Starting phenix.real_space_refine on Thu Sep 18 16:58:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jk8_61547/09_2025/9jk8_61547.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jk8_61547/09_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_61547/09_2025/9jk8_61547.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jk8_61547/09_2025/9jk8_61547.map" model { file = "/net/cci-nas-00/data/ceres_data/9jk8_61547/09_2025/9jk8_61547.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jk8_61547/09_2025/9jk8_61547.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.019 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: B, C, D, E, F Time building chain proxies: 3.08, per 1000 atoms: 0.17 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 B 145 " - pdb=" SG CYS B 149 " distance=2.03 Simple disulfide: pdb=" SG CYS C 145 " - pdb=" SG CYS C 149 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 149 " distance=2.03 Simple disulfide: pdb=" SG CYS E 145 " - pdb=" SG CYS E 149 " distance=2.03 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: 1.84 Conformation dependent library (CDL) restraints added in 936.0 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.72 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: 4.12 Time building geometry restraints manager: 2.39 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.650 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: 0.030 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.810 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:8.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- 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 : 13.47 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.32 (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 ARG 0.010 0.001 ARG E 181 TYR 0.016 0.002 TYR D 283 PHE 0.021 0.002 PHE D 369 TRP 0.022 0.003 TRP E 168 HIS 0.003 0.001 HIS F 234 Details of bonding type rmsd covalent geometry : bond 0.00472 (18924) covalent geometry : angle 0.82219 (25602) SS BOND : bond 0.00249 ( 6) SS BOND : angle 0.47913 ( 12) hydrogen bonds : bond 0.13597 ( 1146) hydrogen bonds : angle 6.63072 ( 3318) *********************** 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 : 0.735 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: 0.7291 time to fit residues: 331.3074 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 : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.0060 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0070 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.0870 chunk 200 optimal weight: 1.9990 chunk 212 optimal weight: 0.8980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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 341 ASN E 473 ASN E 512 HIS ** F 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN F 425 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.164578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.124163 restraints weight = 20316.319| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.80 r_work: 0.3334 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3186 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18930 Z= 0.129 Angle : 0.562 10.290 25614 Z= 0.294 Chirality : 0.041 0.169 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.529 23.275 2514 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.62 % Allowed : 9.21 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.17), residues: 2220 helix: 0.76 (0.13), residues: 1374 sheet: -0.28 (0.35), residues: 192 loop : -0.98 (0.22), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 334 TYR 0.013 0.002 TYR C 200 PHE 0.028 0.002 PHE D 196 TRP 0.014 0.002 TRP D 138 HIS 0.006 0.001 HIS A 234 Details of bonding type rmsd covalent geometry : bond 0.00284 (18924) covalent geometry : angle 0.56169 (25602) SS BOND : bond 0.00076 ( 6) SS BOND : angle 0.48423 ( 12) hydrogen bonds : bond 0.03487 ( 1146) hydrogen bonds : angle 4.62018 ( 3318) *********************** 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 386 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 334 time to evaluate : 0.461 Fit side-chains REVERT: A 172 PHE cc_start: 0.7587 (t80) cc_final: 0.7217 (t80) REVERT: A 174 LYS cc_start: 0.7939 (ptpp) cc_final: 0.7668 (mmtt) REVERT: A 207 ARG cc_start: 0.7300 (mmm-85) cc_final: 0.6764 (mmm-85) REVERT: A 334 ARG cc_start: 0.6870 (tpp80) cc_final: 0.6519 (tpp-160) REVERT: A 373 GLN cc_start: 0.7265 (tt0) cc_final: 0.6796 (tt0) REVERT: A 446 SER cc_start: 0.8454 (m) cc_final: 0.8145 (p) REVERT: B 172 PHE cc_start: 0.7458 (t80) cc_final: 0.7143 (t80) REVERT: B 179 MET cc_start: 0.8791 (mtm) cc_final: 0.8560 (mtm) REVERT: B 207 ARG cc_start: 0.7301 (mmm-85) cc_final: 0.6725 (mmm-85) REVERT: B 267 LEU cc_start: 0.8899 (mt) cc_final: 0.8692 (mp) REVERT: B 285 LYS cc_start: 0.7956 (OUTLIER) cc_final: 0.7501 (ttpp) REVERT: B 300 PHE cc_start: 0.8251 (m-80) cc_final: 0.7534 (m-10) REVERT: B 304 LYS cc_start: 0.7663 (tttt) cc_final: 0.7069 (mppt) REVERT: B 334 ARG cc_start: 0.6852 (mtp-110) cc_final: 0.6531 (tpp-160) REVERT: B 373 GLN cc_start: 0.7839 (tt0) cc_final: 0.7380 (tp40) REVERT: B 413 ARG cc_start: 0.8568 (mmt90) cc_final: 0.8307 (mmt90) REVERT: C 172 PHE cc_start: 0.7701 (t80) cc_final: 0.7410 (t80) REVERT: C 207 ARG cc_start: 0.7281 (mmm-85) cc_final: 0.6537 (mmm-85) REVERT: C 249 MET cc_start: 0.8767 (tpt) cc_final: 0.8519 (mmm) REVERT: C 300 PHE cc_start: 0.8204 (m-80) cc_final: 0.7810 (m-80) REVERT: C 334 ARG cc_start: 0.6778 (tpp80) cc_final: 0.6516 (mtp-110) REVERT: C 346 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7560 (tt0) REVERT: C 351 GLU cc_start: 0.7979 (tt0) cc_final: 0.7638 (mt-10) REVERT: C 373 GLN cc_start: 0.7001 (tt0) cc_final: 0.6715 (tt0) REVERT: C 420 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7990 (tpp) REVERT: C 446 SER cc_start: 0.8352 (m) cc_final: 0.8133 (p) REVERT: C 456 ASP cc_start: 0.8207 (p0) cc_final: 0.7951 (p0) REVERT: C 516 LEU cc_start: 0.8606 (tp) cc_final: 0.8381 (tm) REVERT: D 124 PHE cc_start: 0.7501 (t80) cc_final: 0.7185 (t80) REVERT: D 174 LYS cc_start: 0.7914 (ptpp) cc_final: 0.7016 (mmtt) REVERT: D 207 ARG cc_start: 0.6793 (mmm-85) cc_final: 0.6549 (mmm-85) REVERT: D 263 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7569 (mtp180) REVERT: D 267 LEU cc_start: 0.8741 (mt) cc_final: 0.8511 (mp) REVERT: D 285 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7547 (ttpp) REVERT: D 300 PHE cc_start: 0.8048 (m-80) cc_final: 0.7552 (m-80) REVERT: D 373 GLN cc_start: 0.7485 (tt0) cc_final: 0.7127 (tt0) REVERT: D 455 LYS cc_start: 0.8015 (mttp) cc_final: 0.7788 (mmtt) REVERT: E 172 PHE cc_start: 0.7444 (t80) cc_final: 0.7087 (t80) REVERT: E 207 ARG cc_start: 0.7026 (mmm-85) cc_final: 0.6592 (mmm-85) REVERT: E 247 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: E 334 ARG cc_start: 0.7064 (tpp80) cc_final: 0.6562 (tpp-160) REVERT: E 346 GLU cc_start: 0.8038 (tt0) cc_final: 0.7646 (tm-30) REVERT: E 373 GLN cc_start: 0.7439 (tt0) cc_final: 0.6951 (tt0) REVERT: E 413 ARG cc_start: 0.8293 (mpt-90) cc_final: 0.7730 (mtm180) REVERT: E 420 MET cc_start: 0.8318 (OUTLIER) cc_final: 0.7723 (ttm) REVERT: E 456 ASP cc_start: 0.8040 (p0) cc_final: 0.7821 (p0) REVERT: F 148 ILE cc_start: 0.7264 (mm) cc_final: 0.6938 (tt) REVERT: F 174 LYS cc_start: 0.7846 (ptpp) cc_final: 0.7274 (mmtm) REVERT: F 207 ARG cc_start: 0.6903 (mmm-85) cc_final: 0.6504 (mmm-85) REVERT: F 300 PHE cc_start: 0.8203 (m-80) cc_final: 0.7544 (m-10) REVERT: F 346 GLU cc_start: 0.8040 (tt0) cc_final: 0.7807 (tt0) REVERT: F 373 GLN cc_start: 0.7762 (tt0) cc_final: 0.7240 (tp40) REVERT: F 389 ASP cc_start: 0.7148 (p0) cc_final: 0.6935 (p0) REVERT: F 413 ARG cc_start: 0.8365 (mmt90) cc_final: 0.8153 (mmt90) outliers start: 52 outliers final: 17 residues processed: 361 average time/residue: 0.7044 time to fit residues: 280.7683 Evaluate side-chains 309 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 286 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 B residue 154 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 446 SER 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 420 MET Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 233 ILE Chi-restraints excluded: chain D residue 263 ARG Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 247 GLN Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 119 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 214 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 164 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 350 HIS C 406 GLN D 221 GLN D 247 GLN D 293 ASN D 350 HIS D 416 ASN D 473 ASN E 234 HIS E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS F 234 HIS F 247 GLN ** F 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 406 GLN F 425 GLN F 512 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.154532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.113970 restraints weight = 20164.879| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.74 r_work: 0.3201 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18930 Z= 0.172 Angle : 0.592 10.072 25614 Z= 0.305 Chirality : 0.043 0.162 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.573 22.466 2514 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.82 % Allowed : 12.89 % Favored : 84.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.86 (0.17), residues: 2220 helix: 1.23 (0.14), residues: 1380 sheet: 0.14 (0.39), residues: 180 loop : -0.58 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 334 TYR 0.017 0.002 TYR F 453 PHE 0.024 0.002 PHE C 196 TRP 0.020 0.002 TRP C 458 HIS 0.007 0.002 HIS D 426 Details of bonding type rmsd covalent geometry : bond 0.00402 (18924) covalent geometry : angle 0.59233 (25602) SS BOND : bond 0.00059 ( 6) SS BOND : angle 0.44374 ( 12) hydrogen bonds : bond 0.03755 ( 1146) hydrogen bonds : angle 4.44208 ( 3318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 309 time to evaluate : 0.736 Fit side-chains REVERT: A 172 PHE cc_start: 0.7550 (t80) cc_final: 0.7218 (t80) REVERT: A 174 LYS cc_start: 0.8029 (ptpp) cc_final: 0.7396 (mmtm) REVERT: A 196 PHE cc_start: 0.7207 (t80) cc_final: 0.6968 (t80) REVERT: A 207 ARG cc_start: 0.7351 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: A 273 GLN cc_start: 0.8700 (mt0) cc_final: 0.8241 (mt0) REVERT: A 304 LYS cc_start: 0.7631 (tttt) cc_final: 0.7061 (mttp) REVERT: A 334 ARG cc_start: 0.7128 (tpp80) cc_final: 0.6637 (tpp-160) REVERT: A 373 GLN cc_start: 0.7642 (tt0) cc_final: 0.7152 (tt0) REVERT: A 420 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7847 (ttm) REVERT: B 207 ARG cc_start: 0.7379 (mmm-85) cc_final: 0.6545 (mmm-85) REVERT: B 285 LYS cc_start: 0.8255 (OUTLIER) cc_final: 0.7830 (ttpp) REVERT: B 334 ARG cc_start: 0.7047 (mtp-110) cc_final: 0.6639 (tpp-160) REVERT: B 373 GLN cc_start: 0.7993 (tt0) cc_final: 0.7509 (tp40) REVERT: B 413 ARG cc_start: 0.8528 (mmt90) cc_final: 0.8196 (mmt90) REVERT: B 438 LYS cc_start: 0.8603 (OUTLIER) cc_final: 0.8380 (tptt) REVERT: C 172 PHE cc_start: 0.7696 (t80) cc_final: 0.7386 (t80) REVERT: C 207 ARG cc_start: 0.7369 (mmm-85) cc_final: 0.6558 (mmm-85) REVERT: C 273 GLN cc_start: 0.8706 (mt0) cc_final: 0.8394 (mt0) REVERT: C 300 PHE cc_start: 0.8206 (m-80) cc_final: 0.7802 (m-10) REVERT: C 334 ARG cc_start: 0.7009 (tpp80) cc_final: 0.6670 (mtp-110) REVERT: C 346 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7522 (tt0) REVERT: C 351 GLU cc_start: 0.7994 (tt0) cc_final: 0.7758 (tt0) REVERT: C 367 GLU cc_start: 0.7895 (mt-10) cc_final: 0.7171 (mm-30) REVERT: C 373 GLN cc_start: 0.7463 (tt0) cc_final: 0.7136 (tt0) REVERT: C 493 ASN cc_start: 0.8515 (p0) cc_final: 0.8106 (p0) REVERT: C 516 LEU cc_start: 0.8672 (tp) cc_final: 0.8466 (tm) REVERT: D 124 PHE cc_start: 0.7452 (t80) cc_final: 0.7235 (t80) REVERT: D 174 LYS cc_start: 0.8281 (ptpp) cc_final: 0.7412 (mmtt) REVERT: D 207 ARG cc_start: 0.7094 (mmm-85) cc_final: 0.6691 (mmm-85) REVERT: D 247 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8115 (tt0) REVERT: D 285 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7894 (ttpp) REVERT: D 300 PHE cc_start: 0.8108 (m-80) cc_final: 0.7724 (m-10) REVERT: D 334 ARG cc_start: 0.7048 (tpp80) cc_final: 0.6619 (tpp-160) REVERT: D 373 GLN cc_start: 0.7622 (tt0) cc_final: 0.7222 (tt0) REVERT: D 493 ASN cc_start: 0.8493 (p0) cc_final: 0.8116 (p0) REVERT: E 172 PHE cc_start: 0.7591 (t80) cc_final: 0.7231 (t80) REVERT: E 207 ARG cc_start: 0.7242 (mmm-85) cc_final: 0.6700 (mmm-85) REVERT: E 215 ASN cc_start: 0.7279 (p0) cc_final: 0.7031 (t0) REVERT: E 247 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: E 273 GLN cc_start: 0.8678 (mt0) cc_final: 0.8120 (mt0) REVERT: E 346 GLU cc_start: 0.8059 (tt0) cc_final: 0.7661 (tm-30) REVERT: E 367 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7296 (mm-30) REVERT: E 373 GLN cc_start: 0.7915 (tt0) cc_final: 0.7360 (tt0) REVERT: E 413 ARG cc_start: 0.8429 (mpt-90) cc_final: 0.8225 (mmt180) REVERT: E 420 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7866 (ttm) REVERT: F 148 ILE cc_start: 0.7201 (mm) cc_final: 0.6995 (tt) REVERT: F 156 MET cc_start: 0.8307 (ttt) cc_final: 0.8093 (ttt) REVERT: F 172 PHE cc_start: 0.7840 (t80) cc_final: 0.7626 (t80) REVERT: F 174 LYS cc_start: 0.8170 (ptpp) cc_final: 0.7549 (mmtm) REVERT: F 207 ARG cc_start: 0.7057 (mmm-85) cc_final: 0.6554 (mmm-85) REVERT: F 346 GLU cc_start: 0.8048 (tt0) cc_final: 0.7847 (tt0) REVERT: F 373 GLN cc_start: 0.7886 (tt0) cc_final: 0.7356 (tt0) REVERT: F 389 ASP cc_start: 0.7471 (p0) cc_final: 0.7181 (p0) outliers start: 56 outliers final: 24 residues processed: 344 average time/residue: 0.6605 time to fit residues: 251.5757 Evaluate side-chains 319 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 288 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 438 LYS Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 209 LEU Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain D residue 155 SER 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 247 GLN Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 57 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 198 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 174 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 157 optimal weight: 4.9990 chunk 189 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 ASN B 247 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 425 GLN F 425 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114109 restraints weight = 20406.323| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.76 r_work: 0.3202 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 18930 Z= 0.152 Angle : 0.569 10.503 25614 Z= 0.290 Chirality : 0.041 0.153 2922 Planarity : 0.005 0.038 3186 Dihedral : 4.429 22.289 2514 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.78 % Allowed : 13.39 % Favored : 82.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.18), residues: 2220 helix: 1.42 (0.14), residues: 1380 sheet: 0.43 (0.40), residues: 180 loop : -0.37 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 334 TYR 0.013 0.002 TYR B 453 PHE 0.028 0.002 PHE E 196 TRP 0.021 0.002 TRP C 458 HIS 0.005 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00354 (18924) covalent geometry : angle 0.56877 (25602) SS BOND : bond 0.00077 ( 6) SS BOND : angle 0.47257 ( 12) hydrogen bonds : bond 0.03511 ( 1146) hydrogen bonds : angle 4.29261 ( 3318) *********************** 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 375 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 300 time to evaluate : 0.752 Fit side-chains REVERT: A 172 PHE cc_start: 0.7638 (t80) cc_final: 0.7318 (t80) REVERT: A 174 LYS cc_start: 0.8100 (ptpp) cc_final: 0.7293 (mmtm) REVERT: A 207 ARG cc_start: 0.7356 (mmm-85) cc_final: 0.6708 (mmm-85) REVERT: A 334 ARG cc_start: 0.7122 (tpp80) cc_final: 0.6754 (tpp-160) REVERT: A 346 GLU cc_start: 0.8074 (tt0) cc_final: 0.7672 (tm-30) REVERT: A 367 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7304 (mm-30) REVERT: A 373 GLN cc_start: 0.7627 (tt0) cc_final: 0.7237 (tt0) REVERT: A 389 ASP cc_start: 0.7312 (p0) cc_final: 0.7061 (p0) REVERT: A 420 MET cc_start: 0.8376 (OUTLIER) cc_final: 0.7799 (ttm) REVERT: B 172 PHE cc_start: 0.7663 (t80) cc_final: 0.7210 (t80) REVERT: B 207 ARG cc_start: 0.7372 (mmm-85) cc_final: 0.6516 (mmm-85) REVERT: B 285 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7820 (ttpp) REVERT: B 373 GLN cc_start: 0.7979 (tt0) cc_final: 0.7525 (tt0) REVERT: C 172 PHE cc_start: 0.7713 (t80) cc_final: 0.7405 (t80) REVERT: C 207 ARG cc_start: 0.7340 (mmm-85) cc_final: 0.6630 (mmm-85) REVERT: C 273 GLN cc_start: 0.8692 (mt0) cc_final: 0.8310 (mt0) REVERT: C 300 PHE cc_start: 0.8143 (m-80) cc_final: 0.7749 (m-10) REVERT: C 346 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7510 (tt0) REVERT: C 351 GLU cc_start: 0.7987 (tt0) cc_final: 0.7748 (tt0) REVERT: C 373 GLN cc_start: 0.7462 (tt0) cc_final: 0.7150 (tt0) REVERT: C 420 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7864 (tpp) REVERT: D 174 LYS cc_start: 0.8293 (ptpp) cc_final: 0.7439 (mmtt) REVERT: D 207 ARG cc_start: 0.7065 (mmm-85) cc_final: 0.6659 (mmm-85) REVERT: D 285 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7785 (ttpp) REVERT: D 300 PHE cc_start: 0.8198 (m-80) cc_final: 0.7758 (m-10) REVERT: D 334 ARG cc_start: 0.6879 (tpp80) cc_final: 0.6481 (tpp-160) REVERT: D 373 GLN cc_start: 0.7705 (tt0) cc_final: 0.7366 (tt0) REVERT: D 487 ASP cc_start: 0.7877 (m-30) cc_final: 0.7672 (m-30) REVERT: E 156 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8092 (ttp) REVERT: E 172 PHE cc_start: 0.7651 (t80) cc_final: 0.7299 (t80) REVERT: E 207 ARG cc_start: 0.7348 (mmm-85) cc_final: 0.6820 (mmm-85) REVERT: E 215 ASN cc_start: 0.7227 (p0) cc_final: 0.6986 (t0) REVERT: E 247 GLN cc_start: 0.8435 (tp-100) cc_final: 0.8129 (tt0) REVERT: E 273 GLN cc_start: 0.8720 (mt0) cc_final: 0.8215 (mt0) REVERT: E 334 ARG cc_start: 0.7051 (mmm160) cc_final: 0.6582 (tpp-160) REVERT: E 346 GLU cc_start: 0.8075 (tt0) cc_final: 0.7677 (tm-30) REVERT: E 367 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7274 (mm-30) REVERT: E 373 GLN cc_start: 0.7818 (tt0) cc_final: 0.7356 (tt0) REVERT: E 420 MET cc_start: 0.8300 (OUTLIER) cc_final: 0.7766 (ttm) REVERT: F 156 MET cc_start: 0.8456 (ttt) cc_final: 0.8239 (ttt) REVERT: F 174 LYS cc_start: 0.8317 (ptpp) cc_final: 0.7594 (mmtm) REVERT: F 207 ARG cc_start: 0.7004 (mmm-85) cc_final: 0.6424 (mmm-85) REVERT: F 334 ARG cc_start: 0.6978 (mmm160) cc_final: 0.6637 (tpp-160) REVERT: F 346 GLU cc_start: 0.8047 (tt0) cc_final: 0.7845 (tt0) REVERT: F 373 GLN cc_start: 0.7847 (tt0) cc_final: 0.7396 (tt0) REVERT: F 389 ASP cc_start: 0.7480 (p0) cc_final: 0.7209 (p0) outliers start: 75 outliers final: 29 residues processed: 345 average time/residue: 0.7234 time to fit residues: 276.1748 Evaluate side-chains 321 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 286 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 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 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 233 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 239 VAL 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 155 SER Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 298 SER Chi-restraints excluded: chain E residue 371 HIS Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 119 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 149 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 216 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 77 optimal weight: 0.0170 overall best weight: 0.6618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 273 GLN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN D 247 GLN E 215 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 425 GLN F 215 ASN F 425 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.153817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113579 restraints weight = 20303.338| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.73 r_work: 0.3195 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18930 Z= 0.155 Angle : 0.574 10.501 25614 Z= 0.291 Chirality : 0.041 0.177 2922 Planarity : 0.005 0.038 3186 Dihedral : 4.389 22.079 2514 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.83 % Allowed : 14.80 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.31 (0.18), residues: 2220 helix: 1.48 (0.14), residues: 1380 sheet: 0.50 (0.40), residues: 180 loop : -0.20 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 334 TYR 0.013 0.002 TYR C 453 PHE 0.025 0.002 PHE E 196 TRP 0.021 0.002 TRP C 458 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00363 (18924) covalent geometry : angle 0.57390 (25602) SS BOND : bond 0.00095 ( 6) SS BOND : angle 0.58578 ( 12) hydrogen bonds : bond 0.03525 ( 1146) hydrogen bonds : angle 4.25523 ( 3318) *********************** 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 364 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 288 time to evaluate : 0.906 Fit side-chains REVERT: A 172 PHE cc_start: 0.7663 (t80) cc_final: 0.7305 (t80) REVERT: A 174 LYS cc_start: 0.8152 (ptpp) cc_final: 0.7321 (mmtm) REVERT: A 181 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7429 (mtt180) REVERT: A 207 ARG cc_start: 0.7326 (mmm-85) cc_final: 0.6641 (mmm-85) REVERT: A 334 ARG cc_start: 0.7196 (tpp80) cc_final: 0.6839 (tpp-160) REVERT: A 346 GLU cc_start: 0.8092 (tt0) cc_final: 0.7692 (tm-30) REVERT: A 367 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7289 (mm-30) REVERT: A 373 GLN cc_start: 0.7761 (tt0) cc_final: 0.7325 (tt0) REVERT: A 389 ASP cc_start: 0.7347 (p0) cc_final: 0.7061 (p0) REVERT: A 420 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7809 (ttm) REVERT: B 174 LYS cc_start: 0.8756 (OUTLIER) cc_final: 0.7810 (mmtt) REVERT: B 207 ARG cc_start: 0.7262 (mmm-85) cc_final: 0.6742 (mmm-85) REVERT: B 215 ASN cc_start: 0.7187 (OUTLIER) cc_final: 0.6928 (t0) REVERT: B 285 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7866 (ttmm) REVERT: B 334 ARG cc_start: 0.7229 (tpp80) cc_final: 0.6925 (mtp-110) REVERT: B 373 GLN cc_start: 0.7992 (tt0) cc_final: 0.7539 (tt0) REVERT: C 172 PHE cc_start: 0.7745 (t80) cc_final: 0.7449 (t80) REVERT: C 207 ARG cc_start: 0.7330 (mmm-85) cc_final: 0.6577 (mmm-85) REVERT: C 263 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8455 (mmm160) REVERT: C 300 PHE cc_start: 0.8114 (m-80) cc_final: 0.7731 (m-10) REVERT: C 346 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7517 (tt0) REVERT: C 351 GLU cc_start: 0.8023 (tt0) cc_final: 0.7781 (tt0) REVERT: C 367 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7222 (mm-30) REVERT: C 373 GLN cc_start: 0.7509 (tt0) cc_final: 0.7187 (tt0) REVERT: C 420 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.7853 (tpp) REVERT: C 493 ASN cc_start: 0.8446 (p0) cc_final: 0.8093 (p0) REVERT: D 174 LYS cc_start: 0.8300 (ptpp) cc_final: 0.7453 (mmtt) REVERT: D 207 ARG cc_start: 0.7119 (mmm-85) cc_final: 0.6686 (mmm-85) REVERT: D 247 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: D 285 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7894 (ttpp) REVERT: D 300 PHE cc_start: 0.8196 (m-80) cc_final: 0.7946 (m-80) REVERT: D 334 ARG cc_start: 0.6942 (tpp80) cc_final: 0.6546 (tpp-160) REVERT: D 373 GLN cc_start: 0.7698 (tt0) cc_final: 0.7377 (tt0) REVERT: D 487 ASP cc_start: 0.7866 (m-30) cc_final: 0.7622 (m-30) REVERT: E 172 PHE cc_start: 0.7649 (t80) cc_final: 0.7272 (t80) REVERT: E 207 ARG cc_start: 0.7382 (mmm-85) cc_final: 0.6788 (mmm-85) REVERT: E 215 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6917 (t0) REVERT: E 334 ARG cc_start: 0.7135 (mmm160) cc_final: 0.6576 (tpp-160) REVERT: E 346 GLU cc_start: 0.8083 (tt0) cc_final: 0.7693 (tm-30) REVERT: E 367 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7215 (mm-30) REVERT: E 373 GLN cc_start: 0.7789 (tt0) cc_final: 0.7389 (tt0) REVERT: E 420 MET cc_start: 0.8357 (OUTLIER) cc_final: 0.7819 (ttm) REVERT: F 174 LYS cc_start: 0.8345 (ptpp) cc_final: 0.7600 (mmtm) REVERT: F 207 ARG cc_start: 0.7114 (mmm-85) cc_final: 0.6540 (mmm-85) REVERT: F 215 ASN cc_start: 0.7174 (OUTLIER) cc_final: 0.6965 (t0) REVERT: F 334 ARG cc_start: 0.6951 (mmm160) cc_final: 0.6612 (tpp-160) REVERT: F 367 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7024 (mm-30) REVERT: F 373 GLN cc_start: 0.7796 (tt0) cc_final: 0.7581 (tt0) REVERT: F 389 ASP cc_start: 0.7529 (p0) cc_final: 0.7260 (p0) outliers start: 76 outliers final: 32 residues processed: 332 average time/residue: 0.6454 time to fit residues: 238.4480 Evaluate side-chains 317 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 274 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 233 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 239 VAL Chi-restraints excluded: chain C residue 263 ARG Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 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 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 298 SER Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 446 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU Chi-restraints excluded: chain F residue 215 ASN 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 104 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 180 optimal weight: 0.9990 chunk 158 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 73 optimal weight: 0.0170 chunk 157 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 114 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 117 optimal weight: 0.3980 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 GLN D 215 ASN D 247 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 425 GLN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.114302 restraints weight = 20154.135| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.73 r_work: 0.3210 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18930 Z= 0.139 Angle : 0.566 10.608 25614 Z= 0.286 Chirality : 0.041 0.181 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.300 21.729 2514 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.78 % Allowed : 15.31 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.45 (0.18), residues: 2220 helix: 1.56 (0.14), residues: 1380 sheet: 0.63 (0.39), residues: 186 loop : -0.12 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 334 TYR 0.014 0.002 TYR F 216 PHE 0.027 0.002 PHE E 196 TRP 0.020 0.002 TRP C 458 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00321 (18924) covalent geometry : angle 0.56618 (25602) SS BOND : bond 0.00114 ( 6) SS BOND : angle 0.61175 ( 12) hydrogen bonds : bond 0.03397 ( 1146) hydrogen bonds : angle 4.20302 ( 3318) *********************** 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 355 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 280 time to evaluate : 0.824 Fit side-chains REVERT: A 172 PHE cc_start: 0.7603 (t80) cc_final: 0.7220 (t80) REVERT: A 174 LYS cc_start: 0.8140 (ptpp) cc_final: 0.7329 (mmtm) REVERT: A 181 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.7824 (mmt90) REVERT: A 207 ARG cc_start: 0.7205 (mmm-85) cc_final: 0.6484 (mmm-85) REVERT: A 249 MET cc_start: 0.8987 (mmm) cc_final: 0.8675 (mmt) REVERT: A 334 ARG cc_start: 0.7218 (tpp80) cc_final: 0.6852 (tpp-160) REVERT: A 346 GLU cc_start: 0.8093 (tt0) cc_final: 0.7690 (tm-30) REVERT: A 367 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7270 (mm-30) REVERT: A 373 GLN cc_start: 0.7779 (tt0) cc_final: 0.7339 (tt0) REVERT: A 389 ASP cc_start: 0.7318 (p0) cc_final: 0.7029 (p0) REVERT: A 420 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7771 (ttm) REVERT: B 174 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.7824 (mmtt) REVERT: B 207 ARG cc_start: 0.7197 (mmm-85) cc_final: 0.6674 (mmm-85) REVERT: B 215 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.6985 (t0) REVERT: B 285 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7720 (ttmm) REVERT: B 304 LYS cc_start: 0.7855 (mtpt) cc_final: 0.6841 (mptt) REVERT: B 334 ARG cc_start: 0.7240 (tpp80) cc_final: 0.6641 (tpp-160) REVERT: B 373 GLN cc_start: 0.7991 (tt0) cc_final: 0.7527 (tt0) REVERT: B 420 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7937 (ttm) REVERT: C 172 PHE cc_start: 0.7632 (t80) cc_final: 0.7327 (t80) REVERT: C 207 ARG cc_start: 0.7296 (mmm-85) cc_final: 0.6545 (mmm-85) REVERT: C 215 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7041 (t0) REVERT: C 300 PHE cc_start: 0.8103 (m-80) cc_final: 0.7723 (m-10) REVERT: C 346 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7523 (tt0) REVERT: C 351 GLU cc_start: 0.8032 (tt0) cc_final: 0.7794 (tt0) REVERT: C 373 GLN cc_start: 0.7444 (tt0) cc_final: 0.7161 (tt0) REVERT: C 420 MET cc_start: 0.8522 (OUTLIER) cc_final: 0.7915 (tpp) REVERT: D 124 PHE cc_start: 0.7365 (t80) cc_final: 0.7146 (t80) REVERT: D 174 LYS cc_start: 0.8271 (ptpp) cc_final: 0.7482 (mmtt) REVERT: D 207 ARG cc_start: 0.7090 (mmm-85) cc_final: 0.6644 (mmm-85) REVERT: D 247 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8283 (tt0) REVERT: D 285 LYS cc_start: 0.8078 (OUTLIER) cc_final: 0.7780 (ttpp) REVERT: D 300 PHE cc_start: 0.8176 (m-80) cc_final: 0.7940 (m-80) REVERT: D 334 ARG cc_start: 0.6934 (tpp80) cc_final: 0.6537 (tpp-160) REVERT: D 373 GLN cc_start: 0.7662 (tt0) cc_final: 0.7340 (tt0) REVERT: D 487 ASP cc_start: 0.7861 (m-30) cc_final: 0.7627 (m-30) REVERT: E 172 PHE cc_start: 0.7572 (t80) cc_final: 0.7177 (t80) REVERT: E 181 ARG cc_start: 0.8037 (mmm-85) cc_final: 0.7503 (mtt180) REVERT: E 207 ARG cc_start: 0.7312 (mmm-85) cc_final: 0.6731 (mmm-85) REVERT: E 228 ASP cc_start: 0.7882 (m-30) cc_final: 0.7436 (m-30) REVERT: E 334 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6656 (mtp-110) REVERT: E 346 GLU cc_start: 0.8081 (tt0) cc_final: 0.7691 (tm-30) REVERT: E 367 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7328 (mm-30) REVERT: E 373 GLN cc_start: 0.7786 (tt0) cc_final: 0.7437 (tt0) REVERT: E 389 ASP cc_start: 0.7417 (p0) cc_final: 0.7122 (p0) REVERT: E 420 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7783 (ttm) REVERT: F 124 PHE cc_start: 0.7437 (t80) cc_final: 0.6187 (m-10) REVERT: F 174 LYS cc_start: 0.8337 (ptpp) cc_final: 0.7606 (mmtm) REVERT: F 207 ARG cc_start: 0.7108 (mmm-85) cc_final: 0.6502 (mmm-85) REVERT: F 334 ARG cc_start: 0.6915 (mmm160) cc_final: 0.6559 (tpp-160) REVERT: F 373 GLN cc_start: 0.7776 (tt0) cc_final: 0.7563 (tt0) REVERT: F 389 ASP cc_start: 0.7510 (p0) cc_final: 0.7232 (p0) outliers start: 75 outliers final: 33 residues processed: 329 average time/residue: 0.6796 time to fit residues: 249.4929 Evaluate side-chains 318 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 275 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 233 ILE Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 ASN 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 B residue 420 MET 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 233 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 446 SER Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 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 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 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 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 169 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 134 optimal weight: 0.5980 chunk 187 optimal weight: 8.9990 chunk 129 optimal weight: 0.8980 chunk 213 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 212 optimal weight: 0.0670 chunk 133 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 406 GLN C 519 GLN D 215 ASN E 215 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS F 215 ASN ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 425 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.113011 restraints weight = 20274.325| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.73 r_work: 0.3192 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18930 Z= 0.156 Angle : 0.583 10.545 25614 Z= 0.293 Chirality : 0.041 0.185 2922 Planarity : 0.004 0.037 3186 Dihedral : 4.325 22.022 2514 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.52 % Allowed : 16.01 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.18), residues: 2220 helix: 1.56 (0.14), residues: 1380 sheet: 0.63 (0.39), residues: 186 loop : -0.05 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 334 TYR 0.012 0.002 TYR D 453 PHE 0.029 0.002 PHE C 429 TRP 0.021 0.002 TRP C 138 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00366 (18924) covalent geometry : angle 0.58330 (25602) SS BOND : bond 0.00126 ( 6) SS BOND : angle 0.64355 ( 12) hydrogen bonds : bond 0.03501 ( 1146) hydrogen bonds : angle 4.20416 ( 3318) *********************** 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 354 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 0.825 Fit side-chains REVERT: A 172 PHE cc_start: 0.7536 (t80) cc_final: 0.7138 (t80) REVERT: A 174 LYS cc_start: 0.8146 (ptpp) cc_final: 0.7290 (mmtm) REVERT: A 181 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7912 (mmt90) REVERT: A 207 ARG cc_start: 0.7088 (mmm-85) cc_final: 0.6426 (mmm-85) REVERT: A 334 ARG cc_start: 0.7205 (tpp80) cc_final: 0.6962 (mtp-110) REVERT: A 346 GLU cc_start: 0.8109 (tt0) cc_final: 0.7708 (tm-30) REVERT: A 367 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7266 (mm-30) REVERT: A 373 GLN cc_start: 0.7786 (tt0) cc_final: 0.7372 (tt0) REVERT: A 389 ASP cc_start: 0.7358 (p0) cc_final: 0.7074 (p0) REVERT: A 420 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.7830 (ttm) REVERT: B 174 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.7830 (mmtt) REVERT: B 207 ARG cc_start: 0.7265 (mmm-85) cc_final: 0.6712 (mmm-85) REVERT: B 215 ASN cc_start: 0.7293 (OUTLIER) cc_final: 0.7078 (t0) REVERT: B 285 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7946 (ttmm) REVERT: B 373 GLN cc_start: 0.8017 (tt0) cc_final: 0.7553 (tt0) REVERT: C 172 PHE cc_start: 0.7601 (t80) cc_final: 0.7298 (t80) REVERT: C 174 LYS cc_start: 0.8299 (ptpp) cc_final: 0.7544 (mmtt) REVERT: C 207 ARG cc_start: 0.7181 (mmm-85) cc_final: 0.6460 (mmm-85) REVERT: C 215 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7117 (t0) REVERT: C 300 PHE cc_start: 0.8015 (m-80) cc_final: 0.7764 (m-80) REVERT: C 334 ARG cc_start: 0.6733 (tpp80) cc_final: 0.6347 (tpp-160) REVERT: C 346 GLU cc_start: 0.7966 (mm-30) cc_final: 0.7542 (tt0) REVERT: C 351 GLU cc_start: 0.8041 (tt0) cc_final: 0.7799 (tt0) REVERT: C 373 GLN cc_start: 0.7570 (tt0) cc_final: 0.7269 (tt0) REVERT: C 493 ASN cc_start: 0.8448 (p0) cc_final: 0.8095 (p0) REVERT: D 124 PHE cc_start: 0.7397 (t80) cc_final: 0.7153 (t80) REVERT: D 174 LYS cc_start: 0.8300 (ptpp) cc_final: 0.7487 (mmtt) REVERT: D 207 ARG cc_start: 0.7169 (mmm-85) cc_final: 0.6720 (mmm-85) REVERT: D 247 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8234 (tt0) REVERT: D 285 LYS cc_start: 0.8184 (OUTLIER) cc_final: 0.7896 (ttpp) REVERT: D 300 PHE cc_start: 0.8167 (m-80) cc_final: 0.7895 (m-80) REVERT: D 334 ARG cc_start: 0.6931 (tpp80) cc_final: 0.6361 (tpp-160) REVERT: D 373 GLN cc_start: 0.7791 (tt0) cc_final: 0.7499 (tt0) REVERT: D 487 ASP cc_start: 0.7919 (m-30) cc_final: 0.7680 (m-30) REVERT: E 172 PHE cc_start: 0.7586 (t80) cc_final: 0.7174 (t80) REVERT: E 174 LYS cc_start: 0.8162 (ptpp) cc_final: 0.7383 (mmtt) REVERT: E 181 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7503 (mtt180) REVERT: E 207 ARG cc_start: 0.7386 (mmm-85) cc_final: 0.6818 (mmm-85) REVERT: E 228 ASP cc_start: 0.7838 (m-30) cc_final: 0.7371 (m-30) REVERT: E 334 ARG cc_start: 0.7078 (mmm160) cc_final: 0.6659 (mtp-110) REVERT: E 346 GLU cc_start: 0.8095 (tt0) cc_final: 0.7708 (tm-30) REVERT: E 367 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7325 (mm-30) REVERT: E 373 GLN cc_start: 0.7801 (tt0) cc_final: 0.7454 (tt0) REVERT: E 389 ASP cc_start: 0.7463 (p0) cc_final: 0.7168 (p0) REVERT: E 420 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.7794 (ttm) REVERT: F 124 PHE cc_start: 0.7444 (t80) cc_final: 0.6240 (m-10) REVERT: F 158 PHE cc_start: 0.8373 (m-80) cc_final: 0.8149 (m-10) REVERT: F 174 LYS cc_start: 0.8412 (ptpp) cc_final: 0.7648 (mmtm) REVERT: F 207 ARG cc_start: 0.7132 (mmm-85) cc_final: 0.6518 (mmm-85) REVERT: F 373 GLN cc_start: 0.7850 (tt0) cc_final: 0.7640 (tt0) REVERT: F 389 ASP cc_start: 0.7560 (p0) cc_final: 0.7277 (p0) REVERT: F 454 ASP cc_start: 0.8051 (m-30) cc_final: 0.7848 (m-30) outliers start: 70 outliers final: 32 residues processed: 329 average time/residue: 0.6881 time to fit residues: 252.2504 Evaluate side-chains 312 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 273 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 446 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 ASN Chi-restraints excluded: chain B residue 233 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 446 SER Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 285 LYS Chi-restraints excluded: chain D residue 446 SER Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 371 HIS Chi-restraints excluded: chain E residue 375 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain F residue 155 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 209 LEU 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 1 optimal weight: 0.0270 chunk 12 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 159 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 146 optimal weight: 0.2980 chunk 107 optimal weight: 0.7980 chunk 43 optimal weight: 0.0000 overall best weight: 0.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN C 247 GLN C 406 GLN D 215 ASN E 215 ASN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS E 371 HIS F 215 ASN F 425 GLN F 519 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.116531 restraints weight = 20048.829| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.72 r_work: 0.3235 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3493 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= 0.119 Angle : 0.560 11.261 25614 Z= 0.278 Chirality : 0.040 0.186 2922 Planarity : 0.004 0.040 3186 Dihedral : 4.170 21.537 2514 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.27 % Allowed : 17.27 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.61 (0.18), residues: 2220 helix: 1.73 (0.14), residues: 1374 sheet: 0.55 (0.41), residues: 180 loop : -0.08 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 334 TYR 0.017 0.001 TYR C 216 PHE 0.026 0.002 PHE C 429 TRP 0.022 0.002 TRP A 138 HIS 0.008 0.001 HIS E 371 Details of bonding type rmsd covalent geometry : bond 0.00268 (18924) covalent geometry : angle 0.55984 (25602) SS BOND : bond 0.00100 ( 6) SS BOND : angle 0.59531 ( 12) hydrogen bonds : bond 0.03223 ( 1146) hydrogen bonds : angle 4.12756 ( 3318) *********************** 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 335 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 290 time to evaluate : 0.751 Fit side-chains REVERT: A 172 PHE cc_start: 0.7405 (t80) cc_final: 0.6962 (t80) REVERT: A 174 LYS cc_start: 0.8079 (ptpp) cc_final: 0.7421 (mmtt) REVERT: A 181 ARG cc_start: 0.8157 (mmm-85) cc_final: 0.7740 (mmt90) REVERT: A 195 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7290 (tp) REVERT: A 207 ARG cc_start: 0.7009 (mmm-85) cc_final: 0.6380 (mmm-85) REVERT: A 334 ARG cc_start: 0.7179 (tpp80) cc_final: 0.6905 (mtp-110) REVERT: A 346 GLU cc_start: 0.8089 (tt0) cc_final: 0.7676 (tm-30) REVERT: A 367 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7226 (mm-30) REVERT: A 373 GLN cc_start: 0.7696 (tt0) cc_final: 0.7338 (tt0) REVERT: A 389 ASP cc_start: 0.7392 (p0) cc_final: 0.7103 (p0) REVERT: A 420 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7743 (ttm) REVERT: B 174 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7821 (mmtt) REVERT: B 207 ARG cc_start: 0.7193 (mmm-85) cc_final: 0.6641 (mmm-85) REVERT: B 285 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7608 (ttpp) REVERT: B 304 LYS cc_start: 0.7867 (mtpt) cc_final: 0.6866 (mptt) REVERT: B 373 GLN cc_start: 0.7968 (tt0) cc_final: 0.7528 (tt0) REVERT: C 172 PHE cc_start: 0.7589 (t80) cc_final: 0.7268 (t80) REVERT: C 181 ARG cc_start: 0.8232 (mmm-85) cc_final: 0.7732 (mmt90) REVERT: C 207 ARG cc_start: 0.7056 (mmm-85) cc_final: 0.6433 (mmm-85) REVERT: C 215 ASN cc_start: 0.7364 (OUTLIER) cc_final: 0.7145 (t0) REVERT: C 300 PHE cc_start: 0.8027 (m-80) cc_final: 0.7648 (m-10) REVERT: C 334 ARG cc_start: 0.6782 (tpp80) cc_final: 0.6373 (tpp-160) REVERT: C 346 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7533 (tt0) REVERT: C 351 GLU cc_start: 0.7953 (tt0) cc_final: 0.7733 (tt0) REVERT: C 373 GLN cc_start: 0.7490 (tt0) cc_final: 0.7180 (tt0) REVERT: C 420 MET cc_start: 0.8474 (tmm) cc_final: 0.7883 (tpp) REVERT: D 174 LYS cc_start: 0.8270 (ptpp) cc_final: 0.7479 (mmtt) REVERT: D 207 ARG cc_start: 0.7052 (mmm-85) cc_final: 0.6616 (mmm-85) REVERT: D 300 PHE cc_start: 0.8203 (m-80) cc_final: 0.7800 (m-10) REVERT: D 334 ARG cc_start: 0.6972 (tpp80) cc_final: 0.6403 (tpp-160) REVERT: D 373 GLN cc_start: 0.7726 (tt0) cc_final: 0.7428 (tt0) REVERT: D 487 ASP cc_start: 0.7841 (m-30) cc_final: 0.7591 (m-30) REVERT: E 181 ARG cc_start: 0.7887 (mmm-85) cc_final: 0.7262 (mtt180) REVERT: E 207 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.6735 (mmm-85) REVERT: E 228 ASP cc_start: 0.7811 (m-30) cc_final: 0.7411 (m-30) REVERT: E 334 ARG cc_start: 0.7117 (mmm160) cc_final: 0.6711 (mtp-110) REVERT: E 346 GLU cc_start: 0.8072 (tt0) cc_final: 0.7679 (tm-30) REVERT: E 367 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7252 (mm-30) REVERT: E 373 GLN cc_start: 0.7756 (tt0) cc_final: 0.7387 (tt0) REVERT: E 389 ASP cc_start: 0.7456 (p0) cc_final: 0.7234 (p0) REVERT: E 420 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7719 (ttm) REVERT: F 124 PHE cc_start: 0.7372 (t80) cc_final: 0.6219 (m-10) REVERT: F 158 PHE cc_start: 0.8436 (m-80) cc_final: 0.8158 (m-10) REVERT: F 174 LYS cc_start: 0.8382 (ptpp) cc_final: 0.7666 (mmtm) REVERT: F 178 ASP cc_start: 0.8372 (m-30) cc_final: 0.7995 (m-30) REVERT: F 207 ARG cc_start: 0.7044 (mmm-85) cc_final: 0.6429 (mmm-85) REVERT: F 304 LYS cc_start: 0.7841 (mtpt) cc_final: 0.6849 (mppt) REVERT: F 334 ARG cc_start: 0.7137 (tpp80) cc_final: 0.6926 (mtp-110) REVERT: F 373 GLN cc_start: 0.7815 (tt0) cc_final: 0.7610 (tt0) REVERT: F 389 ASP cc_start: 0.7359 (p0) cc_final: 0.7085 (p0) outliers start: 45 outliers final: 23 residues processed: 327 average time/residue: 0.6923 time to fit residues: 251.7262 Evaluate side-chains 297 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 268 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 195 LEU 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 B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS 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 215 ASN Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 239 VAL Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain C residue 493 ASN Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain D residue 493 ASN Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 420 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 32 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 205 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 142 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS ** 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 = 0.3853 r_free = 0.3853 target = 0.154475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.113303 restraints weight = 20148.220| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.75 r_work: 0.3195 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 18930 Z= 0.165 Angle : 0.592 10.633 25614 Z= 0.296 Chirality : 0.041 0.190 2922 Planarity : 0.005 0.039 3186 Dihedral : 4.331 22.357 2514 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.06 % Allowed : 17.77 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.18), residues: 2220 helix: 1.69 (0.14), residues: 1374 sheet: 0.55 (0.39), residues: 186 loop : -0.02 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 334 TYR 0.012 0.002 TYR C 453 PHE 0.027 0.002 PHE C 429 TRP 0.023 0.003 TRP B 138 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00388 (18924) covalent geometry : angle 0.59181 (25602) SS BOND : bond 0.00156 ( 6) SS BOND : angle 0.71846 ( 12) hydrogen bonds : bond 0.03570 ( 1146) hydrogen bonds : angle 4.17976 ( 3318) *********************** 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 322 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 281 time to evaluate : 0.707 Fit side-chains REVERT: A 172 PHE cc_start: 0.7577 (t80) cc_final: 0.7173 (t80) REVERT: A 174 LYS cc_start: 0.8164 (ptpp) cc_final: 0.7340 (mmtm) REVERT: A 181 ARG cc_start: 0.8310 (mmm-85) cc_final: 0.7620 (mtt180) REVERT: A 207 ARG cc_start: 0.7049 (mmm-85) cc_final: 0.6385 (mmm-85) REVERT: A 334 ARG cc_start: 0.7198 (tpp80) cc_final: 0.6940 (mtp-110) REVERT: A 346 GLU cc_start: 0.8130 (tt0) cc_final: 0.7733 (tm-30) REVERT: A 367 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7291 (mm-30) REVERT: A 373 GLN cc_start: 0.7783 (tt0) cc_final: 0.7391 (tt0) REVERT: A 389 ASP cc_start: 0.7426 (p0) cc_final: 0.7155 (p0) REVERT: A 420 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7835 (ttm) REVERT: B 174 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7909 (mmtt) REVERT: B 207 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6609 (mmm-85) REVERT: B 285 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7968 (ttmm) REVERT: B 304 LYS cc_start: 0.7877 (mtpt) cc_final: 0.6859 (mptt) REVERT: B 373 GLN cc_start: 0.8045 (tt0) cc_final: 0.7617 (tt0) REVERT: C 172 PHE cc_start: 0.7612 (t80) cc_final: 0.7313 (t80) REVERT: C 174 LYS cc_start: 0.8305 (ptpp) cc_final: 0.7585 (mmtt) REVERT: C 207 ARG cc_start: 0.7176 (mmm-85) cc_final: 0.6514 (mmm-85) REVERT: C 215 ASN cc_start: 0.7389 (OUTLIER) cc_final: 0.6993 (t0) REVERT: C 300 PHE cc_start: 0.8005 (m-80) cc_final: 0.7789 (m-80) REVERT: C 334 ARG cc_start: 0.6796 (tpp80) cc_final: 0.6387 (tpp-160) REVERT: C 346 GLU cc_start: 0.7983 (mm-30) cc_final: 0.7545 (tt0) REVERT: C 351 GLU cc_start: 0.8056 (tt0) cc_final: 0.7802 (tt0) REVERT: C 367 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7233 (mm-30) REVERT: C 373 GLN cc_start: 0.7658 (tt0) cc_final: 0.7358 (tt0) REVERT: C 420 MET cc_start: 0.8466 (tmm) cc_final: 0.7918 (tpp) REVERT: C 493 ASN cc_start: 0.8475 (p0) cc_final: 0.8118 (p0) REVERT: D 124 PHE cc_start: 0.7355 (t80) cc_final: 0.7108 (t80) REVERT: D 174 LYS cc_start: 0.8318 (ptpp) cc_final: 0.7533 (mmtt) REVERT: D 207 ARG cc_start: 0.7133 (mmm-85) cc_final: 0.6555 (mmm-85) REVERT: D 300 PHE cc_start: 0.8170 (m-80) cc_final: 0.7951 (m-80) REVERT: D 334 ARG cc_start: 0.7015 (tpp80) cc_final: 0.6450 (tpp-160) REVERT: D 373 GLN cc_start: 0.7944 (tt0) cc_final: 0.7677 (tt0) REVERT: D 487 ASP cc_start: 0.7889 (m-30) cc_final: 0.7674 (m-30) REVERT: D 493 ASN cc_start: 0.8526 (p0) cc_final: 0.8207 (p0) REVERT: E 172 PHE cc_start: 0.7604 (t80) cc_final: 0.7221 (t80) REVERT: E 181 ARG cc_start: 0.8077 (mmm-85) cc_final: 0.7506 (mtt180) REVERT: E 207 ARG cc_start: 0.7380 (mmm-85) cc_final: 0.6708 (mmm-85) REVERT: E 228 ASP cc_start: 0.7796 (m-30) cc_final: 0.7339 (m-30) REVERT: E 334 ARG cc_start: 0.7125 (mmm160) cc_final: 0.6716 (mtp-110) REVERT: E 346 GLU cc_start: 0.8132 (tt0) cc_final: 0.7749 (tm-30) REVERT: E 367 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7332 (mm-30) REVERT: E 373 GLN cc_start: 0.7819 (tt0) cc_final: 0.7444 (tt0) REVERT: E 389 ASP cc_start: 0.7452 (p0) cc_final: 0.7195 (p0) REVERT: E 420 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7875 (ttm) REVERT: F 124 PHE cc_start: 0.7424 (t80) cc_final: 0.6256 (m-10) REVERT: F 158 PHE cc_start: 0.8375 (m-80) cc_final: 0.8117 (m-10) REVERT: F 174 LYS cc_start: 0.8437 (ptpp) cc_final: 0.7671 (mmtm) REVERT: F 178 ASP cc_start: 0.8496 (m-30) cc_final: 0.8142 (m-30) REVERT: F 181 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7717 (mmt90) REVERT: F 207 ARG cc_start: 0.7035 (mmm-85) cc_final: 0.6426 (mmm-85) REVERT: F 334 ARG cc_start: 0.7138 (tpp80) cc_final: 0.6656 (tpp-160) REVERT: F 373 GLN cc_start: 0.7910 (tt0) cc_final: 0.7700 (tt0) REVERT: F 389 ASP cc_start: 0.7562 (p0) cc_final: 0.7292 (p0) outliers start: 41 outliers final: 25 residues processed: 313 average time/residue: 0.6617 time to fit residues: 230.6982 Evaluate side-chains 298 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 268 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 195 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 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain C residue 155 SER 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 375 LEU Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 155 SER Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain E residue 209 LEU Chi-restraints excluded: chain E residue 233 ILE Chi-restraints excluded: chain E residue 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 375 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 222 random chunks: chunk 133 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 123 optimal weight: 0.5980 chunk 183 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 187 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 106 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN B 215 ASN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN ** C 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 273 GLN D 519 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS F 425 GLN F 519 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.155648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115765 restraints weight = 21257.606| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.82 r_work: 0.3272 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 18930 Z= 0.175 Angle : 0.606 11.213 25614 Z= 0.303 Chirality : 0.042 0.192 2922 Planarity : 0.005 0.038 3186 Dihedral : 4.392 22.404 2514 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.01 % Allowed : 17.62 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.18), residues: 2220 helix: 1.67 (0.14), residues: 1374 sheet: 0.42 (0.38), residues: 186 loop : -0.01 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 334 TYR 0.018 0.002 TYR C 216 PHE 0.034 0.002 PHE D 196 TRP 0.022 0.003 TRP F 138 HIS 0.004 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00415 (18924) covalent geometry : angle 0.60623 (25602) SS BOND : bond 0.00165 ( 6) SS BOND : angle 0.70998 ( 12) hydrogen bonds : bond 0.03627 ( 1146) hydrogen bonds : angle 4.21594 ( 3318) ********************** 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 320 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.701 Fit side-chains REVERT: A 172 PHE cc_start: 0.7530 (t80) cc_final: 0.7143 (t80) REVERT: A 174 LYS cc_start: 0.8252 (ptpp) cc_final: 0.7382 (mmtm) REVERT: A 181 ARG cc_start: 0.8352 (mmm-85) cc_final: 0.7656 (mtt180) REVERT: A 207 ARG cc_start: 0.7115 (mmm-85) cc_final: 0.6458 (mmm-85) REVERT: A 334 ARG cc_start: 0.7199 (tpp80) cc_final: 0.6917 (mtp-110) REVERT: A 346 GLU cc_start: 0.8214 (tt0) cc_final: 0.7829 (tm-30) REVERT: A 367 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7372 (mm-30) REVERT: A 373 GLN cc_start: 0.7861 (tt0) cc_final: 0.7535 (tt0) REVERT: A 389 ASP cc_start: 0.7515 (p0) cc_final: 0.7197 (p0) REVERT: A 420 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7762 (ttm) REVERT: B 174 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.7947 (mmtt) REVERT: B 207 ARG cc_start: 0.7273 (mmm-85) cc_final: 0.6585 (mmm-85) REVERT: B 285 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7938 (ttmm) REVERT: B 373 GLN cc_start: 0.8047 (tt0) cc_final: 0.7719 (tt0) REVERT: C 172 PHE cc_start: 0.7623 (t80) cc_final: 0.7333 (t80) REVERT: C 174 LYS cc_start: 0.8353 (ptpp) cc_final: 0.7606 (mmtt) REVERT: C 207 ARG cc_start: 0.7192 (mmm-85) cc_final: 0.6584 (mmm-85) REVERT: C 215 ASN cc_start: 0.7382 (OUTLIER) cc_final: 0.7179 (t0) REVERT: C 300 PHE cc_start: 0.8075 (m-80) cc_final: 0.7849 (m-80) REVERT: C 334 ARG cc_start: 0.6880 (tpp80) cc_final: 0.6422 (tpp-160) REVERT: C 346 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7632 (tt0) REVERT: C 351 GLU cc_start: 0.7964 (tt0) cc_final: 0.7743 (tt0) REVERT: C 367 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7353 (mm-30) REVERT: C 373 GLN cc_start: 0.7757 (tt0) cc_final: 0.7495 (tt0) REVERT: C 420 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7886 (tpp) REVERT: C 493 ASN cc_start: 0.8471 (p0) cc_final: 0.8057 (p0) REVERT: D 174 LYS cc_start: 0.8388 (ptpp) cc_final: 0.7580 (mmtt) REVERT: D 207 ARG cc_start: 0.7186 (mmm-85) cc_final: 0.6635 (mmm-85) REVERT: D 300 PHE cc_start: 0.8202 (m-80) cc_final: 0.7979 (m-80) REVERT: D 334 ARG cc_start: 0.7185 (tpp80) cc_final: 0.6606 (tpp-160) REVERT: D 373 GLN cc_start: 0.7920 (tt0) cc_final: 0.7693 (tt0) REVERT: D 420 MET cc_start: 0.7785 (tpp) cc_final: 0.7491 (tpt) REVERT: D 456 ASP cc_start: 0.8270 (p0) cc_final: 0.8026 (p0) REVERT: D 493 ASN cc_start: 0.8511 (p0) cc_final: 0.8134 (p0) REVERT: E 172 PHE cc_start: 0.7616 (t80) cc_final: 0.7250 (t80) REVERT: E 174 LYS cc_start: 0.8202 (ptpp) cc_final: 0.7363 (mmtm) REVERT: E 176 ARG cc_start: 0.7540 (mtp180) cc_final: 0.7175 (mtp85) REVERT: E 181 ARG cc_start: 0.8131 (mmm-85) cc_final: 0.7562 (mtt180) REVERT: E 207 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.6753 (mmm-85) REVERT: E 228 ASP cc_start: 0.7896 (m-30) cc_final: 0.7468 (m-30) REVERT: E 334 ARG cc_start: 0.7115 (mmm160) cc_final: 0.6717 (mtp-110) REVERT: E 346 GLU cc_start: 0.8173 (tt0) cc_final: 0.7790 (tm-30) REVERT: E 367 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7357 (mm-30) REVERT: E 373 GLN cc_start: 0.7844 (tt0) cc_final: 0.7566 (tt0) REVERT: E 389 ASP cc_start: 0.7586 (p0) cc_final: 0.7295 (p0) REVERT: E 420 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7758 (ttm) REVERT: F 124 PHE cc_start: 0.7495 (t80) cc_final: 0.6327 (m-10) REVERT: F 158 PHE cc_start: 0.8411 (m-80) cc_final: 0.8137 (m-10) REVERT: F 174 LYS cc_start: 0.8491 (ptpp) cc_final: 0.7839 (mmtt) REVERT: F 181 ARG cc_start: 0.8251 (mmm-85) cc_final: 0.7783 (mmt90) REVERT: F 207 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6476 (mmm-85) REVERT: F 334 ARG cc_start: 0.7205 (tpp80) cc_final: 0.6657 (tpp-160) REVERT: F 389 ASP cc_start: 0.7732 (p0) cc_final: 0.7459 (p0) outliers start: 40 outliers final: 23 residues processed: 310 average time/residue: 0.6345 time to fit residues: 218.6866 Evaluate side-chains 304 residues out of total 1986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 174 LYS Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 285 LYS Chi-restraints excluded: chain C residue 155 SER 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 375 LEU Chi-restraints excluded: chain C residue 420 MET Chi-restraints excluded: chain C residue 459 LEU Chi-restraints excluded: chain D residue 155 SER Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 239 VAL 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 F residue 155 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 87 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 162 optimal weight: 0.0770 chunk 73 optimal weight: 10.0000 chunk 139 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 201 optimal weight: 0.5980 chunk 172 optimal weight: 0.0030 chunk 113 optimal weight: 5.9990 overall best weight: 0.4348 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN A 519 GLN ** B 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN C 215 ASN C 247 GLN C 416 ASN D 215 ASN ** D 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 519 GLN ** E 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 371 HIS E 519 GLN F 519 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.157819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118269 restraints weight = 21368.927| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.83 r_work: 0.3288 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18930 Z= 0.129 Angle : 0.573 11.161 25614 Z= 0.284 Chirality : 0.040 0.190 2922 Planarity : 0.004 0.043 3186 Dihedral : 4.213 21.647 2514 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.61 % Allowed : 18.58 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.18), residues: 2220 helix: 1.80 (0.14), residues: 1374 sheet: 0.54 (0.40), residues: 186 loop : 0.02 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 334 TYR 0.012 0.001 TYR D 453 PHE 0.032 0.002 PHE D 196 TRP 0.024 0.002 TRP A 138 HIS 0.004 0.001 HIS D 269 Details of bonding type rmsd covalent geometry : bond 0.00298 (18924) covalent geometry : angle 0.57290 (25602) SS BOND : bond 0.00136 ( 6) SS BOND : angle 0.64840 ( 12) hydrogen bonds : bond 0.03292 ( 1146) hydrogen bonds : angle 4.12652 ( 3318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8082.91 seconds wall clock time: 138 minutes 7.30 seconds (8287.30 seconds total)