Starting phenix.real_space_refine on Mon May 19 12:40:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk8_61547/05_2025/9jk8_61547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk8_61547/05_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_61547/05_2025/9jk8_61547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk8_61547/05_2025/9jk8_61547.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk8_61547/05_2025/9jk8_61547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk8_61547/05_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-5687/modules/chem_data/mon_lib" Total number of atoms: 18504 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3084 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 13, 'TRANS': 362} Chain breaks: 2 Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 7.62, per 1000 atoms: 0.41 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: 4.33 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: 1.92 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: 5.87 Time building geometry restraints manager: 5.06 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: 4.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.070 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.460 ------------------------------------------------------------------------------- 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 : 2.051 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: 1.5076 time to fit residues: 686.6388 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 : 1.955 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.122164 restraints weight = 20116.580| |-----------------------------------------------------------------------------| 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 10.493 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 4.65379 ( 3318) SS BOND : bond 0.00085 ( 6) SS BOND : angle 0.51033 ( 12) covalent geometry : bond 0.00311 (18924) covalent geometry : angle 0.57171 (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 : 2.055 Fit side-chains REVERT: A 172 PHE cc_start: 0.7635 (t80) cc_final: 0.7290 (t80) REVERT: A 174 LYS cc_start: 0.7947 (ptpp) cc_final: 0.7659 (mmtt) REVERT: A 207 ARG cc_start: 0.7307 (mmm-85) cc_final: 0.6774 (mmm-85) REVERT: A 334 ARG cc_start: 0.6898 (tpp80) cc_final: 0.6506 (tpp-160) REVERT: A 373 GLN cc_start: 0.7426 (tt0) cc_final: 0.6967 (tt0) REVERT: A 420 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7667 (ttm) REVERT: A 446 SER cc_start: 0.8460 (m) cc_final: 0.8144 (p) REVERT: B 172 PHE cc_start: 0.7468 (t80) cc_final: 0.7085 (t80) REVERT: B 179 MET cc_start: 0.8902 (mtm) cc_final: 0.8695 (mtm) REVERT: B 207 ARG cc_start: 0.7322 (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: 0.7588 (ttpp) REVERT: B 334 ARG cc_start: 0.6890 (mtp-110) cc_final: 0.6548 (tpp-160) REVERT: B 373 GLN cc_start: 0.7865 (tt0) cc_final: 0.7409 (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: 0.7298 (mmm-85) cc_final: 0.6549 (mmm-85) REVERT: C 249 MET cc_start: 0.8803 (tpt) cc_final: 0.8558 (mmm) REVERT: C 300 PHE cc_start: 0.8231 (m-80) cc_final: 0.7878 (m-80) REVERT: C 334 ARG cc_start: 0.6794 (tpp80) cc_final: 0.6523 (mtp-110) REVERT: C 346 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7569 (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: 0.6929 (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: 0.8155 (p0) cc_final: 0.7898 (p0) REVERT: C 516 LEU cc_start: 0.8580 (tp) cc_final: 0.8357 (tm) REVERT: D 124 PHE cc_start: 0.7512 (t80) cc_final: 0.7256 (t80) REVERT: D 174 LYS cc_start: 0.7987 (ptpp) cc_final: 0.7102 (mmtt) REVERT: D 207 ARG cc_start: 0.6946 (mmm-85) cc_final: 0.6659 (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: 0.7633 (m-80) REVERT: D 373 GLN cc_start: 0.7525 (tt0) cc_final: 0.7149 (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: 0.7102 (tpp80) cc_final: 0.6589 (tpp-160) REVERT: E 346 GLU cc_start: 0.8063 (tt0) cc_final: 0.7671 (tm-30) REVERT: E 373 GLN cc_start: 0.7481 (tt0) cc_final: 0.6998 (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: 0.7768 (ttm) REVERT: E 456 ASP cc_start: 0.8042 (p0) cc_final: 0.7826 (p0) REVERT: F 148 ILE cc_start: 0.7272 (mm) cc_final: 0.6941 (tt) REVERT: F 174 LYS cc_start: 0.7941 (ptpp) cc_final: 0.7388 (mmtm) REVERT: F 207 ARG cc_start: 0.6955 (mmm-85) cc_final: 0.6504 (mmm-85) REVERT: F 346 GLU cc_start: 0.8066 (tt0) cc_final: 0.7846 (tt0) REVERT: F 373 GLN cc_start: 0.7765 (tt0) cc_final: 0.7273 (tp40) REVERT: F 389 ASP cc_start: 0.7205 (p0) cc_final: 0.6983 (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: 1.3567 time to fit residues: 545.5420 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 : 2.201 ------------------------------------------------------------------------------- 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: 0.6980 chunk 54 optimal weight: 0.5980 chunk 133 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 207 optimal weight: 0.7980 chunk 106 optimal weight: 0.4980 chunk 208 optimal weight: 0.7980 chunk 191 optimal weight: 0.0770 chunk 55 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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 350 HIS D 416 ASN E 234 HIS ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 234 HIS F 247 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN F 425 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.159901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.118997 restraints weight = 20173.902| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.78 r_work: 0.3271 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18930 Z= 0.136 Angle : 0.558 10.757 25614 Z= 0.286 Chirality : 0.041 0.162 2922 Planarity : 0.005 0.038 3186 Dihedral : 4.395 22.006 2514 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.67 % Allowed : 13.80 % Favored : 83.53 % 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: 0.91 (0.17), residues: 2220 helix: 1.29 (0.14), residues: 1380 sheet: 0.16 (0.39), residues: 180 loop : -0.60 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 458 HIS 0.005 0.001 HIS D 426 PHE 0.025 0.002 PHE C 196 TYR 0.014 0.002 TYR F 453 ARG 0.007 0.000 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 1146) hydrogen bonds : angle 4.37982 ( 3318) SS BOND : bond 0.00054 ( 6) SS BOND : angle 0.43247 ( 12) covalent geometry : bond 0.00310 (18924) covalent geometry : angle 0.55821 (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 360 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 307 time to evaluate : 2.101 Fit side-chains REVERT: A 172 PHE cc_start: 0.7663 (t80) cc_final: 0.7350 (t80) REVERT: A 174 LYS cc_start: 0.7986 (ptpp) cc_final: 0.7357 (mmtm) REVERT: A 196 PHE cc_start: 0.7152 (t80) cc_final: 0.6921 (t80) REVERT: A 200 TYR cc_start: 0.7710 (m-80) cc_final: 0.7478 (m-80) REVERT: A 207 ARG cc_start: 0.7235 (mmm-85) cc_final: 0.6748 (mmm-85) REVERT: A 334 ARG cc_start: 0.7095 (tpp80) cc_final: 0.6661 (tpp-160) REVERT: A 367 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7313 (mm-30) REVERT: A 373 GLN cc_start: 0.7596 (tt0) cc_final: 0.7142 (tt0) REVERT: A 420 MET cc_start: 0.8335 (OUTLIER) cc_final: 0.7801 (ttm) REVERT: B 207 ARG cc_start: 0.7357 (mmm-85) cc_final: 0.6563 (mmm-85) REVERT: B 285 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7630 (ttpp) REVERT: B 334 ARG cc_start: 0.6950 (mtp-110) cc_final: 0.6589 (tpp-160) REVERT: B 373 GLN cc_start: 0.7938 (tt0) cc_final: 0.7440 (tp40) REVERT: B 413 ARG cc_start: 0.8542 (mmt90) cc_final: 0.8190 (mmt90) REVERT: C 172 PHE cc_start: 0.7665 (t80) cc_final: 0.7367 (t80) REVERT: C 207 ARG cc_start: 0.7311 (mmm-85) cc_final: 0.6549 (mmm-85) REVERT: C 267 LEU cc_start: 0.8823 (mt) cc_final: 0.8614 (mp) REVERT: C 300 PHE cc_start: 0.8264 (m-80) cc_final: 0.7865 (m-10) REVERT: C 346 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7614 (tt0) REVERT: C 351 GLU cc_start: 0.7978 (tt0) cc_final: 0.7756 (tt0) REVERT: C 373 GLN cc_start: 0.7408 (tt0) cc_final: 0.7085 (tt0) REVERT: D 124 PHE cc_start: 0.7403 (t80) cc_final: 0.7170 (t80) REVERT: D 174 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7268 (mmtt) REVERT: D 207 ARG cc_start: 0.6985 (mmm-85) cc_final: 0.6620 (mmm-85) REVERT: D 263 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7608 (mtp180) REVERT: D 267 LEU cc_start: 0.8776 (mt) cc_final: 0.8562 (mp) REVERT: D 285 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.7677 (ttpp) REVERT: D 300 PHE cc_start: 0.8095 (m-80) cc_final: 0.7683 (m-80) REVERT: D 334 ARG cc_start: 0.7076 (tpp80) cc_final: 0.6661 (tpp-160) REVERT: D 373 GLN cc_start: 0.7563 (tt0) cc_final: 0.7167 (tt0) REVERT: D 455 LYS cc_start: 0.8100 (mttp) cc_final: 0.7893 (mmtt) REVERT: E 172 PHE cc_start: 0.7697 (t80) cc_final: 0.7334 (t80) REVERT: E 207 ARG cc_start: 0.7102 (mmm-85) cc_final: 0.6651 (mmm-85) REVERT: E 247 GLN cc_start: 0.8576 (tp-100) cc_final: 0.8227 (tt0) REVERT: E 334 ARG cc_start: 0.7165 (tpp80) cc_final: 0.6660 (tpp-160) REVERT: E 346 GLU cc_start: 0.8063 (tt0) cc_final: 0.7669 (tm-30) REVERT: E 367 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7310 (mm-30) REVERT: E 373 GLN cc_start: 0.7765 (tt0) cc_final: 0.7240 (tt0) REVERT: E 413 ARG cc_start: 0.8330 (mpt-90) cc_final: 0.8097 (mmt90) REVERT: E 420 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7806 (ttm) REVERT: F 119 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6081 (tm) REVERT: F 156 MET cc_start: 0.8359 (ttt) cc_final: 0.8158 (ttt) REVERT: F 174 LYS cc_start: 0.8083 (ptpp) cc_final: 0.7500 (mmtm) REVERT: F 207 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6534 (mmm-85) REVERT: F 304 LYS cc_start: 0.7720 (tttt) cc_final: 0.7128 (mptt) REVERT: F 373 GLN cc_start: 0.7893 (tt0) cc_final: 0.7388 (tt0) REVERT: F 389 ASP cc_start: 0.7325 (p0) cc_final: 0.7114 (p0) REVERT: F 413 ARG cc_start: 0.8479 (mmt90) cc_final: 0.8212 (mmt90) outliers start: 53 outliers final: 23 residues processed: 336 average time/residue: 1.4079 time to fit residues: 526.5797 Evaluate side-chains 316 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 287 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 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 B residue 446 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 D residue 155 SER 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: 0.7980 chunk 138 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 199 optimal weight: 0.5980 chunk 213 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 493 ASN D 247 GLN D 406 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.156245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.114832 restraints weight = 20136.340| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.79 r_work: 0.3216 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18930 Z= 0.159 Angle : 0.573 10.251 25614 Z= 0.292 Chirality : 0.042 0.154 2922 Planarity : 0.005 0.038 3186 Dihedral : 4.429 22.178 2514 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.42 % Allowed : 13.85 % Favored : 82.73 % 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: 1.21 (0.18), residues: 2220 helix: 1.45 (0.14), residues: 1380 sheet: 0.45 (0.40), residues: 180 loop : -0.36 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 458 HIS 0.005 0.001 HIS F 234 PHE 0.023 0.002 PHE C 196 TYR 0.015 0.002 TYR F 453 ARG 0.006 0.000 ARG D 334 Details of bonding type rmsd hydrogen bonds : bond 0.03582 ( 1146) hydrogen bonds : angle 4.30078 ( 3318) SS BOND : bond 0.00080 ( 6) SS BOND : angle 0.53341 ( 12) covalent geometry : bond 0.00372 (18924) covalent geometry : angle 0.57290 (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 373 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 305 time to evaluate : 1.990 Fit side-chains REVERT: A 172 PHE cc_start: 0.7653 (t80) cc_final: 0.7342 (t80) REVERT: A 174 LYS cc_start: 0.8112 (ptpp) cc_final: 0.7300 (mmtm) REVERT: A 207 ARG cc_start: 0.7331 (mmm-85) cc_final: 0.6678 (mmm-85) REVERT: A 334 ARG cc_start: 0.7140 (tpp80) cc_final: 0.6635 (tpp-160) REVERT: A 346 GLU cc_start: 0.8096 (tt0) cc_final: 0.7704 (tm-30) REVERT: A 367 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7322 (mm-30) REVERT: A 373 GLN cc_start: 0.7636 (tt0) cc_final: 0.7185 (tt0) REVERT: A 389 ASP cc_start: 0.7260 (p0) cc_final: 0.7034 (p0) REVERT: A 403 ARG cc_start: 0.8310 (tpt-90) cc_final: 0.8106 (ttt90) REVERT: A 420 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7968 (ttm) REVERT: B 174 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7710 (mmtt) REVERT: B 207 ARG cc_start: 0.7268 (mmm-85) cc_final: 0.6573 (mmm-85) REVERT: B 285 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7819 (ttpp) REVERT: B 373 GLN cc_start: 0.8050 (tt0) cc_final: 0.7568 (tt0) REVERT: B 438 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8371 (tptt) REVERT: C 172 PHE cc_start: 0.7714 (t80) cc_final: 0.7416 (t80) REVERT: C 207 ARG cc_start: 0.7321 (mmm-85) cc_final: 0.6507 (mmm-85) REVERT: C 273 GLN cc_start: 0.8692 (mt0) cc_final: 0.8332 (mt0) REVERT: C 300 PHE cc_start: 0.8090 (m-80) cc_final: 0.7848 (m-80) REVERT: C 346 GLU cc_start: 0.7962 (mm-30) cc_final: 0.7538 (tt0) REVERT: C 351 GLU cc_start: 0.8011 (tt0) cc_final: 0.7769 (tt0) REVERT: C 367 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7201 (mm-30) REVERT: C 373 GLN cc_start: 0.7498 (tt0) cc_final: 0.7188 (tt0) REVERT: C 420 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8132 (tpp) REVERT: D 174 LYS cc_start: 0.8289 (ptpp) cc_final: 0.7447 (mmtt) REVERT: D 207 ARG cc_start: 0.7025 (mmm-85) cc_final: 0.6608 (mmm-85) REVERT: D 247 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: D 285 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.7911 (ttpp) REVERT: D 300 PHE cc_start: 0.8175 (m-80) cc_final: 0.7754 (m-10) REVERT: D 334 ARG cc_start: 0.6884 (tpp80) cc_final: 0.6494 (tpp-160) REVERT: D 373 GLN cc_start: 0.7701 (tt0) cc_final: 0.7354 (tt0) REVERT: E 172 PHE cc_start: 0.7617 (t80) cc_final: 0.7233 (t80) REVERT: E 207 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.6812 (mmm-85) REVERT: E 215 ASN cc_start: 0.7211 (p0) cc_final: 0.6970 (t0) REVERT: E 334 ARG cc_start: 0.7116 (tpp80) cc_final: 0.6861 (mtp-110) REVERT: E 346 GLU cc_start: 0.8085 (tt0) cc_final: 0.7690 (tm-30) REVERT: E 367 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7307 (mm-30) REVERT: E 373 GLN cc_start: 0.7890 (tt0) cc_final: 0.7353 (tt0) REVERT: E 420 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7864 (ttm) REVERT: F 156 MET cc_start: 0.8490 (ttt) cc_final: 0.8255 (ttt) REVERT: F 174 LYS cc_start: 0.8242 (ptpp) cc_final: 0.7577 (mmtm) REVERT: F 207 ARG cc_start: 0.7039 (mmm-85) cc_final: 0.6405 (mmm-85) REVERT: F 334 ARG cc_start: 0.7105 (mmm160) cc_final: 0.6642 (tpp-160) REVERT: F 373 GLN cc_start: 0.7878 (tt0) cc_final: 0.7391 (tt0) REVERT: F 389 ASP cc_start: 0.7478 (p0) cc_final: 0.7233 (p0) outliers start: 68 outliers final: 25 residues processed: 343 average time/residue: 1.3451 time to fit residues: 514.7720 Evaluate side-chains 318 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 285 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 155 SER 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 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain 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 371 HIS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 208 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 117 optimal weight: 0.0270 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: 0.8980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 416 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 247 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.157192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.116118 restraints weight = 20248.876| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.77 r_work: 0.3237 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18930 Z= 0.138 Angle : 0.561 10.481 25614 Z= 0.283 Chirality : 0.041 0.160 2922 Planarity : 0.004 0.038 3186 Dihedral : 4.299 21.869 2514 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.32 % Allowed : 15.26 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.18), residues: 2220 helix: 1.56 (0.14), residues: 1380 sheet: 0.55 (0.41), residues: 180 loop : -0.22 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 458 HIS 0.006 0.001 HIS E 371 PHE 0.022 0.002 PHE E 196 TYR 0.012 0.002 TYR F 453 ARG 0.008 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03387 ( 1146) hydrogen bonds : angle 4.21254 ( 3318) SS BOND : bond 0.00058 ( 6) SS BOND : angle 0.56543 ( 12) covalent geometry : bond 0.00321 (18924) covalent geometry : angle 0.56068 (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 357 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 291 time to evaluate : 2.007 Fit side-chains REVERT: A 172 PHE cc_start: 0.7655 (t80) cc_final: 0.7305 (t80) REVERT: A 174 LYS cc_start: 0.8133 (ptpp) cc_final: 0.7311 (mmtm) REVERT: A 207 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.6620 (mmm-85) REVERT: A 334 ARG cc_start: 0.7199 (tpp80) cc_final: 0.6846 (tpp-160) REVERT: A 346 GLU cc_start: 0.8096 (tt0) cc_final: 0.7699 (tm-30) REVERT: A 367 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7307 (mm-30) REVERT: A 373 GLN cc_start: 0.7655 (tt0) cc_final: 0.7232 (tt0) REVERT: A 389 ASP cc_start: 0.7324 (p0) cc_final: 0.7085 (p0) REVERT: A 420 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7922 (ttm) REVERT: B 174 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.7722 (mmtt) REVERT: B 207 ARG cc_start: 0.7228 (mmm-85) cc_final: 0.6714 (mmm-85) REVERT: B 285 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7673 (ttpp) REVERT: B 334 ARG cc_start: 0.7261 (tpp80) cc_final: 0.7016 (mtp-110) REVERT: B 373 GLN cc_start: 0.7981 (tt0) cc_final: 0.7524 (tt0) REVERT: B 438 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8267 (tptp) REVERT: C 172 PHE cc_start: 0.7711 (t80) cc_final: 0.7409 (t80) REVERT: C 207 ARG cc_start: 0.7310 (mmm-85) cc_final: 0.6595 (mmm-85) REVERT: C 300 PHE cc_start: 0.8034 (m-80) cc_final: 0.7643 (m-10) REVERT: C 346 GLU cc_start: 0.7995 (mm-30) cc_final: 0.7571 (tt0) REVERT: C 351 GLU cc_start: 0.8026 (tt0) cc_final: 0.7785 (tt0) REVERT: C 373 GLN cc_start: 0.7508 (tt0) cc_final: 0.7205 (tt0) REVERT: C 420 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8132 (tpp) REVERT: D 174 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7435 (mmtt) REVERT: D 207 ARG cc_start: 0.6963 (mmm-85) cc_final: 0.6558 (mmm-85) REVERT: D 247 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: D 285 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7781 (ttpp) REVERT: D 300 PHE cc_start: 0.8186 (m-80) cc_final: 0.7757 (m-10) REVERT: D 334 ARG cc_start: 0.6909 (tpp80) cc_final: 0.6534 (tpp-160) REVERT: D 373 GLN cc_start: 0.7701 (tt0) cc_final: 0.7378 (tt0) REVERT: D 455 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7785 (mmtt) REVERT: D 487 ASP cc_start: 0.7803 (m-30) cc_final: 0.7575 (m-30) REVERT: E 172 PHE cc_start: 0.7551 (t80) cc_final: 0.7177 (t80) REVERT: E 207 ARG cc_start: 0.7327 (mmm-85) cc_final: 0.6764 (mmm-85) REVERT: E 215 ASN cc_start: 0.7284 (p0) cc_final: 0.7021 (t0) REVERT: E 334 ARG cc_start: 0.7148 (tpp80) cc_final: 0.6893 (mtp-110) REVERT: E 346 GLU cc_start: 0.8098 (tt0) cc_final: 0.7706 (tm-30) REVERT: E 367 GLU cc_start: 0.7832 (mt-10) cc_final: 0.7236 (mm-30) REVERT: E 373 GLN cc_start: 0.7742 (tt0) cc_final: 0.7349 (tt0) REVERT: E 389 ASP cc_start: 0.7370 (p0) cc_final: 0.7110 (p0) REVERT: E 420 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.7826 (ttm) REVERT: F 174 LYS cc_start: 0.8308 (ptpp) cc_final: 0.7600 (mmtm) REVERT: F 207 ARG cc_start: 0.6953 (mmm-85) cc_final: 0.6337 (mmm-85) REVERT: F 334 ARG cc_start: 0.7101 (mmm160) cc_final: 0.6656 (tpp-160) REVERT: F 373 GLN cc_start: 0.7798 (tt0) cc_final: 0.7390 (tt0) REVERT: F 389 ASP cc_start: 0.7443 (p0) cc_final: 0.7201 (p0) REVERT: F 454 ASP cc_start: 0.7984 (m-30) cc_final: 0.7779 (m-30) outliers start: 66 outliers final: 23 residues processed: 326 average time/residue: 1.2968 time to fit residues: 472.0953 Evaluate side-chains 303 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 271 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 VAL 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 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 438 LYS Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 247 GLN Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 298 SER Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL 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 209 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: 0.2980 chunk 145 optimal weight: 0.1980 chunk 162 optimal weight: 0.9990 chunk 140 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 chunk 95 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 198 optimal weight: 0.1980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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 273 GLN C 425 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.158555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.117710 restraints weight = 20394.669| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.78 r_work: 0.3256 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18930 Z= 0.121 Angle : 0.543 10.440 25614 Z= 0.273 Chirality : 0.040 0.148 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.152 21.409 2514 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.68 % Allowed : 15.36 % Favored : 80.97 % 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: 1.56 (0.18), residues: 2220 helix: 1.66 (0.14), residues: 1380 sheet: 0.78 (0.40), residues: 186 loop : -0.14 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 138 HIS 0.005 0.001 HIS C 269 PHE 0.025 0.002 PHE F 196 TYR 0.012 0.002 TYR E 453 ARG 0.007 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03231 ( 1146) hydrogen bonds : angle 4.12792 ( 3318) SS BOND : bond 0.00091 ( 6) SS BOND : angle 0.59770 ( 12) covalent geometry : bond 0.00276 (18924) covalent geometry : angle 0.54303 (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 359 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 286 time to evaluate : 2.013 Fit side-chains REVERT: A 172 PHE cc_start: 0.7450 (t80) cc_final: 0.7065 (t80) REVERT: A 174 LYS cc_start: 0.8092 (ptpp) cc_final: 0.7243 (mmtm) REVERT: A 181 ARG cc_start: 0.8114 (mmm-85) cc_final: 0.7709 (mmt90) REVERT: A 207 ARG cc_start: 0.7216 (mmm-85) cc_final: 0.6572 (mmm-85) REVERT: A 273 GLN cc_start: 0.8535 (mt0) cc_final: 0.8326 (mt0) REVERT: A 334 ARG cc_start: 0.7188 (tpp80) cc_final: 0.6834 (tpp-160) REVERT: A 346 GLU cc_start: 0.8090 (tt0) cc_final: 0.7681 (tm-30) REVERT: A 367 GLU cc_start: 0.7852 (mt-10) cc_final: 0.7251 (mm-30) REVERT: A 373 GLN cc_start: 0.7683 (tt0) cc_final: 0.7263 (tt0) REVERT: A 389 ASP cc_start: 0.7310 (p0) cc_final: 0.7044 (p0) REVERT: B 174 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.7730 (mmtt) REVERT: B 207 ARG cc_start: 0.7114 (mmm-85) cc_final: 0.6626 (mmm-85) REVERT: B 285 LYS cc_start: 0.7987 (OUTLIER) cc_final: 0.7565 (ttpp) REVERT: B 304 LYS cc_start: 0.7611 (ttmm) cc_final: 0.6919 (mptt) REVERT: B 334 ARG cc_start: 0.7252 (tpp80) cc_final: 0.6981 (mtp-110) REVERT: B 373 GLN cc_start: 0.8001 (tt0) cc_final: 0.7540 (tt0) REVERT: C 172 PHE cc_start: 0.7658 (t80) cc_final: 0.7343 (t80) REVERT: C 181 ARG cc_start: 0.8169 (mmm-85) cc_final: 0.7742 (mmt90) REVERT: C 207 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6611 (mmm-85) REVERT: C 300 PHE cc_start: 0.8016 (m-80) cc_final: 0.7623 (m-10) REVERT: C 346 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7549 (tt0) REVERT: C 351 GLU cc_start: 0.7967 (tt0) cc_final: 0.7741 (tt0) REVERT: C 373 GLN cc_start: 0.7409 (tt0) cc_final: 0.7117 (tt0) REVERT: C 420 MET cc_start: 0.8396 (OUTLIER) cc_final: 0.8038 (tpp) REVERT: D 124 PHE cc_start: 0.7345 (t80) cc_final: 0.7114 (t80) REVERT: D 181 ARG cc_start: 0.8171 (mmm-85) cc_final: 0.7701 (mmt90) REVERT: D 207 ARG cc_start: 0.7028 (mmm-85) cc_final: 0.6604 (mmm-85) REVERT: D 247 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8273 (tt0) REVERT: D 300 PHE cc_start: 0.8177 (m-80) cc_final: 0.7747 (m-10) REVERT: D 334 ARG cc_start: 0.6908 (tpp80) cc_final: 0.6364 (tpp-160) REVERT: D 373 GLN cc_start: 0.7647 (tt0) cc_final: 0.7327 (tt0) REVERT: D 487 ASP cc_start: 0.7754 (m-30) cc_final: 0.7498 (m-30) REVERT: E 207 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6730 (mmm-85) REVERT: E 215 ASN cc_start: 0.7256 (OUTLIER) cc_final: 0.6931 (t0) REVERT: E 334 ARG cc_start: 0.7144 (tpp80) cc_final: 0.6875 (mtp-110) REVERT: E 346 GLU cc_start: 0.8090 (tt0) cc_final: 0.7698 (tm-30) REVERT: E 367 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7346 (mm-30) REVERT: E 373 GLN cc_start: 0.7708 (tt0) cc_final: 0.7252 (tt0) REVERT: E 389 ASP cc_start: 0.7385 (p0) cc_final: 0.7144 (p0) REVERT: E 420 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7767 (ttm) REVERT: F 124 PHE cc_start: 0.7438 (t80) cc_final: 0.6175 (m-10) REVERT: F 174 LYS cc_start: 0.8282 (ptpp) cc_final: 0.7595 (mmtm) REVERT: F 181 ARG cc_start: 0.8070 (mmm-85) cc_final: 0.7615 (mmt90) REVERT: F 207 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6458 (mmm-85) REVERT: F 215 ASN cc_start: 0.7158 (OUTLIER) cc_final: 0.6934 (t0) REVERT: F 334 ARG cc_start: 0.7083 (mmm160) cc_final: 0.6653 (tpp-160) REVERT: F 373 GLN cc_start: 0.7743 (tt0) cc_final: 0.7330 (tt0) REVERT: F 389 ASP cc_start: 0.7264 (p0) cc_final: 0.7028 (p0) outliers start: 73 outliers final: 27 residues processed: 337 average time/residue: 1.2484 time to fit residues: 472.9790 Evaluate side-chains 305 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 271 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 233 ILE 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 209 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 420 MET 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 298 SER 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 298 SER Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 215 ASN Chi-restraints excluded: chain F residue 371 HIS 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: 0.0980 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 80 optimal weight: 0.0870 chunk 135 optimal weight: 0.6980 chunk 78 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 178 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 416 ASN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN C 247 GLN C 406 GLN C 416 ASN C 519 GLN D 215 ASN D 247 GLN D 406 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: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.157863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.116966 restraints weight = 20232.391| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.77 r_work: 0.3244 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 18930 Z= 0.130 Angle : 0.561 10.530 25614 Z= 0.280 Chirality : 0.040 0.184 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.148 21.450 2514 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.07 % Allowed : 16.52 % Favored : 80.41 % 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: 1.64 (0.18), residues: 2220 helix: 1.72 (0.14), residues: 1380 sheet: 0.75 (0.40), residues: 186 loop : -0.08 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 138 HIS 0.005 0.001 HIS C 269 PHE 0.026 0.002 PHE C 429 TYR 0.012 0.002 TYR E 453 ARG 0.007 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 1146) hydrogen bonds : angle 4.11440 ( 3318) SS BOND : bond 0.00101 ( 6) SS BOND : angle 0.62824 ( 12) covalent geometry : bond 0.00299 (18924) covalent geometry : angle 0.56088 (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 334 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 273 time to evaluate : 1.987 Fit side-chains REVERT: A 181 ARG cc_start: 0.8068 (mmm-85) cc_final: 0.7672 (mmt90) REVERT: A 207 ARG cc_start: 0.7101 (mmm-85) cc_final: 0.6471 (mmm-85) REVERT: A 334 ARG cc_start: 0.7183 (tpp80) cc_final: 0.6954 (mtp-110) REVERT: A 346 GLU cc_start: 0.8087 (tt0) cc_final: 0.7688 (tm-30) REVERT: A 367 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7259 (mm-30) REVERT: A 373 GLN cc_start: 0.7752 (tt0) cc_final: 0.7333 (tt0) REVERT: A 389 ASP cc_start: 0.7345 (p0) cc_final: 0.7074 (p0) REVERT: A 420 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7802 (ttm) REVERT: B 174 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7795 (mmtt) REVERT: B 207 ARG cc_start: 0.7144 (mmm-85) cc_final: 0.6621 (mmm-85) REVERT: B 285 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7593 (ttpp) REVERT: B 373 GLN cc_start: 0.7994 (tt0) cc_final: 0.7531 (tt0) REVERT: C 172 PHE cc_start: 0.7660 (t80) cc_final: 0.7344 (t80) REVERT: C 207 ARG cc_start: 0.7143 (mmm-85) cc_final: 0.6511 (mmm-85) REVERT: C 215 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.7025 (t0) REVERT: C 300 PHE cc_start: 0.8004 (m-80) cc_final: 0.7635 (m-10) REVERT: C 346 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7535 (tt0) REVERT: C 351 GLU cc_start: 0.7957 (tt0) cc_final: 0.7734 (tt0) REVERT: C 373 GLN cc_start: 0.7435 (tt0) cc_final: 0.7143 (tt0) REVERT: C 420 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.8095 (tpp) REVERT: D 124 PHE cc_start: 0.7332 (t80) cc_final: 0.7097 (t80) REVERT: D 207 ARG cc_start: 0.7033 (mmm-85) cc_final: 0.6586 (mmm-85) REVERT: D 273 GLN cc_start: 0.8376 (mt0) cc_final: 0.7897 (mt0) REVERT: D 300 PHE cc_start: 0.8183 (m-80) cc_final: 0.7731 (m-10) REVERT: D 334 ARG cc_start: 0.6938 (tpp80) cc_final: 0.6396 (tpp-160) REVERT: D 373 GLN cc_start: 0.7676 (tt0) cc_final: 0.7379 (tt0) REVERT: D 487 ASP cc_start: 0.7749 (m-30) cc_final: 0.7491 (m-30) REVERT: E 207 ARG cc_start: 0.7274 (mmm-85) cc_final: 0.6710 (mmm-85) REVERT: E 215 ASN cc_start: 0.7132 (p0) cc_final: 0.6925 (t0) REVERT: E 334 ARG cc_start: 0.7121 (tpp80) cc_final: 0.6843 (mtp-110) REVERT: E 346 GLU cc_start: 0.8102 (tt0) cc_final: 0.7712 (tm-30) REVERT: E 367 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7313 (mm-30) REVERT: E 373 GLN cc_start: 0.7719 (tt0) cc_final: 0.7258 (tt0) REVERT: E 420 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7788 (ttm) REVERT: F 124 PHE cc_start: 0.7363 (t80) cc_final: 0.6210 (m-10) REVERT: F 174 LYS cc_start: 0.8316 (ptpp) cc_final: 0.7648 (mmtm) REVERT: F 178 ASP cc_start: 0.8452 (m-30) cc_final: 0.8065 (m-30) REVERT: F 207 ARG cc_start: 0.7047 (mmm-85) cc_final: 0.6426 (mmm-85) REVERT: F 220 VAL cc_start: 0.7695 (t) cc_final: 0.7490 (t) REVERT: F 373 GLN cc_start: 0.7814 (tt0) cc_final: 0.7440 (tt0) REVERT: F 389 ASP cc_start: 0.7293 (p0) cc_final: 0.7072 (p0) outliers start: 61 outliers final: 29 residues processed: 317 average time/residue: 1.2222 time to fit residues: 435.8193 Evaluate side-chains 299 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 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 238 ILE Chi-restraints excluded: chain B residue 285 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 215 ASN 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 197 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 298 SER 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 233 ILE Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 371 HIS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 371 HIS 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: 0.6980 chunk 136 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 204 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 216 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 142 optimal weight: 0.8980 chunk 201 optimal weight: 0.5980 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 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN C 406 GLN C 416 ASN D 215 ASN E 215 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS E 371 HIS E 493 ASN F 215 ASN F 425 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.155193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.114051 restraints weight = 20235.494| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.76 r_work: 0.3206 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 18930 Z= 0.164 Angle : 0.595 10.952 25614 Z= 0.299 Chirality : 0.042 0.188 2922 Planarity : 0.005 0.040 3186 Dihedral : 4.310 22.066 2514 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.57 % Allowed : 17.32 % 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: 1.58 (0.18), residues: 2220 helix: 1.71 (0.14), residues: 1374 sheet: 0.41 (0.40), residues: 180 loop : -0.07 (0.24), residues: 666 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 0.026 0.002 PHE C 429 TYR 0.012 0.002 TYR C 453 ARG 0.010 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03554 ( 1146) hydrogen bonds : angle 4.17385 ( 3318) SS BOND : bond 0.00119 ( 6) SS BOND : angle 0.66630 ( 12) covalent geometry : bond 0.00385 (18924) covalent geometry : angle 0.59532 (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 324 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 273 time to evaluate : 2.345 Fit side-chains REVERT: A 172 PHE cc_start: 0.7434 (t80) cc_final: 0.7052 (t80) REVERT: A 174 LYS cc_start: 0.8090 (ptpp) cc_final: 0.7266 (mmtm) REVERT: A 181 ARG cc_start: 0.8244 (mmm-85) cc_final: 0.7788 (mmt90) REVERT: A 207 ARG cc_start: 0.7055 (mmm-85) cc_final: 0.6382 (mmm-85) REVERT: A 334 ARG cc_start: 0.7238 (tpp80) cc_final: 0.6969 (mtp-110) REVERT: A 346 GLU cc_start: 0.8112 (tt0) cc_final: 0.7715 (tm-30) REVERT: A 367 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7303 (mm-30) REVERT: A 373 GLN cc_start: 0.7845 (tt0) cc_final: 0.7394 (tt0) REVERT: A 389 ASP cc_start: 0.7410 (p0) cc_final: 0.7116 (p0) REVERT: A 420 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.7920 (ttm) REVERT: B 174 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.7855 (mmtt) REVERT: B 207 ARG cc_start: 0.7247 (mmm-85) cc_final: 0.6687 (mmm-85) REVERT: B 285 LYS cc_start: 0.8254 (OUTLIER) cc_final: 0.7888 (ttmm) REVERT: B 373 GLN cc_start: 0.8014 (tt0) cc_final: 0.7615 (tt0) REVERT: C 172 PHE cc_start: 0.7681 (t80) cc_final: 0.7383 (t80) REVERT: C 174 LYS cc_start: 0.8322 (ptpp) cc_final: 0.7580 (mmtt) REVERT: C 207 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6524 (mmm-85) REVERT: C 215 ASN cc_start: 0.7354 (OUTLIER) cc_final: 0.7070 (t0) REVERT: C 300 PHE cc_start: 0.8022 (m-80) cc_final: 0.7815 (m-80) REVERT: C 346 GLU cc_start: 0.7984 (mm-30) cc_final: 0.7547 (tt0) REVERT: C 351 GLU cc_start: 0.8052 (tt0) cc_final: 0.7810 (tt0) REVERT: C 367 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7233 (mm-30) REVERT: C 373 GLN cc_start: 0.7621 (tt0) cc_final: 0.7327 (tt0) REVERT: C 420 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: C 493 ASN cc_start: 0.8479 (p0) cc_final: 0.8121 (p0) REVERT: D 124 PHE cc_start: 0.7413 (t80) cc_final: 0.7178 (t80) REVERT: D 207 ARG cc_start: 0.7122 (mmm-85) cc_final: 0.6659 (mmm-85) REVERT: D 300 PHE cc_start: 0.8162 (m-80) cc_final: 0.7891 (m-80) REVERT: D 334 ARG cc_start: 0.6930 (tpp80) cc_final: 0.6388 (tpp-160) REVERT: D 373 GLN cc_start: 0.7778 (tt0) cc_final: 0.7478 (tt0) REVERT: D 420 MET cc_start: 0.7788 (tpp) cc_final: 0.7519 (tpt) REVERT: E 207 ARG cc_start: 0.7411 (mmm-85) cc_final: 0.6772 (mmm-85) REVERT: E 228 ASP cc_start: 0.7896 (m-30) cc_final: 0.7373 (m-30) REVERT: E 334 ARG cc_start: 0.7149 (tpp80) cc_final: 0.6868 (mtp-110) REVERT: E 346 GLU cc_start: 0.8144 (tt0) cc_final: 0.7760 (tm-30) REVERT: E 367 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7329 (mm-30) REVERT: E 373 GLN cc_start: 0.7856 (tt0) cc_final: 0.7442 (tt0) REVERT: E 420 MET cc_start: 0.8427 (OUTLIER) cc_final: 0.7893 (ttm) REVERT: F 124 PHE cc_start: 0.7393 (t80) cc_final: 0.6218 (m-10) REVERT: F 158 PHE cc_start: 0.8386 (m-80) cc_final: 0.8119 (m-10) REVERT: F 174 LYS cc_start: 0.8414 (ptpp) cc_final: 0.7675 (mmtm) REVERT: F 181 ARG cc_start: 0.8166 (mmm-85) cc_final: 0.7681 (mmt90) REVERT: F 207 ARG cc_start: 0.7064 (mmm-85) cc_final: 0.6426 (mmm-85) REVERT: F 373 GLN cc_start: 0.7862 (tt0) cc_final: 0.7655 (tt0) REVERT: F 389 ASP cc_start: 0.7537 (p0) cc_final: 0.7283 (p0) outliers start: 51 outliers final: 25 residues processed: 308 average time/residue: 1.2644 time to fit residues: 437.9016 Evaluate side-chains 299 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 268 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain 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 239 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER 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 375 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 210 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 186 optimal weight: 0.5980 chunk 218 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 68 optimal weight: 0.0030 chunk 2 optimal weight: 8.9990 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.4790 ------------------------------------------------------------------------------- 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** C 406 GLN C 416 ASN D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 519 GLN E 215 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 215 ASN F 425 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.156909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.115979 restraints weight = 20259.800| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.77 r_work: 0.3232 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18930 Z= 0.134 Angle : 0.574 10.871 25614 Z= 0.286 Chirality : 0.040 0.189 2922 Planarity : 0.004 0.039 3186 Dihedral : 4.210 21.763 2514 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.06 % Allowed : 17.72 % Favored : 80.21 % 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: 1.70 (0.18), residues: 2220 helix: 1.79 (0.14), residues: 1374 sheet: 0.53 (0.39), residues: 186 loop : -0.01 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 138 HIS 0.004 0.001 HIS D 269 PHE 0.024 0.002 PHE C 429 TYR 0.012 0.002 TYR C 453 ARG 0.009 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 1146) hydrogen bonds : angle 4.14042 ( 3318) SS BOND : bond 0.00109 ( 6) SS BOND : angle 0.65037 ( 12) covalent geometry : bond 0.00309 (18924) covalent geometry : angle 0.57434 (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 311 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 270 time to evaluate : 2.145 Fit side-chains REVERT: A 174 LYS cc_start: 0.8066 (ptpp) cc_final: 0.7256 (mmtm) REVERT: A 181 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7837 (mmt90) REVERT: A 207 ARG cc_start: 0.7024 (mmm-85) cc_final: 0.6371 (mmm-85) REVERT: A 334 ARG cc_start: 0.7227 (tpp80) cc_final: 0.6961 (mtp-110) REVERT: A 346 GLU cc_start: 0.8102 (tt0) cc_final: 0.7698 (tm-30) REVERT: A 367 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7270 (mm-30) REVERT: A 373 GLN cc_start: 0.7749 (tt0) cc_final: 0.7387 (tt0) REVERT: A 389 ASP cc_start: 0.7377 (p0) cc_final: 0.7090 (p0) REVERT: A 420 MET cc_start: 0.8372 (OUTLIER) cc_final: 0.7801 (ttm) REVERT: B 174 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.7909 (mmtt) REVERT: B 207 ARG cc_start: 0.7221 (mmm-85) cc_final: 0.6674 (mmm-85) REVERT: B 285 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7695 (ttmm) REVERT: B 373 GLN cc_start: 0.7995 (tt0) cc_final: 0.7637 (tt0) REVERT: C 172 PHE cc_start: 0.7534 (t80) cc_final: 0.7221 (t80) REVERT: C 174 LYS cc_start: 0.8313 (ptpp) cc_final: 0.7592 (mmtt) REVERT: C 207 ARG cc_start: 0.7149 (mmm-85) cc_final: 0.6523 (mmm-85) REVERT: C 300 PHE cc_start: 0.8025 (m-80) cc_final: 0.7648 (m-10) REVERT: C 346 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7552 (tt0) REVERT: C 351 GLU cc_start: 0.8020 (tt0) cc_final: 0.7783 (tt0) REVERT: C 373 GLN cc_start: 0.7609 (tt0) cc_final: 0.7305 (tt0) REVERT: C 420 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8138 (tpp) REVERT: D 124 PHE cc_start: 0.7281 (t80) cc_final: 0.7054 (t80) REVERT: D 207 ARG cc_start: 0.7046 (mmm-85) cc_final: 0.6614 (mmm-85) REVERT: D 300 PHE cc_start: 0.8177 (m-80) cc_final: 0.7774 (m-10) REVERT: D 334 ARG cc_start: 0.6942 (tpp80) cc_final: 0.6406 (tpp-160) REVERT: D 373 GLN cc_start: 0.7766 (tt0) cc_final: 0.7468 (tt0) REVERT: D 487 ASP cc_start: 0.7773 (m-30) cc_final: 0.7547 (m-30) REVERT: E 207 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.6719 (mmm-85) REVERT: E 228 ASP cc_start: 0.7879 (m-30) cc_final: 0.7365 (m-30) REVERT: E 334 ARG cc_start: 0.7118 (tpp80) cc_final: 0.6864 (mtp-110) REVERT: E 346 GLU cc_start: 0.8123 (tt0) cc_final: 0.7733 (tm-30) REVERT: E 367 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7318 (mm-30) REVERT: E 373 GLN cc_start: 0.7761 (tt0) cc_final: 0.7312 (tt0) REVERT: E 420 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7817 (ttm) REVERT: F 124 PHE cc_start: 0.7415 (t80) cc_final: 0.6270 (m-10) REVERT: F 158 PHE cc_start: 0.8380 (m-80) cc_final: 0.8084 (m-10) REVERT: F 174 LYS cc_start: 0.8389 (ptpp) cc_final: 0.7677 (mmtm) REVERT: F 178 ASP cc_start: 0.8444 (m-30) cc_final: 0.8074 (m-30) REVERT: F 181 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7649 (mmt90) REVERT: F 207 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6399 (mmm-85) REVERT: F 334 ARG cc_start: 0.6905 (mtp-110) cc_final: 0.6560 (tpp-160) REVERT: F 373 GLN cc_start: 0.7837 (tt0) cc_final: 0.7635 (tt0) REVERT: F 389 ASP cc_start: 0.7362 (p0) cc_final: 0.7134 (p0) outliers start: 41 outliers final: 26 residues processed: 297 average time/residue: 1.3063 time to fit residues: 434.5099 Evaluate side-chains 289 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 233 ILE 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 238 ILE Chi-restraints excluded: chain B residue 285 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 197 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 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 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 159 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 128 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 GLN A 519 GLN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 247 GLN C 416 ASN D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 519 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 E 519 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN F 425 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.153345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.112035 restraints weight = 20326.553| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 1.76 r_work: 0.3173 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 18930 Z= 0.188 Angle : 0.627 10.521 25614 Z= 0.313 Chirality : 0.042 0.192 2922 Planarity : 0.005 0.051 3186 Dihedral : 4.457 23.079 2514 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.17 % Allowed : 17.72 % 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: 1.55 (0.18), residues: 2220 helix: 1.73 (0.14), residues: 1350 sheet: 0.32 (0.38), residues: 186 loop : -0.06 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 458 HIS 0.005 0.001 HIS C 269 PHE 0.031 0.002 PHE E 429 TYR 0.013 0.002 TYR F 453 ARG 0.010 0.001 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03762 ( 1146) hydrogen bonds : angle 4.25558 ( 3318) SS BOND : bond 0.00134 ( 6) SS BOND : angle 0.73237 ( 12) covalent geometry : bond 0.00449 (18924) covalent geometry : angle 0.62700 (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 313 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 270 time to evaluate : 1.943 Fit side-chains REVERT: A 172 PHE cc_start: 0.7527 (t80) cc_final: 0.7137 (t80) REVERT: A 174 LYS cc_start: 0.8250 (ptpp) cc_final: 0.7324 (mmtm) REVERT: A 181 ARG cc_start: 0.8318 (mmm-85) cc_final: 0.7974 (mmt90) REVERT: A 207 ARG cc_start: 0.7184 (mmm-85) cc_final: 0.6445 (mmm-85) REVERT: A 334 ARG cc_start: 0.7204 (tpp80) cc_final: 0.6893 (mtp-110) REVERT: A 346 GLU cc_start: 0.8122 (tt0) cc_final: 0.7726 (tm-30) REVERT: A 367 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7326 (mm-30) REVERT: A 373 GLN cc_start: 0.7849 (tt0) cc_final: 0.7508 (tt0) REVERT: A 389 ASP cc_start: 0.7491 (p0) cc_final: 0.7181 (p0) REVERT: A 420 MET cc_start: 0.8434 (OUTLIER) cc_final: 0.7882 (ttm) REVERT: B 174 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7912 (mmtt) REVERT: B 207 ARG cc_start: 0.7295 (mmm-85) cc_final: 0.6580 (mmm-85) REVERT: B 285 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7959 (ttmm) REVERT: C 172 PHE cc_start: 0.7626 (t80) cc_final: 0.7345 (t80) REVERT: C 174 LYS cc_start: 0.8368 (ptpp) cc_final: 0.7603 (mmtt) REVERT: C 207 ARG cc_start: 0.7212 (mmm-85) cc_final: 0.6620 (mmm-85) REVERT: C 300 PHE cc_start: 0.8024 (m-80) cc_final: 0.7824 (m-80) REVERT: C 346 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7534 (tt0) REVERT: C 351 GLU cc_start: 0.8003 (tt0) cc_final: 0.7755 (tt0) REVERT: C 367 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7257 (mm-30) REVERT: C 373 GLN cc_start: 0.7866 (tt0) cc_final: 0.7577 (tt0) REVERT: C 420 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8061 (tpp) REVERT: C 493 ASN cc_start: 0.8546 (p0) cc_final: 0.8138 (p0) REVERT: D 124 PHE cc_start: 0.7419 (t80) cc_final: 0.7196 (t80) REVERT: D 174 LYS cc_start: 0.8291 (ptpp) cc_final: 0.7504 (mmtt) REVERT: D 207 ARG cc_start: 0.7257 (mmm-85) cc_final: 0.6645 (mmm-85) REVERT: D 300 PHE cc_start: 0.8144 (m-80) cc_final: 0.7906 (m-80) REVERT: D 334 ARG cc_start: 0.7055 (tpp80) cc_final: 0.6509 (tpp-160) REVERT: D 373 GLN cc_start: 0.7889 (tt0) cc_final: 0.7636 (tt0) REVERT: D 456 ASP cc_start: 0.8308 (p0) cc_final: 0.8059 (p0) REVERT: E 172 PHE cc_start: 0.7603 (t80) cc_final: 0.7221 (t80) REVERT: E 174 LYS cc_start: 0.8158 (ptpp) cc_final: 0.7258 (mmtm) REVERT: E 207 ARG cc_start: 0.7438 (mmm-85) cc_final: 0.6674 (mmm-85) REVERT: E 228 ASP cc_start: 0.7803 (m-30) cc_final: 0.7332 (m-30) REVERT: E 334 ARG cc_start: 0.7094 (tpp80) cc_final: 0.6829 (mtp-110) REVERT: E 346 GLU cc_start: 0.8154 (tt0) cc_final: 0.7771 (tm-30) REVERT: E 367 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7344 (mm-30) REVERT: E 373 GLN cc_start: 0.7835 (tt0) cc_final: 0.7495 (tt0) REVERT: E 420 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7845 (ttm) REVERT: F 124 PHE cc_start: 0.7420 (t80) cc_final: 0.6292 (m-10) REVERT: F 158 PHE cc_start: 0.8392 (m-80) cc_final: 0.8111 (m-10) REVERT: F 174 LYS cc_start: 0.8487 (ptpp) cc_final: 0.7669 (mmtm) REVERT: F 178 ASP cc_start: 0.8563 (m-30) cc_final: 0.8193 (m-30) REVERT: F 207 ARG cc_start: 0.7061 (mmm-85) cc_final: 0.6471 (mmm-85) REVERT: F 334 ARG cc_start: 0.6923 (mtp-110) cc_final: 0.6573 (tpp-160) REVERT: F 389 ASP cc_start: 0.7639 (p0) cc_final: 0.6908 (p0) outliers start: 43 outliers final: 26 residues processed: 300 average time/residue: 1.2356 time to fit residues: 416.0806 Evaluate side-chains 286 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 255 time to evaluate : 1.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 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 285 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 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 197 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 371 HIS 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 209 LEU 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: 0.7980 chunk 3 optimal weight: 20.0000 chunk 71 optimal weight: 0.0980 chunk 97 optimal weight: 0.5980 chunk 75 optimal weight: 0.6980 chunk 175 optimal weight: 0.7980 chunk 204 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 ASN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 416 ASN D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 493 ASN F 425 GLN F 519 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.153570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.113245 restraints weight = 20021.977| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.72 r_work: 0.3193 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18930 Z= 0.150 Angle : 0.599 11.298 25614 Z= 0.297 Chirality : 0.041 0.191 2922 Planarity : 0.005 0.042 3186 Dihedral : 4.319 22.454 2514 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.96 % Allowed : 18.18 % Favored : 79.86 % 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: 1.63 (0.18), residues: 2220 helix: 1.73 (0.14), residues: 1374 sheet: 0.39 (0.39), residues: 186 loop : 0.03 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 138 HIS 0.004 0.001 HIS C 269 PHE 0.032 0.002 PHE D 196 TYR 0.012 0.002 TYR C 453 ARG 0.010 0.000 ARG B 334 Details of bonding type rmsd hydrogen bonds : bond 0.03482 ( 1146) hydrogen bonds : angle 4.19498 ( 3318) SS BOND : bond 0.00123 ( 6) SS BOND : angle 0.68627 ( 12) covalent geometry : bond 0.00352 (18924) covalent geometry : angle 0.59866 (25602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15080.42 seconds wall clock time: 259 minutes 41.55 seconds (15581.55 seconds total)