Starting phenix.real_space_refine on Wed Mar 4 12:43:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7rtf_24681/03_2026/7rtf_24681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtf_24681/03_2026/7rtf_24681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7rtf_24681/03_2026/7rtf_24681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtf_24681/03_2026/7rtf_24681.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtf_24681/03_2026/7rtf_24681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtf_24681/03_2026/7rtf_24681.map" } resolution = 2.9 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= 0.007 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: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 9052 2.51 5 N 2088 2.21 5 O 2284 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13460 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3134 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 24, 'TRANS': 370} Chain breaks: 1 Chain: "A" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 231 Unusual residues: {'PGW': 12} Classifications: {'RNA': 1, 'undetermined': 12} Modifications used: {'rna3p': 1} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 403 Unresolved non-hydrogen angles: 478 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'PGW:plan-1': 10, 'PGW:plan-2': 10, 'PGW:plan-3': 5} Unresolved non-hydrogen planarities: 95 Restraints were copied for chains: B, C, D Time building chain proxies: 2.71, per 1000 atoms: 0.20 Number of scatterers: 13460 At special positions: 0 Unit cell: (105.827, 105.827, 120.01, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2284 8.00 N 2088 7.00 C 9052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.11 Conformation dependent library (CDL) restraints added in 625.7 milliseconds 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3000 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 8 sheets defined 67.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 10 through 36 removed outlier: 3.511A pdb=" N TRP A 18 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.505A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 56 removed outlier: 3.539A pdb=" N LEU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 63 Processing helix chain 'A' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU A 85 " --> pdb=" O ARG A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 101 through 106 removed outlier: 3.871A pdb=" N LEU A 106 " --> pdb=" O SER A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.962A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 removed outlier: 3.975A pdb=" N SER A 117 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG A 124 " --> pdb=" O ALA A 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 158 removed outlier: 3.647A pdb=" N ARG A 136 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU A 137 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 182 Processing helix chain 'A' and resid 193 through 223 Processing helix chain 'A' and resid 227 through 246 removed outlier: 3.639A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 246 " --> pdb=" O PHE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 268 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 280 through 292 Processing helix chain 'A' and resid 294 through 299 removed outlier: 3.739A pdb=" N LYS A 298 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 299 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE A 310 " --> pdb=" O GLY A 306 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.297A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 394 through 402 Processing helix chain 'A' and resid 404 through 415 Processing helix chain 'B' and resid 11 through 36 removed outlier: 3.510A pdb=" N TRP B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.506A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 56 removed outlier: 3.538A pdb=" N LEU B 49 " --> pdb=" O PRO B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU B 85 " --> pdb=" O ARG B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 101 through 106 removed outlier: 3.872A pdb=" N LEU B 106 " --> pdb=" O SER B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 112 removed outlier: 3.962A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 126 removed outlier: 3.974A pdb=" N SER B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG B 124 " --> pdb=" O ALA B 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 158 removed outlier: 3.647A pdb=" N ARG B 136 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU B 137 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 Processing helix chain 'B' and resid 193 through 223 Processing helix chain 'B' and resid 227 through 246 removed outlier: 3.639A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 268 Processing helix chain 'B' and resid 271 through 276 Processing helix chain 'B' and resid 280 through 292 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.739A pdb=" N LYS B 298 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 299 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE B 310 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.297A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 394 through 402 Processing helix chain 'B' and resid 404 through 415 Processing helix chain 'C' and resid 11 through 36 removed outlier: 3.511A pdb=" N TRP C 18 " --> pdb=" O VAL C 14 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ILE C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.505A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 56 removed outlier: 3.538A pdb=" N LEU C 49 " --> pdb=" O PRO C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 63 Processing helix chain 'C' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU C 85 " --> pdb=" O ARG C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 101 through 106 removed outlier: 3.872A pdb=" N LEU C 106 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 112 removed outlier: 3.961A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 126 removed outlier: 3.975A pdb=" N SER C 117 " --> pdb=" O LEU C 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG C 124 " --> pdb=" O ALA C 120 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 158 removed outlier: 3.646A pdb=" N ARG C 136 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU C 137 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 182 Processing helix chain 'C' and resid 193 through 223 Processing helix chain 'C' and resid 227 through 246 removed outlier: 3.639A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS C 246 " --> pdb=" O PHE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 268 Processing helix chain 'C' and resid 271 through 276 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.739A pdb=" N LYS C 298 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL C 299 " --> pdb=" O ILE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE C 310 " --> pdb=" O GLY C 306 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.296A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 394 through 402 Processing helix chain 'C' and resid 404 through 415 Processing helix chain 'D' and resid 11 through 36 removed outlier: 3.510A pdb=" N TRP D 18 " --> pdb=" O VAL D 14 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ILE D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.505A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 56 removed outlier: 3.538A pdb=" N LEU D 49 " --> pdb=" O PRO D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 63 Processing helix chain 'D' and resid 81 through 87 removed outlier: 3.723A pdb=" N LEU D 85 " --> pdb=" O ARG D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 101 through 106 removed outlier: 3.872A pdb=" N LEU D 106 " --> pdb=" O SER D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 112 removed outlier: 3.962A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 126 removed outlier: 3.974A pdb=" N SER D 117 " --> pdb=" O LEU D 113 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG D 124 " --> pdb=" O ALA D 120 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 158 removed outlier: 3.646A pdb=" N ARG D 136 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU D 137 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 182 Processing helix chain 'D' and resid 193 through 223 Processing helix chain 'D' and resid 227 through 246 removed outlier: 3.640A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS D 246 " --> pdb=" O PHE D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 280 through 292 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.740A pdb=" N LYS D 298 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 299 " --> pdb=" O ILE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.808A pdb=" N ILE D 310 " --> pdb=" O GLY D 306 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.297A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 394 through 402 Processing helix chain 'D' and resid 404 through 415 Processing sheet with id=AA1, first strand: chain 'A' and resid 318 through 320 Processing sheet with id=AA2, first strand: chain 'A' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL A 381 " --> pdb=" O ILE A 328 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 358 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 318 through 320 Processing sheet with id=AA4, first strand: chain 'B' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL B 381 " --> pdb=" O ILE B 328 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 358 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 318 through 320 Processing sheet with id=AA6, first strand: chain 'C' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL C 381 " --> pdb=" O ILE C 328 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA C 358 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 318 through 320 Processing sheet with id=AA8, first strand: chain 'D' and resid 327 through 329 removed outlier: 6.607A pdb=" N VAL D 381 " --> pdb=" O ILE D 328 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA D 358 " --> pdb=" O VAL D 348 " (cutoff:3.500A) 725 hydrogen bonds defined for protein. 2079 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: 2.08 Time building geometry restraints manager: 1.51 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: 3774 1.34 - 1.46: 1908 1.46 - 1.57: 7966 1.57 - 1.69: 12 1.69 - 1.81: 52 Bond restraints: 13712 Sorted by residual: bond pdb=" C10 PGW B 507 " pdb=" C9 PGW B 507 " ideal model delta sigma weight residual 1.333 1.524 -0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C10 PGW C 507 " pdb=" C9 PGW C 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C10 PGW A 507 " pdb=" C9 PGW A 507 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.01e+01 bond pdb=" C10 PGW A 513 " pdb=" C9 PGW A 513 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 9.00e+01 bond pdb=" C10 PGW D 513 " pdb=" C9 PGW D 513 " ideal model delta sigma weight residual 1.333 1.523 -0.190 2.00e-02 2.50e+03 8.98e+01 ... (remaining 13707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.44: 18010 3.44 - 6.88: 330 6.88 - 10.32: 28 10.32 - 13.76: 0 13.76 - 17.21: 48 Bond angle restraints: 18416 Sorted by residual: angle pdb=" C06 PGW C 504 " pdb=" C10 PGW C 504 " pdb=" C9 PGW C 504 " ideal model delta sigma weight residual 126.92 109.71 17.21 3.00e+00 1.11e-01 3.29e+01 angle pdb=" C06 PGW A 504 " pdb=" C10 PGW A 504 " pdb=" C9 PGW A 504 " ideal model delta sigma weight residual 126.92 109.75 17.17 3.00e+00 1.11e-01 3.28e+01 angle pdb=" C06 PGW B 504 " pdb=" C10 PGW B 504 " pdb=" C9 PGW B 504 " ideal model delta sigma weight residual 126.92 109.76 17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C06 PGW D 504 " pdb=" C10 PGW D 504 " pdb=" C9 PGW D 504 " ideal model delta sigma weight residual 126.92 109.77 17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" C06 PGW D 509 " pdb=" C10 PGW D 509 " pdb=" C9 PGW D 509 " ideal model delta sigma weight residual 126.92 109.83 17.09 3.00e+00 1.11e-01 3.24e+01 ... (remaining 18411 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.49: 7960 33.49 - 66.98: 384 66.98 - 100.46: 32 100.46 - 133.95: 16 133.95 - 167.44: 24 Dihedral angle restraints: 8416 sinusoidal: 3768 harmonic: 4648 Sorted by residual: dihedral pdb=" C5' CMP D 501 " pdb=" O5' CMP D 501 " pdb=" P CMP D 501 " pdb=" O1P CMP D 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.49 -110.49 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" C5' CMP C 501 " pdb=" O5' CMP C 501 " pdb=" P CMP C 501 " pdb=" O1P CMP C 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.46 -110.46 1 2.00e+01 2.50e-03 3.24e+01 dihedral pdb=" C5' CMP A 501 " pdb=" O5' CMP A 501 " pdb=" P CMP A 501 " pdb=" O1P CMP A 501 " ideal model delta sinusoidal sigma weight residual 60.00 170.44 -110.44 1 2.00e+01 2.50e-03 3.24e+01 ... (remaining 8413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1653 0.060 - 0.119: 372 0.119 - 0.179: 83 0.179 - 0.238: 4 0.238 - 0.298: 4 Chirality restraints: 2116 Sorted by residual: chirality pdb=" CB ILE C 58 " pdb=" CA ILE C 58 " pdb=" CG1 ILE C 58 " pdb=" CG2 ILE C 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE B 58 " pdb=" CA ILE B 58 " pdb=" CG1 ILE B 58 " pdb=" CG2 ILE B 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 2113 not shown) Planarity restraints: 2212 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 PGW A 509 " 0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW A 509 " -0.155 2.00e-02 2.50e+03 pdb=" C8 PGW A 509 " 0.164 2.00e-02 2.50e+03 pdb=" C9 PGW A 509 " -0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW D 509 " -0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW D 509 " 0.155 2.00e-02 2.50e+03 pdb=" C8 PGW D 509 " -0.164 2.00e-02 2.50e+03 pdb=" C9 PGW D 509 " 0.170 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 PGW C 509 " -0.161 2.00e-02 2.50e+03 1.62e-01 2.64e+02 pdb=" C10 PGW C 509 " 0.155 2.00e-02 2.50e+03 pdb=" C8 PGW C 509 " -0.164 2.00e-02 2.50e+03 pdb=" C9 PGW C 509 " 0.170 2.00e-02 2.50e+03 ... (remaining 2209 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3207 2.80 - 3.33: 11880 3.33 - 3.85: 20553 3.85 - 4.38: 24240 4.38 - 4.90: 42168 Nonbonded interactions: 102048 Sorted by model distance: nonbonded pdb=" OH TYR A 186 " pdb=" OG1 THR B 180 " model vdw 2.280 3.040 nonbonded pdb=" OH TYR C 186 " pdb=" OG1 THR D 180 " model vdw 2.297 3.040 nonbonded pdb=" OG1 THR A 180 " pdb=" OH TYR D 186 " model vdw 2.304 3.040 nonbonded pdb=" OH TYR B 186 " pdb=" OG1 THR C 180 " model vdw 2.306 3.040 nonbonded pdb=" OH TYR D 327 " pdb=" OE2 GLU D 353 " model vdw 2.307 3.040 ... (remaining 102043 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.200 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.009 0.191 13712 Z= 0.460 Angle : 1.363 17.206 18416 Z= 0.553 Chirality : 0.053 0.298 2116 Planarity : 0.013 0.162 2212 Dihedral : 21.044 167.438 5416 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.41 % Allowed : 7.94 % Favored : 90.65 % 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 are not related in a simple way. whole: -0.52 (0.22), residues: 1564 helix: 0.21 (0.18), residues: 952 sheet: -0.45 (0.53), residues: 88 loop : -1.19 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 273 TYR 0.013 0.001 TYR D 199 PHE 0.007 0.001 PHE D 40 TRP 0.014 0.002 TRP A 264 HIS 0.002 0.000 HIS D 316 Details of bonding type rmsd covalent geometry : bond 0.00919 (13712) covalent geometry : angle 1.36273 (18416) hydrogen bonds : bond 0.13584 ( 725) hydrogen bonds : angle 6.02781 ( 2079) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.430 Fit side-chains REVERT: B 334 MET cc_start: 0.7348 (mmp) cc_final: 0.7090 (mmt) REVERT: C 334 MET cc_start: 0.7328 (mmp) cc_final: 0.7063 (mmt) outliers start: 19 outliers final: 4 residues processed: 150 average time/residue: 0.7044 time to fit residues: 113.8488 Evaluate side-chains 145 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.0870 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.182613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.140268 restraints weight = 12892.786| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 1.41 r_work: 0.3104 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 13712 Z= 0.183 Angle : 0.752 10.776 18416 Z= 0.356 Chirality : 0.048 0.192 2116 Planarity : 0.006 0.048 2212 Dihedral : 20.595 160.567 2464 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.56 % Allowed : 12.91 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.22), residues: 1564 helix: 0.65 (0.18), residues: 956 sheet: -0.07 (0.59), residues: 88 loop : -1.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 399 TYR 0.011 0.002 TYR D 175 PHE 0.007 0.001 PHE D 366 TRP 0.010 0.002 TRP D 176 HIS 0.003 0.001 HIS B 281 Details of bonding type rmsd covalent geometry : bond 0.00460 (13712) covalent geometry : angle 0.75212 (18416) hydrogen bonds : bond 0.05931 ( 725) hydrogen bonds : angle 4.21921 ( 2079) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.484 Fit side-chains REVERT: C 382 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7706 (mmm160) outliers start: 21 outliers final: 12 residues processed: 135 average time/residue: 0.6574 time to fit residues: 96.1645 Evaluate side-chains 140 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 128 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 235 ARG Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 116 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.183228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.140054 restraints weight = 12950.075| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.50 r_work: 0.3075 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13712 Z= 0.162 Angle : 0.686 8.816 18416 Z= 0.328 Chirality : 0.046 0.203 2116 Planarity : 0.005 0.044 2212 Dihedral : 18.494 149.057 2464 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.89 % Allowed : 14.32 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.22), residues: 1564 helix: 0.98 (0.18), residues: 960 sheet: 0.10 (0.59), residues: 88 loop : -0.97 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 254 TYR 0.011 0.002 TYR A 199 PHE 0.006 0.001 PHE C 366 TRP 0.010 0.002 TRP D 176 HIS 0.003 0.001 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00404 (13712) covalent geometry : angle 0.68630 (18416) hydrogen bonds : bond 0.05552 ( 725) hydrogen bonds : angle 4.03974 ( 2079) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 131 time to evaluate : 0.506 Fit side-chains REVERT: A 414 LEU cc_start: 0.4573 (OUTLIER) cc_final: 0.4119 (tm) REVERT: B 414 LEU cc_start: 0.4642 (OUTLIER) cc_final: 0.4197 (tm) REVERT: C 414 LEU cc_start: 0.4661 (OUTLIER) cc_final: 0.4204 (tm) REVERT: D 414 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.4210 (tm) outliers start: 39 outliers final: 20 residues processed: 159 average time/residue: 0.7032 time to fit residues: 120.4925 Evaluate side-chains 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 0.3980 chunk 86 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 95 optimal weight: 0.4980 chunk 33 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.182538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.140767 restraints weight = 12942.233| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.31 r_work: 0.3075 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13712 Z= 0.162 Angle : 0.674 8.875 18416 Z= 0.322 Chirality : 0.046 0.211 2116 Planarity : 0.005 0.041 2212 Dihedral : 17.925 142.116 2464 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.56 % Allowed : 15.95 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1564 helix: 1.10 (0.18), residues: 960 sheet: 0.19 (0.60), residues: 88 loop : -0.97 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 391 TYR 0.011 0.002 TYR A 404 PHE 0.007 0.001 PHE D 366 TRP 0.010 0.002 TRP C 176 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00405 (13712) covalent geometry : angle 0.67409 (18416) hydrogen bonds : bond 0.05467 ( 725) hydrogen bonds : angle 3.94293 ( 2079) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 134 time to evaluate : 0.527 Fit side-chains REVERT: A 235 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.8107 (ttt180) REVERT: A 382 ARG cc_start: 0.8029 (mmm160) cc_final: 0.7689 (mmm160) REVERT: A 414 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.4188 (tm) REVERT: B 382 ARG cc_start: 0.8025 (mmm160) cc_final: 0.7724 (mmm160) REVERT: B 414 LEU cc_start: 0.4801 (OUTLIER) cc_final: 0.4286 (tm) REVERT: C 382 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7722 (mmm160) REVERT: C 414 LEU cc_start: 0.4805 (OUTLIER) cc_final: 0.4381 (tm) REVERT: D 414 LEU cc_start: 0.4809 (OUTLIER) cc_final: 0.4319 (tm) outliers start: 48 outliers final: 25 residues processed: 168 average time/residue: 0.6186 time to fit residues: 113.3500 Evaluate side-chains 164 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 134 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 152 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 86 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.180994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.136048 restraints weight = 12949.532| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.40 r_work: 0.3016 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 13712 Z= 0.195 Angle : 0.735 10.800 18416 Z= 0.348 Chirality : 0.048 0.219 2116 Planarity : 0.005 0.043 2212 Dihedral : 17.905 138.526 2464 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.93 % Allowed : 17.06 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1564 helix: 1.04 (0.17), residues: 964 sheet: 0.31 (0.60), residues: 88 loop : -0.90 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 391 TYR 0.015 0.002 TYR A 404 PHE 0.008 0.002 PHE D 366 TRP 0.011 0.002 TRP A 176 HIS 0.003 0.001 HIS D 281 Details of bonding type rmsd covalent geometry : bond 0.00500 (13712) covalent geometry : angle 0.73495 (18416) hydrogen bonds : bond 0.06124 ( 725) hydrogen bonds : angle 3.96615 ( 2079) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 159 time to evaluate : 0.446 Fit side-chains REVERT: A 235 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8151 (ttt180) REVERT: A 384 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.7989 (mtm180) REVERT: A 414 LEU cc_start: 0.4603 (OUTLIER) cc_final: 0.4225 (tm) REVERT: B 414 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4242 (tm) REVERT: C 414 LEU cc_start: 0.4684 (OUTLIER) cc_final: 0.4244 (tm) REVERT: D 414 LEU cc_start: 0.4688 (OUTLIER) cc_final: 0.4259 (tm) outliers start: 53 outliers final: 28 residues processed: 194 average time/residue: 0.6240 time to fit residues: 131.3494 Evaluate side-chains 193 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 380 THR Chi-restraints excluded: chain A residue 384 ARG Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 380 THR Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 380 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 380 THR Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.184544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.139821 restraints weight = 12876.183| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.38 r_work: 0.3060 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 13712 Z= 0.128 Angle : 0.633 8.961 18416 Z= 0.299 Chirality : 0.044 0.226 2116 Planarity : 0.004 0.038 2212 Dihedral : 16.864 139.034 2464 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 3.19 % Allowed : 18.40 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.23), residues: 1564 helix: 1.46 (0.18), residues: 952 sheet: 0.30 (0.59), residues: 88 loop : -0.92 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 391 TYR 0.016 0.001 TYR B 199 PHE 0.006 0.001 PHE D 366 TRP 0.007 0.001 TRP B 176 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00294 (13712) covalent geometry : angle 0.63289 (18416) hydrogen bonds : bond 0.04694 ( 725) hydrogen bonds : angle 3.83960 ( 2079) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 150 time to evaluate : 0.387 Fit side-chains REVERT: A 382 ARG cc_start: 0.7995 (mmm160) cc_final: 0.7723 (mmm160) REVERT: A 388 ASP cc_start: 0.8096 (t70) cc_final: 0.7582 (t0) REVERT: A 414 LEU cc_start: 0.4653 (OUTLIER) cc_final: 0.4243 (tm) REVERT: B 382 ARG cc_start: 0.8005 (mmm160) cc_final: 0.7730 (mmm160) REVERT: B 414 LEU cc_start: 0.4511 (OUTLIER) cc_final: 0.4260 (tm) REVERT: C 243 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7891 (mp) REVERT: C 382 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7759 (mmm160) REVERT: C 414 LEU cc_start: 0.4510 (OUTLIER) cc_final: 0.4251 (tm) REVERT: D 414 LEU cc_start: 0.4669 (OUTLIER) cc_final: 0.4255 (tm) outliers start: 43 outliers final: 20 residues processed: 183 average time/residue: 0.6106 time to fit residues: 121.2687 Evaluate side-chains 173 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 59 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.2980 chunk 96 optimal weight: 0.8980 chunk 22 optimal weight: 0.0020 chunk 147 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.185912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.142159 restraints weight = 12868.550| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.37 r_work: 0.3138 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13712 Z= 0.119 Angle : 0.614 8.636 18416 Z= 0.289 Chirality : 0.043 0.229 2116 Planarity : 0.004 0.036 2212 Dihedral : 15.797 136.391 2464 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.26 % Allowed : 18.25 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.23), residues: 1564 helix: 1.67 (0.18), residues: 952 sheet: 0.45 (0.59), residues: 88 loop : -0.86 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 391 TYR 0.017 0.001 TYR D 199 PHE 0.006 0.001 PHE C 242 TRP 0.005 0.001 TRP B 176 HIS 0.001 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00265 (13712) covalent geometry : angle 0.61405 (18416) hydrogen bonds : bond 0.04262 ( 725) hydrogen bonds : angle 3.73188 ( 2079) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 157 time to evaluate : 0.488 Fit side-chains REVERT: A 243 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7985 (mp) REVERT: A 382 ARG cc_start: 0.7941 (mmm160) cc_final: 0.7700 (mmm160) REVERT: A 388 ASP cc_start: 0.7976 (t70) cc_final: 0.7575 (t0) REVERT: A 414 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4282 (tm) REVERT: B 243 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7949 (mp) REVERT: B 273 ARG cc_start: 0.8087 (mtt-85) cc_final: 0.7876 (mtt-85) REVERT: B 277 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7481 (mtmp) REVERT: B 382 ARG cc_start: 0.7949 (mmm160) cc_final: 0.7505 (ttt90) REVERT: B 388 ASP cc_start: 0.7981 (t70) cc_final: 0.7579 (t0) REVERT: B 414 LEU cc_start: 0.4526 (OUTLIER) cc_final: 0.4278 (tm) REVERT: C 243 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7850 (mp) REVERT: C 382 ARG cc_start: 0.7962 (mmm160) cc_final: 0.7525 (ttt90) REVERT: C 388 ASP cc_start: 0.8030 (t70) cc_final: 0.7604 (t0) REVERT: C 414 LEU cc_start: 0.4523 (OUTLIER) cc_final: 0.4279 (tm) REVERT: D 243 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.7984 (mp) REVERT: D 414 LEU cc_start: 0.4539 (OUTLIER) cc_final: 0.4292 (tm) outliers start: 44 outliers final: 21 residues processed: 188 average time/residue: 0.5959 time to fit residues: 121.8012 Evaluate side-chains 175 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 14 optimal weight: 0.0770 chunk 148 optimal weight: 7.9990 chunk 59 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 150 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.186393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.143278 restraints weight = 12806.553| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.36 r_work: 0.3101 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13712 Z= 0.118 Angle : 0.618 11.154 18416 Z= 0.287 Chirality : 0.043 0.230 2116 Planarity : 0.004 0.035 2212 Dihedral : 15.092 134.312 2464 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.45 % Allowed : 19.29 % Favored : 78.26 % 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 are not related in a simple way. whole: 1.29 (0.23), residues: 1564 helix: 1.78 (0.18), residues: 956 sheet: 0.59 (0.59), residues: 88 loop : -0.84 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 391 TYR 0.018 0.001 TYR D 199 PHE 0.006 0.001 PHE C 366 TRP 0.005 0.001 TRP B 176 HIS 0.001 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00263 (13712) covalent geometry : angle 0.61848 (18416) hydrogen bonds : bond 0.04144 ( 725) hydrogen bonds : angle 3.64538 ( 2079) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 155 time to evaluate : 0.330 Fit side-chains REVERT: A 243 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 382 ARG cc_start: 0.7899 (mmm160) cc_final: 0.7666 (mmm160) REVERT: A 388 ASP cc_start: 0.7905 (t70) cc_final: 0.7614 (t0) REVERT: A 414 LEU cc_start: 0.4669 (OUTLIER) cc_final: 0.4430 (tm) REVERT: B 243 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7955 (mp) REVERT: B 382 ARG cc_start: 0.7909 (mmm160) cc_final: 0.7516 (ttt90) REVERT: B 388 ASP cc_start: 0.7894 (t70) cc_final: 0.7658 (t0) REVERT: B 414 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4361 (tm) REVERT: C 243 LEU cc_start: 0.8182 (OUTLIER) cc_final: 0.7891 (mp) REVERT: C 277 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7388 (mtmp) REVERT: C 382 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7486 (ttt90) REVERT: C 388 ASP cc_start: 0.7924 (t70) cc_final: 0.7586 (t0) REVERT: C 414 LEU cc_start: 0.4614 (OUTLIER) cc_final: 0.4361 (tm) REVERT: D 243 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7994 (mp) REVERT: D 388 ASP cc_start: 0.7918 (t70) cc_final: 0.7595 (t0) REVERT: D 414 LEU cc_start: 0.4623 (OUTLIER) cc_final: 0.4365 (tm) outliers start: 33 outliers final: 16 residues processed: 182 average time/residue: 0.6488 time to fit residues: 127.7545 Evaluate side-chains 174 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 149 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 414 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 chunk 42 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.185676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.142227 restraints weight = 12898.261| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.37 r_work: 0.3094 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13712 Z= 0.123 Angle : 0.634 12.954 18416 Z= 0.293 Chirality : 0.044 0.233 2116 Planarity : 0.004 0.035 2212 Dihedral : 14.748 136.109 2464 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 2.52 % Allowed : 18.77 % Favored : 78.71 % 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 are not related in a simple way. whole: 1.36 (0.23), residues: 1564 helix: 1.84 (0.18), residues: 956 sheet: 0.63 (0.59), residues: 88 loop : -0.83 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 391 TYR 0.016 0.001 TYR D 199 PHE 0.006 0.001 PHE A 366 TRP 0.006 0.001 TRP C 176 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00279 (13712) covalent geometry : angle 0.63442 (18416) hydrogen bonds : bond 0.04297 ( 725) hydrogen bonds : angle 3.63182 ( 2079) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 0.427 Fit side-chains REVERT: A 243 LEU cc_start: 0.8208 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 273 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7848 (mtt90) REVERT: A 388 ASP cc_start: 0.7937 (t70) cc_final: 0.7655 (t0) REVERT: A 414 LEU cc_start: 0.4692 (OUTLIER) cc_final: 0.4451 (tm) REVERT: B 243 LEU cc_start: 0.8191 (OUTLIER) cc_final: 0.7928 (mp) REVERT: B 388 ASP cc_start: 0.7941 (t70) cc_final: 0.7717 (t0) REVERT: C 243 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7858 (mp) REVERT: C 277 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7560 (mtmp) REVERT: C 382 ARG cc_start: 0.7894 (mmm160) cc_final: 0.7479 (ttt90) REVERT: C 388 ASP cc_start: 0.7941 (t70) cc_final: 0.7625 (t0) REVERT: D 243 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7956 (mp) REVERT: D 277 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7569 (mtmp) REVERT: D 388 ASP cc_start: 0.7970 (t70) cc_final: 0.7677 (t0) outliers start: 34 outliers final: 18 residues processed: 177 average time/residue: 0.6033 time to fit residues: 116.0863 Evaluate side-chains 168 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.183136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.141760 restraints weight = 12818.226| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.30 r_work: 0.3111 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 13712 Z= 0.188 Angle : 0.730 12.941 18416 Z= 0.342 Chirality : 0.048 0.231 2116 Planarity : 0.005 0.039 2212 Dihedral : 15.668 139.772 2464 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.93 % Allowed : 20.18 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.22), residues: 1564 helix: 1.53 (0.17), residues: 964 sheet: 0.64 (0.59), residues: 88 loop : -0.72 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 391 TYR 0.013 0.002 TYR C 404 PHE 0.008 0.001 PHE D 366 TRP 0.011 0.002 TRP A 176 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd covalent geometry : bond 0.00476 (13712) covalent geometry : angle 0.73029 (18416) hydrogen bonds : bond 0.05900 ( 725) hydrogen bonds : angle 3.77189 ( 2079) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3128 Ramachandran restraints generated. 1564 Oldfield, 0 Emsley, 1564 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 147 time to evaluate : 0.311 Fit side-chains REVERT: A 235 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8198 (ttt180) REVERT: A 243 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8183 (mp) REVERT: A 414 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4480 (tm) REVERT: B 243 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8140 (mp) REVERT: B 277 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7626 (mtmp) REVERT: C 243 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 277 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7632 (mtmp) REVERT: D 243 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8186 (mp) REVERT: D 277 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7632 (mtmp) outliers start: 26 outliers final: 16 residues processed: 165 average time/residue: 0.6359 time to fit residues: 113.6040 Evaluate side-chains 175 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain B residue 277 LYS Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 243 LEU Chi-restraints excluded: chain C residue 277 LYS Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 277 LYS Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 346 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 99 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 68 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 164 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.185276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.142885 restraints weight = 12882.049| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 1.39 r_work: 0.3152 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13712 Z= 0.125 Angle : 0.643 11.330 18416 Z= 0.299 Chirality : 0.044 0.253 2116 Planarity : 0.004 0.036 2212 Dihedral : 14.836 139.874 2464 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.08 % Allowed : 20.33 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1564 helix: 1.88 (0.18), residues: 952 sheet: 0.61 (0.60), residues: 88 loop : -0.82 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 399 TYR 0.016 0.001 TYR D 199 PHE 0.007 0.001 PHE D 366 TRP 0.007 0.001 TRP A 15 HIS 0.001 0.000 HIS A 292 Details of bonding type rmsd covalent geometry : bond 0.00283 (13712) covalent geometry : angle 0.64345 (18416) hydrogen bonds : bond 0.04497 ( 725) hydrogen bonds : angle 3.68286 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3754.06 seconds wall clock time: 64 minutes 38.75 seconds (3878.75 seconds total)