_start: 0.8087 (tt0) cc_final: 0.7692 (tm-30) REVERT: E 367 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7315 (mm-30) REVERT: E 373 GLN cc_start: 0.7903 (tt0) cc_final: 0.7363 (tt0) REVERT: E 389 ASP cc_start: 0.7401 (p0) cc_final: 0.7131 (p0) REVERT: E 420 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7901 (ttm) REVERT: F 174 LYS cc_start: 0.8293 (ptpp) cc_final: 0.7615 (mmtm) REVERT: F 207 ARG cc_start: 0.7042 (mmm-85) cc_final: 0.6399 (mmm-85) REVERT: F 334 ARG cc_start: 0.7077 (mmm160) cc_final: 0.6674 (tpp-160) REVERT: F 373 GLN cc_start: 0.7953 (tt0) cc_final: 0.7478 (tt0) REVERT: F 389 ASP cc_start: 0.7506 (p0) cc_final: 0.7252 (p0) outliers start: 71 outliers final: 28 residues processed: 348 average time/residue: 1.3840 time to fit residues: 537.7687 Evaluate side-chains 313 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 277 time to evaluate : 2.157 ------------------------------------------------------------------------------- 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 209 LEU Chi-restraints excluded: chain A residue 233 ILE 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 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS 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 298 SER 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 446 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 247 GLN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 208 optimal weight: 0.5980 chunk 42 optimal weight: 0.0370 chunk 96 optimal weight: 0.5980 chunk 193 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 0.4980 chunk 159 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 247 GLN C 273 GLN 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 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.157527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.116499 restraints weight = 20240.099| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.78 r_work: 0.3241 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18930 Z= 0.133 Angle : 0.558 10.478 25614 Z= 0.282 Chirality : 0.040 0.148 2922 Planarity : 0.004 0.038 3186 Dihedral : 4.309 21.814 2514 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.42 % Allowed : 15.21 % Favored : 81.37 % 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: 1.35 (0.18), residues: 2220 helix: 1.53 (0.14), residues: 1380 sheet: 0.53 (0.41), residues: 180 loop : -0.25 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 458 HIS 0.005 0.001 HIS C 269 PHE 0.023 0.002 PHE E 196 TYR 0.013 0.002 TYR F 453 ARG 0.008 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 1146) hydrogen bonds : angle 4.21671 ( 3318) SS BOND : bond 0.00058 ( 6) SS BOND : angle 0.55374 ( 12) covalent geometry : bond 0.00304 (18924) covalent geometry : angle 0.55770 (25602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 281 time to evaluate : 2.203 Fit side-chains REVERT: A 172 PHE cc_start: 0.7632 (t80) cc_final: 0.7283 (t80) REVERT: A 174 LYS cc_start: 0.8128 (ptpp) cc_final: 0.7323 (mmtm) REVERT: A 181 ARG cc_start: 0.8103 (mmm-85) cc_final: 0.7711 (mmt90) REVERT: A 207 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.6590 (mmm-85) REVERT: A 249 MET cc_start: 0.9011 (mmm) cc_final: 0.8751 (mmt) REVERT: A 334 ARG cc_start: 0.7183 (tpp80) cc_final: 0.6829 (tpp-160) REVERT: A 346 GLU cc_start: 0.8102 (tt0) cc_final: 0.7706 (tm-30) REVERT: A 367 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7293 (mm-30) REVERT: A 373 GLN cc_start: 0.7595 (tt0) cc_final: 0.7174 (tt0) REVERT: A 389 ASP cc_start: 0.7327 (p0) cc_final: 0.7070 (p0) REVERT: A 420 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7818 (ttm) REVERT: B 174 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7721 (mmtt) REVERT: B 207 ARG cc_start: 0.7234 (mmm-85) cc_final: 0.6705 (mmm-85) REVERT: B 285 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7668 (ttpp) REVERT: B 334 ARG cc_start: 0.7258 (tpp80) cc_final: 0.6983 (mtp-110) REVERT: B 373 GLN cc_start: 0.7943 (tt0) cc_final: 0.7486 (tt0) REVERT: B 438 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8268 (tptp) REVERT: C 172 PHE cc_start: 0.7693 (t80) cc_final: 0.7365 (t80) REVERT: C 207 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6561 (mmm-85) REVERT: C 300 PHE cc_start: 0.8106 (m-80) cc_final: 0.7713 (m-10) REVERT: C 346 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7545 (tt0) REVERT: C 351 GLU cc_start: 0.8007 (tt0) cc_final: 0.7767 (tt0) REVERT: C 373 GLN cc_start: 0.7494 (tt0) cc_final: 0.7185 (tt0) REVERT: C 420 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7900 (tpp) REVERT: D 174 LYS cc_start: 0.8260 (ptpp) cc_final: 0.7414 (mmtt) REVERT: D 207 ARG cc_start: 0.6939 (mmm-85) cc_final: 0.6516 (mmm-85) REVERT: D 247 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8272 (tt0) REVERT: D 285 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7731 (ttpp) REVERT: D 300 PHE cc_start: 0.8182 (m-80) cc_final: 0.7753 (m-10) REVERT: D 334 ARG cc_start: 0.6898 (tpp80) cc_final: 0.6513 (tpp-160) REVERT: D 373 GLN cc_start: 0.7667 (tt0) cc_final: 0.7322 (tt0) REVERT: D 487 ASP cc_start: 0.7809 (m-30) cc_final: 0.7574 (m-30) REVERT: E 172 PHE cc_start: 0.7539 (t80) cc_final: 0.7165 (t80) REVERT: E 207 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.6719 (mmm-85) REVERT: E 215 ASN cc_start: 0.7240 (p0) cc_final: 0.6964 (t0) REVERT: E 247 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8270 (tt0) REVERT: E 334 ARG cc_start: 0.7128 (tpp80) cc_final: 0.6871 (mtp-110) REVERT: E 346 GLU cc_start: 0.8091 (tt0) cc_final: 0.7697 (tm-30) REVERT: E 367 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7250 (mm-30) REVERT: E 373 GLN cc_start: 0.7787 (tt0) cc_final: 0.7337 (tt0) REVERT: E 389 ASP cc_start: 0.7362 (p0) cc_final: 0.7090 (p0) REVERT: E 420 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7830 (ttm) REVERT: F 158 PHE cc_start: 0.8415 (m-80) cc_final: 0.8142 (m-10) REVERT: F 174 LYS cc_start: 0.8297 (ptpp) cc_final: 0.7619 (mmtm) REVERT: F 207 ARG cc_start: 0.6928 (mmm-85) cc_final: 0.6293 (mmm-85) REVERT: F 334 ARG cc_start: 0.7068 (mmm160) cc_final: 0.6653 (tpp-160) REVERT: F 373 GLN cc_start: 0.7784 (tt0) cc_final: 0.7366 (tt0) REVERT: F 389 ASP cc_start: 0.7440 (p0) cc_final: 0.7194 (p0) REVERT: F 454 ASP cc_start: 0.7973 (m-30) cc_final: 0.7768 (m-30) outliers start: 68 outliers final: 27 residues processed: 321 average time/residue: 1.3785 time to fit residues: 494.4041 Evaluate side-chains 305 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 155 SER 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 239 VAL Chi-restraints excluded: chain C residue 298 SER 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 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 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 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 375 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 43 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 chunk 162 optimal weight: 0.7980 chunk 140 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 185 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 198 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 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 215 ASN F 425 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.155760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114617 restraints weight = 20437.432| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.78 r_work: 0.3216 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18930 Z= 0.151 Angle : 0.573 10.398 25614 Z= 0.289 Chirality : 0.041 0.149 2922 Planarity : 0.005 0.037 3186 Dihedral : 4.333 22.136 2514 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.98 % Allowed : 15.36 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.18), residues: 2220 helix: 1.57 (0.14), residues: 1380 sheet: 0.54 (0.39), residues: 192 loop : -0.23 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 458 HIS 0.005 0.001 HIS C 269 PHE 0.025 0.002 PHE C 429 TYR 0.013 0.002 TYR F 453 ARG 0.007 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1146) hydrogen bonds : angle 4.20949 ( 3318) SS BOND : bond 0.00107 ( 6) SS BOND : angle 0.63332 ( 12) covalent geometry : bond 0.00354 (18924) covalent geometry : angle 0.57254 (25602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 275 time to evaluate : 1.948 Fit side-chains REVERT: A 172 PHE cc_start: 0.7637 (t80) cc_final: 0.7270 (t80) REVERT: A 174 LYS cc_start: 0.8167 (ptpp) cc_final: 0.7327 (mmtm) REVERT: A 181 ARG cc_start: 0.8225 (mmm-85) cc_final: 0.7784 (mmt90) REVERT: A 207 ARG cc_start: 0.7198 (mmm-85) cc_final: 0.6518 (mmm-85) REVERT: A 249 MET cc_start: 0.9010 (mmm) cc_final: 0.8771 (mmt) REVERT: A 334 ARG cc_start: 0.7233 (tpp80) cc_final: 0.6988 (mtp-110) REVERT: A 346 GLU cc_start: 0.8118 (tt0) cc_final: 0.7722 (tm-30) REVERT: A 367 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7290 (mm-30) REVERT: A 373 GLN cc_start: 0.7806 (tt0) cc_final: 0.7371 (tt0) REVERT: A 389 ASP cc_start: 0.7347 (p0) cc_final: 0.7105 (p0) REVERT: A 420 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7872 (ttm) REVERT: B 174 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7776 (mmtt) REVERT: B 207 ARG cc_start: 0.7243 (mmm-85) cc_final: 0.6734 (mmm-85) REVERT: B 285 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7851 (ttmm) REVERT: B 334 ARG cc_start: 0.7275 (tpp80) cc_final: 0.6692 (tpp-160) REVERT: B 373 GLN cc_start: 0.8018 (tt0) cc_final: 0.7560 (tt0) REVERT: B 438 LYS cc_start: 0.8585 (OUTLIER) cc_final: 0.8374 (tptt) REVERT: C 172 PHE cc_start: 0.7705 (t80) cc_final: 0.7397 (t80) REVERT: C 207 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.6551 (mmm-85) REVERT: C 300 PHE cc_start: 0.8023 (m-80) cc_final: 0.7641 (m-10) REVERT: C 346 GLU cc_start: 0.7958 (mm-30) cc_final: 0.7543 (tt0) REVERT: C 351 GLU cc_start: 0.8024 (tt0) cc_final: 0.7777 (tt0) REVERT: C 367 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7221 (mm-30) REVERT: C 373 GLN cc_start: 0.7563 (tt0) cc_final: 0.7275 (tt0) REVERT: C 420 MET cc_start: 0.8471 (OUTLIER) cc_final: 0.7906 (tpp) REVERT: D 124 PHE cc_start: 0.7420 (t80) cc_final: 0.7175 (t80) REVERT: D 174 LYS cc_start: 0.8310 (ptpp) cc_final: 0.7452 (mmtt) REVERT: D 207 ARG cc_start: 0.7073 (mmm-85) cc_final: 0.6636 (mmm-85) REVERT: D 247 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: D 285 LYS cc_start: 0.8187 (OUTLIER) cc_final: 0.7895 (ttpp) REVERT: D 300 PHE cc_start: 0.8202 (m-80) cc_final: 0.7963 (m-80) REVERT: D 334 ARG cc_start: 0.6927 (tpp80) cc_final: 0.6397 (tpp-160) REVERT: D 373 GLN cc_start: 0.7722 (tt0) cc_final: 0.7412 (tt0) REVERT: D 487 ASP cc_start: 0.7853 (m-30) cc_final: 0.7608 (m-30) REVERT: E 172 PHE cc_start: 0.7578 (t80) cc_final: 0.7188 (t80) REVERT: E 176 ARG cc_start: 0.7448 (mmm160) cc_final: 0.7029 (mmm160) REVERT: E 207 ARG cc_start: 0.7347 (mmm-85) cc_final: 0.6773 (mmm-85) REVERT: E 215 ASN cc_start: 0.7261 (OUTLIER) cc_final: 0.6940 (t0) REVERT: E 334 ARG cc_start: 0.7145 (tpp80) cc_final: 0.6868 (mtp-110) REVERT: E 346 GLU cc_start: 0.8123 (tt0) cc_final: 0.7733 (tm-30) REVERT: E 367 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7359 (mm-30) REVERT: E 373 GLN cc_start: 0.7769 (tt0) cc_final: 0.7348 (tt0) REVERT: E 389 ASP cc_start: 0.7419 (p0) cc_final: 0.7154 (p0) REVERT: E 420 MET cc_start: 0.8421 (OUTLIER) cc_final: 0.7880 (ttm) REVERT: F 158 PHE cc_start: 0.8408 (m-80) cc_final: 0.8141 (m-10) REVERT: F 174 LYS cc_start: 0.8374 (ptpp) cc_final: 0.7639 (mmtm) REVERT: F 207 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6497 (mmm-85) REVERT: F 215 ASN cc_start: 0.7172 (OUTLIER) cc_final: 0.6948 (t0) REVERT: F 304 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7559 (mttt) REVERT: F 334 ARG cc_start: 0.7037 (mmm160) cc_final: 0.6623 (tpp-160) REVERT: F 373 GLN cc_start: 0.7885 (tt0) cc_final: 0.7675 (tt0) REVERT: F 389 ASP cc_start: 0.7495 (p0) cc_final: 0.7247 (p0) outliers start: 79 outliers final: 33 residues processed: 324 average time/residue: 1.3050 time to fit residues: 474.9075 Evaluate side-chains 307 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 263 time to evaluate : 2.038 ------------------------------------------------------------------------------- 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 A residue 446 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 226 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 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 215 ASN 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 446 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 375 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 130 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 135 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 178 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN B 519 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 GLN D 215 ASN D 247 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.155095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113933 restraints weight = 20252.869| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.76 r_work: 0.3206 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 18930 Z= 0.159 Angle : 0.590 10.564 25614 Z= 0.296 Chirality : 0.041 0.184 2922 Planarity : 0.005 0.037 3186 Dihedral : 4.356 22.167 2514 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.78 % Allowed : 15.91 % 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: 1.50 (0.18), residues: 2220 helix: 1.60 (0.14), residues: 1380 sheet: 0.62 (0.39), residues: 186 loop : -0.05 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 138 HIS 0.004 0.001 HIS C 269 PHE 0.026 0.002 PHE C 429 TYR 0.012 0.002 TYR F 453 ARG 0.007 0.000 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 1146) hydrogen bonds : angle 4.21199 ( 3318) SS BOND : bond 0.00111 ( 6) SS BOND : angle 0.64429 ( 12) covalent geometry : bond 0.00374 (18924) covalent geometry : angle 0.59003 (25602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 266 time to evaluate : 2.060 Fit side-chains REVERT: A 172 PHE cc_start: 0.7635 (t80) cc_final: 0.7274 (t80) REVERT: A 174 LYS cc_start: 0.8172 (ptpp) cc_final: 0.7350 (mmtm) REVERT: A 181 ARG cc_start: 0.8214 (mmm-85) cc_final: 0.7859 (mmt90) REVERT: A 207 ARG cc_start: 0.7095 (mmm-85) cc_final: 0.6449 (mmm-85) REVERT: A 249 MET cc_start: 0.9067 (mmm) cc_final: 0.8835 (mmt) REVERT: A 334 ARG cc_start: 0.7206 (tpp80) cc_final: 0.6948 (mtp-110) REVERT: A 346 GLU cc_start: 0.8123 (tt0) cc_final: 0.7727 (tm-30) REVERT: A 367 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7276 (mm-30) REVERT: A 373 GLN cc_start: 0.7814 (tt0) cc_final: 0.7357 (tt0) REVERT: A 389 ASP cc_start: 0.7379 (p0) cc_final: 0.7114 (p0) REVERT: A 420 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7902 (ttm) REVERT: B 174 LYS cc_start: 0.8739 (OUTLIER) cc_final: 0.7846 (mmtt) REVERT: B 207 ARG cc_start: 0.7263 (mmm-85) cc_final: 0.6718 (mmm-85) REVERT: B 285 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7929 (ttmm) REVERT: B 373 GLN cc_start: 0.8048 (tt0) cc_final: 0.7584 (tt0) REVERT: B 420 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.8004 (ttm) REVERT: B 438 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8385 (tptt) REVERT: C 172 PHE cc_start: 0.7632 (t80) cc_final: 0.7331 (t80) REVERT: C 174 LYS cc_start: 0.8302 (ptpp) cc_final: 0.7581 (mmtt) REVERT: C 207 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6543 (mmm-85) REVERT: C 215 ASN cc_start: 0.7414 (OUTLIER) cc_final: 0.7042 (t0) REVERT: C 300 PHE cc_start: 0.8022 (m-80) cc_final: 0.7816 (m-80) REVERT: C 346 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7549 (tt0) REVERT: C 351 GLU cc_start: 0.8033 (tt0) cc_final: 0.7785 (tt0) REVERT: C 367 GLU cc_start: 0.7949 (mt-10) cc_final: 0.7242 (mm-30) REVERT: C 373 GLN cc_start: 0.7569 (tt0) cc_final: 0.7260 (tt0) REVERT: C 420 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.7848 (tpp) REVERT: D 124 PHE cc_start: 0.7424 (t80) cc_final: 0.7178 (t80) REVERT: D 174 LYS cc_start: 0.8318 (ptpp) cc_final: 0.7489 (mmtt) REVERT: D 207 ARG cc_start: 0.7081 (mmm-85) cc_final: 0.6608 (mmm-85) REVERT: D 247 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8333 (tt0) REVERT: D 285 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7922 (ttpp) REVERT: D 300 PHE cc_start: 0.8163 (m-80) cc_final: 0.7892 (m-80) REVERT: D 334 ARG cc_start: 0.6974 (tpp80) cc_final: 0.6413 (tpp-160) REVERT: D 373 GLN cc_start: 0.7824 (tt0) cc_final: 0.7539 (tt0) REVERT: D 487 ASP cc_start: 0.7870 (m-30) cc_final: 0.7626 (m-30) REVERT: E 172 PHE cc_start: 0.7611 (t80) cc_final: 0.7224 (t80) REVERT: E 174 LYS cc_start: 0.8211 (ptpp) cc_final: 0.7340 (mmtm) REVERT: E 207 ARG cc_start: 0.7381 (mmm-85) cc_final: 0.6763 (mmm-85) REVERT: E 215 ASN cc_start: 0.7144 (p0) cc_final: 0.6932 (t0) REVERT: E 228 ASP cc_start: 0.7841 (m-30) cc_final: 0.7454 (m-30) REVERT: E 334 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6836 (mtp-110) REVERT: E 346 GLU cc_start: 0.8134 (tt0) cc_final: 0.7745 (tm-30) REVERT: E 367 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7345 (mm-30) REVERT: E 373 GLN cc_start: 0.7803 (tt0) cc_final: 0.7411 (tt0) REVERT: E 389 ASP cc_start: 0.7397 (p0) cc_final: 0.7141 (p0) REVERT: E 420 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.7862 (ttm) REVERT: F 158 PHE cc_start: 0.8396 (m-80) cc_final: 0.8109 (m-10) REVERT: F 174 LYS cc_start: 0.8400 (ptpp) cc_final: 0.7667 (mmtm) REVERT: F 207 ARG cc_start: 0.7081 (mmm-85) cc_final: 0.6455 (mmm-85) REVERT: F 304 LYS cc_start: 0.7934 (OUTLIER) cc_final: 0.7610 (mttt) REVERT: F 373 GLN cc_start: 0.7869 (tt0) cc_final: 0.7654 (tt0) REVERT: F 389 ASP cc_start: 0.7531 (p0) cc_final: 0.7282 (p0) outliers start: 75 outliers final: 37 residues processed: 317 average time/residue: 1.3201 time to fit residues: 469.5437 Evaluate side-chains 314 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 2.052 ------------------------------------------------------------------------------- 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 A residue 446 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 298 SER 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 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 209 LEU 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 119 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 375 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 195 optimal weight: 4.9990 chunk 136 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 108 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 60 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN D 247 GLN D 273 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113317 restraints weight = 20224.046| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.75 r_work: 0.3196 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18930 Z= 0.165 Angle : 0.597 10.935 25614 Z= 0.299 Chirality : 0.042 0.187 2922 Planarity : 0.005 0.040 3186 Dihedral : 4.379 22.369 2514 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.37 % Allowed : 16.52 % 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: 1.52 (0.18), residues: 2220 helix: 1.63 (0.14), residues: 1374 sheet: 0.49 (0.38), residues: 186 loop : -0.06 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 138 HIS 0.004 0.001 HIS C 269 PHE 0.025 0.002 PHE C 429 TYR 0.013 0.002 TYR C 216 ARG 0.009 0.001 ARG F 334 Details of bonding type rmsd hydrogen bonds : bond 0.03550 ( 1146) hydrogen bonds : angle 4.21685 ( 3318) SS BOND : bond 0.00117 ( 6) SS BOND : angle 0.65924 ( 12) covalent geometry : bond 0.00388 (18924) covalent geometry : angle 0.59731 (25602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 269 time to evaluate : 2.195 Fit side-chains REVERT: A 172 PHE cc_start: 0.7644 (t80) cc_final: 0.7277 (t80) REVERT: A 174 LYS cc_start: 0.8199 (ptpp) cc_final: 0.7345 (mmtm) REVERT: A 181 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.7873 (mmt90) REVERT: A 207 ARG cc_start: 0.7059 (mmm-85) cc_final: 0.6393 (mmm-85) REVERT: A 249 MET cc_start: 0.9084 (mmm) cc_final: 0.8865 (mmt) REVERT: A 334 ARG cc_start: 0.7254 (tpp80) cc_final: 0.6970 (mtp-110) REVERT: A 346 GLU cc_start: 0.8130 (tt0) cc_final: 0.7736 (tm-30) REVERT: A 367 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7296 (mm-30) REVERT: A 373 GLN cc_start: 0.7779 (tt0) cc_final: 0.7390 (tt0) REVERT: A 389 ASP cc_start: 0.7434 (p0) cc_final: 0.7167 (p0) REVERT: A 420 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7880 (ttm) REVERT: B 174 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7885 (mmtt) REVERT: B 207 ARG cc_start: 0.7259 (mmm-85) cc_final: 0.6707 (mmm-85) REVERT: B 285 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7948 (ttmm) REVERT: B 373 GLN cc_start: 0.8016 (tt0) cc_final: 0.7658 (tt0) REVERT: B 438 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8395 (tptt) REVERT: C 172 PHE cc_start: 0.7641 (t80) cc_final: 0.7351 (t80) REVERT: C 174 LYS cc_start: 0.8338 (ptpp) cc_final: 0.7638 (mmtt) REVERT: C 207 ARG cc_start: 0.7163 (mmm-85) cc_final: 0.6540 (mmm-85) REVERT: C 215 ASN cc_start: 0.7331 (OUTLIER) cc_final: 0.7097 (t0) REVERT: C 300 PHE cc_start: 0.8037 (m-80) cc_final: 0.7828 (m-80) REVERT: C 346 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7552 (tt0) REVERT: C 351 GLU cc_start: 0.8042 (tt0) cc_final: 0.7787 (tt0) REVERT: C 367 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7250 (mm-30) REVERT: C 373 GLN cc_start: 0.7678 (tt0) cc_final: 0.7377 (tt0) REVERT: C 420 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7847 (tpp) REVERT: D 124 PHE cc_start: 0.7427 (t80) cc_final: 0.7181 (t80) REVERT: D 174 LYS cc_start: 0.8351 (ptpp) cc_final: 0.7587 (mmtt) REVERT: D 207 ARG cc_start: 0.7122 (mmm-85) cc_final: 0.6663 (mmm-85) REVERT: D 247 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8348 (tt0) REVERT: D 285 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7922 (ttpp) REVERT: D 300 PHE cc_start: 0.8173 (m-80) cc_final: 0.7948 (m-80) REVERT: D 334 ARG cc_start: 0.6958 (tpp80) cc_final: 0.6392 (tpp-160) REVERT: D 373 GLN cc_start: 0.7918 (tt0) cc_final: 0.7633 (tt0) REVERT: D 487 ASP cc_start: 0.7974 (m-30) cc_final: 0.7739 (m-30) REVERT: D 493 ASN cc_start: 0.8510 (p0) cc_final: 0.8184 (p0) REVERT: E 172 PHE cc_start: 0.7599 (t80) cc_final: 0.7212 (t80) REVERT: E 174 LYS cc_start: 0.8208 (ptpp) cc_final: 0.7361 (mmtm) REVERT: E 207 ARG cc_start: 0.7373 (mmm-85) cc_final: 0.6798 (mmm-85) REVERT: E 228 ASP cc_start: 0.7843 (m-30) cc_final: 0.7396 (m-30) REVERT: E 334 ARG cc_start: 0.7100 (tpp80) cc_final: 0.6873 (mtp-110) REVERT: E 346 GLU cc_start: 0.8144 (tt0) cc_final: 0.7756 (tm-30) REVERT: E 367 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7301 (mm-30) REVERT: E 373 GLN cc_start: 0.7765 (tt0) cc_final: 0.7415 (tt0) REVERT: E 389 ASP cc_start: 0.7464 (p0) cc_final: 0.7212 (p0) REVERT: E 420 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7870 (ttm) REVERT: F 124 PHE cc_start: 0.7391 (t80) cc_final: 0.6217 (m-10) REVERT: F 158 PHE cc_start: 0.8400 (m-80) cc_final: 0.8129 (m-10) REVERT: F 174 LYS cc_start: 0.8396 (ptpp) cc_final: 0.7659 (mmtm) REVERT: F 181 ARG cc_start: 0.8179 (mmm-85) cc_final: 0.7682 (mmt90) REVERT: F 207 ARG cc_start: 0.7059 (mmm-85) cc_final: 0.6422 (mmm-85) REVERT: F 304 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7641 (mttt) REVERT: F 334 ARG cc_start: 0.7139 (tpp80) cc_final: 0.6636 (tpp-160) REVERT: F 373 GLN cc_start: 0.7886 (tt0) cc_final: 0.7667 (tt0) REVERT: F 389 ASP cc_start: 0.7568 (p0) cc_final: 0.7321 (p0) outliers start: 67 outliers final: 35 residues processed: 312 average time/residue: 1.3308 time to fit residues: 466.2297 Evaluate side-chains 307 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 262 time to evaluate : 2.096 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 215 ASN Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 298 SER 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 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 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 209 LEU Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 375 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 186 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 159 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN D 247 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.154508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113487 restraints weight = 20261.322| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.77 r_work: 0.3198 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18930 Z= 0.163 Angle : 0.600 10.842 25614 Z= 0.299 Chirality : 0.041 0.189 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.389 22.380 2514 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.02 % Allowed : 16.92 % Favored : 80.06 % 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: 1.54 (0.18), residues: 2220 helix: 1.67 (0.14), residues: 1374 sheet: 0.41 (0.38), residues: 186 loop : -0.04 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 138 HIS 0.004 0.001 HIS C 269 PHE 0.034 0.002 PHE D 196 TYR 0.012 0.002 TYR C 453 ARG 0.009 0.001 ARG D 176 Details of bonding type rmsd hydrogen bonds : bond 0.03556 ( 1146) hydrogen bonds : angle 4.22201 ( 3318) SS BOND : bond 0.00124 ( 6) SS BOND : angle 0.67391 ( 12) covalent geometry : bond 0.00383 (18924) covalent geometry : angle 0.60019 (25602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 264 time to evaluate : 2.085 Fit side-chains REVERT: A 172 PHE cc_start: 0.7591 (t80) cc_final: 0.7229 (t80) REVERT: A 174 LYS cc_start: 0.8232 (ptpp) cc_final: 0.7371 (mmtm) REVERT: A 207 ARG cc_start: 0.7052 (mmm-85) cc_final: 0.6382 (mmm-85) REVERT: A 249 MET cc_start: 0.9119 (mmm) cc_final: 0.8900 (mmt) REVERT: A 334 ARG cc_start: 0.7224 (tpp80) cc_final: 0.6938 (mtp-110) REVERT: A 346 GLU cc_start: 0.8153 (tt0) cc_final: 0.7758 (tm-30) REVERT: A 367 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7304 (mm-30) REVERT: A 373 GLN cc_start: 0.7806 (tt0) cc_final: 0.7419 (tt0) REVERT: A 389 ASP cc_start: 0.7470 (p0) cc_final: 0.7174 (p0) REVERT: A 420 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7884 (ttm) REVERT: B 174 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.7897 (mmtt) REVERT: B 207 ARG cc_start: 0.7251 (mmm-85) cc_final: 0.6679 (mmm-85) REVERT: B 285 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7947 (ttmm) REVERT: B 373 GLN cc_start: 0.8055 (tt0) cc_final: 0.7704 (tt0) REVERT: B 438 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8268 (tptp) REVERT: C 172 PHE cc_start: 0.7625 (t80) cc_final: 0.7337 (t80) REVERT: C 174 LYS cc_start: 0.8356 (ptpp) cc_final: 0.7621 (mmtt) REVERT: C 207 ARG cc_start: 0.7199 (mmm-85) cc_final: 0.6595 (mmm-85) REVERT: C 300 PHE cc_start: 0.8022 (m-80) cc_final: 0.7807 (m-80) REVERT: C 346 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7553 (tt0) REVERT: C 351 GLU cc_start: 0.8015 (tt0) cc_final: 0.7759 (tt0) REVERT: C 367 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7233 (mm-30) REVERT: C 373 GLN cc_start: 0.7697 (tt0) cc_final: 0.7372 (tt0) REVERT: D 174 LYS cc_start: 0.8385 (ptpp) cc_final: 0.7548 (mmtt) REVERT: D 207 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6579 (mmm-85) REVERT: D 285 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7923 (ttpp) REVERT: D 300 PHE cc_start: 0.8152 (m-80) cc_final: 0.7924 (m-80) REVERT: D 334 ARG cc_start: 0.7035 (tpp80) cc_final: 0.6486 (tpp-160) REVERT: D 373 GLN cc_start: 0.7890 (tt0) cc_final: 0.7658 (tt0) REVERT: D 456 ASP cc_start: 0.8281 (p0) cc_final: 0.8023 (p0) REVERT: D 487 ASP cc_start: 0.7989 (m-30) cc_final: 0.7779 (m-30) REVERT: D 493 ASN cc_start: 0.8496 (p0) cc_final: 0.8168 (p0) REVERT: E 172 PHE cc_start: 0.7598 (t80) cc_final: 0.7218 (t80) REVERT: E 174 LYS cc_start: 0.8223 (ptpp) cc_final: 0.7371 (mmtm) REVERT: E 207 ARG cc_start: 0.7347 (mmm-85) cc_final: 0.6709 (mmm-85) REVERT: E 228 ASP cc_start: 0.7958 (m-30) cc_final: 0.7437 (m-30) REVERT: E 334 ARG cc_start: 0.7078 (tpp80) cc_final: 0.6810 (mtp-110) REVERT: E 346 GLU cc_start: 0.8140 (tt0) cc_final: 0.7749 (tm-30) REVERT: E 367 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7316 (mm-30) REVERT: E 373 GLN cc_start: 0.7823 (tt0) cc_final: 0.7495 (tt0) REVERT: E 389 ASP cc_start: 0.7488 (p0) cc_final: 0.7237 (p0) REVERT: E 420 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7889 (ttm) REVERT: F 124 PHE cc_start: 0.7414 (t80) cc_final: 0.6258 (m-10) REVERT: F 158 PHE cc_start: 0.8405 (m-80) cc_final: 0.8118 (m-10) REVERT: F 174 LYS cc_start: 0.8466 (ptpp) cc_final: 0.7677 (mmtm) REVERT: F 178 ASP cc_start: 0.8563 (m-30) cc_final: 0.8236 (m-30) REVERT: F 207 ARG cc_start: 0.7040 (mmm-85) cc_final: 0.6422 (mmm-85) REVERT: F 304 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7656 (mttt) REVERT: F 334 ARG cc_start: 0.7130 (tpp80) cc_final: 0.6625 (tpp-160) REVERT: F 389 ASP cc_start: 0.7638 (p0) cc_final: 0.7370 (p0) outliers start: 60 outliers final: 35 residues processed: 305 average time/residue: 1.2781 time to fit residues: 438.2801 Evaluate side-chains 302 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 2.244 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 SER 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 298 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 459 LEU 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 285 LYS Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 446 SER 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 209 LEU 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 155 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 159 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 143 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 152 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 chunk 128 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 GLN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 247 GLN D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN ** E 221 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 ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.154290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.113468 restraints weight = 20264.051| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.73 r_work: 0.3201 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18930 Z= 0.163 Angle : 0.604 11.176 25614 Z= 0.300 Chirality : 0.041 0.191 2922 Planarity : 0.005 0.043 3186 Dihedral : 4.397 22.387 2514 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.42 % Allowed : 17.42 % Favored : 80.16 % 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: 0.38 (0.38), residues: 186 loop : -0.02 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP F 138 HIS 0.004 0.001 HIS D 269 PHE 0.032 0.002 PHE D 196 TYR 0.012 0.002 TYR D 453 ARG 0.009 0.001 ARG F 334 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 1146) hydrogen bonds : angle 4.21540 ( 3318) SS BOND : bond 0.00130 ( 6) SS BOND : angle 0.69082 ( 12) covalent geometry : bond 0.00384 (18924) covalent geometry : angle 0.60389 (25602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 262 time to evaluate : 2.204 Fit side-chains REVERT: A 172 PHE cc_start: 0.7589 (t80) cc_final: 0.7200 (t80) REVERT: A 174 LYS cc_start: 0.8223 (ptpp) cc_final: 0.7350 (mmtm) REVERT: A 181 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7763 (mmt90) REVERT: A 207 ARG cc_start: 0.7067 (mmm-85) cc_final: 0.6397 (mmm-85) REVERT: A 249 MET cc_start: 0.9107 (mmm) cc_final: 0.8891 (mmt) REVERT: A 334 ARG cc_start: 0.7210 (tpp80) cc_final: 0.6909 (mtp-110) REVERT: A 346 GLU cc_start: 0.8148 (tt0) cc_final: 0.7753 (tm-30) REVERT: A 367 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7309 (mm-30) REVERT: A 373 GLN cc_start: 0.7839 (tt0) cc_final: 0.7498 (tt0) REVERT: A 389 ASP cc_start: 0.7486 (p0) cc_final: 0.7200 (p0) REVERT: A 420 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7877 (ttm) REVERT: B 174 LYS cc_start: 0.8804 (OUTLIER) cc_final: 0.7936 (mmtt) REVERT: B 207 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6554 (mmm-85) REVERT: B 285 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.7951 (ttmm) REVERT: B 438 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8261 (tptp) REVERT: C 172 PHE cc_start: 0.7644 (t80) cc_final: 0.7363 (t80) REVERT: C 174 LYS cc_start: 0.8360 (ptpp) cc_final: 0.7635 (mmtt) REVERT: C 207 ARG cc_start: 0.7204 (mmm-85) cc_final: 0.6635 (mmm-85) REVERT: C 300 PHE cc_start: 0.8022 (m-80) cc_final: 0.7807 (m-80) REVERT: C 346 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7547 (tt0) REVERT: C 351 GLU cc_start: 0.8006 (tt0) cc_final: 0.7751 (tt0) REVERT: C 367 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7258 (mm-30) REVERT: C 373 GLN cc_start: 0.7919 (tt0) cc_final: 0.7655 (tt0) REVERT: C 420 MET cc_start: 0.8482 (tmm) cc_final: 0.8123 (tpp) REVERT: D 174 LYS cc_start: 0.8423 (ptpp) cc_final: 0.7556 (mmtt) REVERT: D 207 ARG cc_start: 0.7161 (mmm-85) cc_final: 0.6591 (mmm-85) REVERT: D 285 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7924 (ttpp) REVERT: D 300 PHE cc_start: 0.8153 (m-80) cc_final: 0.7929 (m-80) REVERT: D 334 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6493 (tpp-160) REVERT: D 373 GLN cc_start: 0.7841 (tt0) cc_final: 0.7631 (tt0) REVERT: D 456 ASP cc_start: 0.8274 (p0) cc_final: 0.8023 (p0) REVERT: D 493 ASN cc_start: 0.8490 (p0) cc_final: 0.8159 (p0) REVERT: E 172 PHE cc_start: 0.7592 (t80) cc_final: 0.7204 (t80) REVERT: E 174 LYS cc_start: 0.8261 (ptpp) cc_final: 0.7380 (mmtm) REVERT: E 207 ARG cc_start: 0.7388 (mmm-85) cc_final: 0.6722 (mmm-85) REVERT: E 228 ASP cc_start: 0.7866 (m-30) cc_final: 0.7414 (m-30) REVERT: E 334 ARG cc_start: 0.7091 (tpp80) cc_final: 0.6824 (mtp-110) REVERT: E 346 GLU cc_start: 0.8134 (tt0) cc_final: 0.7744 (tm-30) REVERT: E 367 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7318 (mm-30) REVERT: E 373 GLN cc_start: 0.7807 (tt0) cc_final: 0.7458 (tt0) REVERT: E 389 ASP cc_start: 0.7492 (p0) cc_final: 0.7228 (p0) REVERT: E 420 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7850 (ttm) REVERT: F 158 PHE cc_start: 0.8353 (m-80) cc_final: 0.8062 (m-10) REVERT: F 174 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7841 (mmtt) REVERT: F 178 ASP cc_start: 0.8567 (m-30) cc_final: 0.8238 (m-30) REVERT: F 181 ARG cc_start: 0.8219 (mmm-85) cc_final: 0.7740 (mmt90) REVERT: F 207 ARG cc_start: 0.7029 (mmm-85) cc_final: 0.6403 (mmm-85) REVERT: F 304 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7663 (mttt) REVERT: F 334 ARG cc_start: 0.7143 (tpp80) cc_final: 0.6635 (tpp-160) REVERT: F 389 ASP cc_start: 0.7653 (p0) cc_final: 0.7406 (p0) outliers start: 48 outliers final: 32 residues processed: 297 average time/residue: 1.3881 time to fit residues: 463.3162 Evaluate side-chains 292 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 2.243 ------------------------------------------------------------------------------- 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 233 ILE 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 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 298 SER Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain C residue 459 LEU 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 285 LYS Chi-restraints excluded: chain D residue 446 SER 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 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 155 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 304 LYS Chi-restraints excluded: chain F residue 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 44 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 97 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 chunk 204 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 215 ASN ** B 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 519 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.151518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110752 restraints weight = 20112.325| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.74 r_work: 0.3165 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 18930 Z= 0.214 Angle : 0.649 10.783 25614 Z= 0.324 Chirality : 0.043 0.193 2922 Planarity : 0.005 0.051 3186 Dihedral : 4.620 23.535 2514 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.77 % Allowed : 17.42 % Favored : 79.81 % 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: 1.38 (0.18), residues: 2220 helix: 1.61 (0.14), residues: 1344 sheet: 0.21 (0.37), residues: 186 loop : -0.15 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP C 458 HIS 0.005 0.002 HIS A 512 PHE 0.032 0.002 PHE D 196 TYR 0.013 0.002 TYR F 453 ARG 0.009 0.001 ARG F 334 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1146) hydrogen bonds : angle 4.34104 ( 3318) SS BOND : bond 0.00152 ( 6) SS BOND : angle 0.78315 ( 12) covalent geometry : bond 0.00513 (18924) covalent geometry : angle 0.64881 (25602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17883.54 seconds wall clock time: 311 minutes 27.31 seconds (18687.31 seconds total)