Starting phenix.real_space_refine on Fri Jul 3 10:38:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtf_24681/07_2026/7rtf_24681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtf_24681/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7rtf_24681/07_2026/7rtf_24681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtf_24681/07_2026/7rtf_24681.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtf_24681/07_2026/7rtf_24681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtf_24681/07_2026/7rtf_24681.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7rtf_24681/07_2026/7rtf_24681.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtf_24681/07_2026/7rtf_24681.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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: 265 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: 2.67, 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: 0.88 Conformation dependent library (CDL) restraints added in 564.1 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: 0.35 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: 1.94 Time building geometry restraints manager: 1.23 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 - 33.03: 7923 33.03 - 66.05: 381 66.05 - 99.08: 28 99.08 - 132.11: 16 132.11 - 165.13: 8 Dihedral angle restraints: 8356 sinusoidal: 3708 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 8353 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.890 Find NCS groups from input model: 0.190 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: 0.010 Load rotamer database and sin/cos tables:8.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 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 : 18.996 165.133 5356 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/Z covalent geometry : bond 0.00919 / 0.46 (13712) covalent geometry : angle 1.36273 / 0.55 (18416) hydrogen bonds : bond 0.13584 / 9.12 ( 725) hydrogen bonds : angle 6.02781 / 4.33 ( 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 : 0.307 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: 0.6112 time to fit residues: 99.4480 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 : 0.338 ------------------------------------------------------------------------------- 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... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.182657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.139811 restraints weight = 12895.216| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.36 r_work: 0.3063 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 13712 Z= 0.181 Angle : 0.752 10.576 18416 Z= 0.355 Chirality : 0.047 0.195 2116 Planarity : 0.006 0.048 2212 Dihedral : 17.500 163.039 2404 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 1.26 % Allowed : 13.20 % 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: 0.01 (0.22), residues: 1564 helix: 0.63 (0.18), residues: 956 sheet: -0.08 (0.59), residues: 88 loop : -1.02 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 399 TYR 0.012 0.002 TYR B 175 PHE 0.006 0.001 PHE C 366 TRP 0.010 0.002 TRP C 176 HIS 0.003 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.18 (13712) covalent geometry : angle 0.75217 / 0.35 (18416) hydrogen bonds : bond 0.06023 / 3.89 ( 725) hydrogen bonds : angle 4.25926 / 3.08 ( 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 144 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.489 Fit side-chains REVERT: A 382 ARG cc_start: 0.7968 (mmm160) cc_final: 0.7688 (mmm160) REVERT: C 382 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7730 (mmm160) outliers start: 17 outliers final: 12 residues processed: 130 average time/residue: 0.6468 time to fit residues: 91.6151 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 : 0.483 ------------------------------------------------------------------------------- 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: 7.9990 chunk 86 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 128 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.180074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.137445 restraints weight = 12951.083| |-----------------------------------------------------------------------------| r_work (start): 0.3458 rms_B_bonded: 1.43 r_work: 0.3038 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.105 13712 Z= 0.236 Angle : 0.795 10.660 18416 Z= 0.381 Chirality : 0.050 0.211 2116 Planarity : 0.006 0.049 2212 Dihedral : 16.927 139.096 2404 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 3.26 % Allowed : 14.54 % Favored : 82.20 % 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: -0.01 (0.22), residues: 1564 helix: 0.62 (0.17), residues: 964 sheet: 0.13 (0.60), residues: 88 loop : -1.10 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 254 TYR 0.014 0.002 TYR A 404 PHE 0.008 0.002 PHE D 366 TRP 0.014 0.003 TRP C 176 HIS 0.004 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.24 (13712) covalent geometry : angle 0.79464 / 0.38 (18416) hydrogen bonds : bond 0.06906 / 4.47 ( 725) hydrogen bonds : angle 4.19149 / 3.03 ( 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 193 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.518 Fit side-chains REVERT: A 235 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8117 (ttt180) REVERT: A 276 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 382 ARG cc_start: 0.8061 (mmm160) cc_final: 0.7837 (mmm160) REVERT: A 414 LEU cc_start: 0.4486 (OUTLIER) cc_final: 0.4048 (tm) REVERT: B 276 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8260 (mp) REVERT: B 414 LEU cc_start: 0.4700 (OUTLIER) cc_final: 0.4206 (tm) REVERT: C 276 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8236 (mp) REVERT: C 382 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7812 (mmm160) REVERT: C 414 LEU cc_start: 0.4728 (OUTLIER) cc_final: 0.4228 (tm) REVERT: D 276 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8415 (mp) REVERT: D 382 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7786 (mmm160) REVERT: D 414 LEU cc_start: 0.4591 (OUTLIER) cc_final: 0.4126 (tm) outliers start: 44 outliers final: 21 residues processed: 173 average time/residue: 0.7031 time to fit residues: 131.4580 Evaluate side-chains 170 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 235 ARG Chi-restraints excluded: chain A residue 276 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 389 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 276 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 193 THR Chi-restraints excluded: chain C residue 276 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 92 ASP Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 276 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.0050 chunk 73 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 20 optimal weight: 0.0170 chunk 144 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 chunk 95 optimal weight: 0.0980 chunk 33 optimal weight: 0.0870 chunk 92 optimal weight: 0.0070 overall best weight: 0.0428 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.188451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.144614 restraints weight = 12981.060| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.40 r_work: 0.3142 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13712 Z= 0.116 Angle : 0.591 7.756 18416 Z= 0.282 Chirality : 0.041 0.202 2116 Planarity : 0.004 0.037 2212 Dihedral : 14.692 133.849 2404 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.45 % Allowed : 17.51 % Favored : 80.04 % 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: 0.74 (0.23), residues: 1564 helix: 1.34 (0.18), residues: 952 sheet: -0.06 (0.57), residues: 88 loop : -0.94 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 391 TYR 0.022 0.001 TYR C 199 PHE 0.009 0.001 PHE B 40 TRP 0.007 0.001 TRP B 176 HIS 0.002 0.001 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (13712) covalent geometry : angle 0.59075 / 0.28 (18416) hydrogen bonds : bond 0.03730 / 2.37 ( 725) hydrogen bonds : angle 3.91013 / 2.82 ( 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 180 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.498 Fit side-chains REVERT: A 388 ASP cc_start: 0.7939 (t70) cc_final: 0.7619 (t0) REVERT: B 388 ASP cc_start: 0.8032 (t70) cc_final: 0.7587 (t0) REVERT: B 414 LEU cc_start: 0.4600 (OUTLIER) cc_final: 0.4163 (tm) REVERT: C 388 ASP cc_start: 0.8027 (t70) cc_final: 0.7571 (t0) REVERT: D 388 ASP cc_start: 0.8047 (t70) cc_final: 0.7579 (t0) REVERT: D 414 LEU cc_start: 0.4627 (OUTLIER) cc_final: 0.4171 (tm) outliers start: 33 outliers final: 9 residues processed: 168 average time/residue: 0.5783 time to fit residues: 105.6562 Evaluate side-chains 158 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 314 ILE Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 314 ILE 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: 6.9990 chunk 126 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 152 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 chunk 127 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.184812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.140916 restraints weight = 12973.654| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.39 r_work: 0.3073 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 13712 Z= 0.129 Angle : 0.631 10.427 18416 Z= 0.294 Chirality : 0.044 0.211 2116 Planarity : 0.004 0.038 2212 Dihedral : 14.230 133.750 2404 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.82 % Allowed : 16.99 % Favored : 80.19 % 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: 0.96 (0.23), residues: 1564 helix: 1.47 (0.18), residues: 952 sheet: 0.20 (0.58), residues: 88 loop : -0.80 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 391 TYR 0.014 0.001 TYR B 199 PHE 0.007 0.001 PHE A 366 TRP 0.006 0.001 TRP B 176 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (13712) covalent geometry : angle 0.63118 / 0.29 (18416) hydrogen bonds : bond 0.04480 / 2.88 ( 725) hydrogen bonds : angle 3.75263 / 2.72 ( 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 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 144 time to evaluate : 0.352 Fit side-chains REVERT: A 388 ASP cc_start: 0.7981 (t70) cc_final: 0.7673 (t0) REVERT: A 414 LEU cc_start: 0.4587 (OUTLIER) cc_final: 0.4136 (tm) REVERT: B 382 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7699 (mmm160) REVERT: B 388 ASP cc_start: 0.8039 (t70) cc_final: 0.7598 (t0) REVERT: B 414 LEU cc_start: 0.4819 (OUTLIER) cc_final: 0.4311 (tm) REVERT: C 388 ASP cc_start: 0.8062 (t70) cc_final: 0.7627 (t0) REVERT: C 414 LEU cc_start: 0.4768 (OUTLIER) cc_final: 0.4290 (tm) REVERT: D 382 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7527 (ttt90) REVERT: D 388 ASP cc_start: 0.8053 (t70) cc_final: 0.7600 (t0) REVERT: D 414 LEU cc_start: 0.4807 (OUTLIER) cc_final: 0.4306 (tm) outliers start: 38 outliers final: 14 residues processed: 169 average time/residue: 0.6340 time to fit residues: 116.3071 Evaluate side-chains 155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 137 time to evaluate : 0.460 ------------------------------------------------------------------------------- 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 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 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 314 ILE Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain D residue 46 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 6.9990 chunk 41 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 111 optimal weight: 0.2980 chunk 43 optimal weight: 7.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.185331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.141224 restraints weight = 12951.807| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.38 r_work: 0.3079 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1828 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= 0.122 Angle : 0.621 11.260 18416 Z= 0.289 Chirality : 0.043 0.216 2116 Planarity : 0.004 0.037 2212 Dihedral : 13.606 133.545 2404 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.82 % Allowed : 16.91 % Favored : 80.27 % 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: 1.17 (0.23), residues: 1564 helix: 1.63 (0.18), residues: 952 sheet: 0.41 (0.58), residues: 88 loop : -0.73 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.014 0.001 TYR D 199 PHE 0.006 0.001 PHE A 366 TRP 0.006 0.001 TRP A 176 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (13712) covalent geometry : angle 0.62108 / 0.29 (18416) hydrogen bonds : bond 0.04308 / 2.76 ( 725) hydrogen bonds : angle 3.69229 / 2.67 ( 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 176 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 138 time to evaluate : 0.348 Fit side-chains REVERT: A 276 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8072 (mp) REVERT: A 388 ASP cc_start: 0.7940 (t70) cc_final: 0.7672 (t0) REVERT: A 414 LEU cc_start: 0.4584 (OUTLIER) cc_final: 0.4099 (tm) REVERT: B 388 ASP cc_start: 0.8089 (t70) cc_final: 0.7693 (t0) REVERT: B 414 LEU cc_start: 0.4786 (OUTLIER) cc_final: 0.4364 (tm) REVERT: C 276 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8094 (mp) REVERT: C 388 ASP cc_start: 0.8047 (t70) cc_final: 0.7654 (t0) REVERT: C 414 LEU cc_start: 0.4784 (OUTLIER) cc_final: 0.4377 (tm) REVERT: D 382 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7500 (ttt90) REVERT: D 388 ASP cc_start: 0.8090 (t70) cc_final: 0.7681 (t0) REVERT: D 414 LEU cc_start: 0.4679 (OUTLIER) cc_final: 0.4269 (tm) outliers start: 38 outliers final: 15 residues processed: 163 average time/residue: 0.5355 time to fit residues: 95.7504 Evaluate side-chains 158 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.454 ------------------------------------------------------------------------------- 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 276 LEU 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 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 46 LEU Chi-restraints excluded: chain C residue 276 LEU 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 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: 0.9980 chunk 9 optimal weight: 0.1980 chunk 68 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 147 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.0370 chunk 81 optimal weight: 0.0670 chunk 55 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.189321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.150902 restraints weight = 12959.695| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.26 r_work: 0.3247 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13712 Z= 0.105 Angle : 0.585 10.817 18416 Z= 0.269 Chirality : 0.042 0.231 2116 Planarity : 0.004 0.035 2212 Dihedral : 12.201 133.704 2404 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.37 % Allowed : 17.58 % Favored : 80.04 % 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: 1.45 (0.23), residues: 1564 helix: 1.84 (0.18), residues: 952 sheet: 0.47 (0.57), residues: 88 loop : -0.57 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.021 0.001 TYR B 199 PHE 0.005 0.001 PHE A 366 TRP 0.004 0.001 TRP A 15 HIS 0.001 0.000 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (13712) covalent geometry : angle 0.58490 / 0.27 (18416) hydrogen bonds : bond 0.03462 / 2.21 ( 725) hydrogen bonds : angle 3.57966 / 2.58 ( 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 182 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.461 Fit side-chains REVERT: A 266 THR cc_start: 0.8021 (p) cc_final: 0.7709 (p) REVERT: A 414 LEU cc_start: 0.4712 (OUTLIER) cc_final: 0.4397 (tm) REVERT: B 243 LEU cc_start: 0.8245 (OUTLIER) cc_final: 0.8025 (mp) REVERT: B 414 LEU cc_start: 0.4785 (OUTLIER) cc_final: 0.4413 (tm) REVERT: C 243 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.8025 (mp) REVERT: C 414 LEU cc_start: 0.4833 (OUTLIER) cc_final: 0.4473 (tm) REVERT: D 414 LEU cc_start: 0.4744 (OUTLIER) cc_final: 0.4391 (tm) outliers start: 32 outliers final: 12 residues processed: 170 average time/residue: 0.5491 time to fit residues: 102.2987 Evaluate side-chains 156 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 138 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ARG 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 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 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 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: 7.9990 chunk 49 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 150 optimal weight: 0.0470 chunk 126 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.183737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.140093 restraints weight = 12814.525| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.36 r_work: 0.3072 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13712 Z= 0.154 Angle : 0.669 12.753 18416 Z= 0.312 Chirality : 0.045 0.224 2116 Planarity : 0.004 0.038 2212 Dihedral : 13.329 133.582 2404 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.08 % Allowed : 17.95 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.40 (0.23), residues: 1564 helix: 1.76 (0.18), residues: 964 sheet: 0.49 (0.58), residues: 88 loop : -0.57 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.010 0.001 TYR B 199 PHE 0.008 0.001 PHE B 366 TRP 0.009 0.002 TRP A 176 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (13712) covalent geometry : angle 0.66874 / 0.31 (18416) hydrogen bonds : bond 0.05156 / 3.32 ( 725) hydrogen bonds : angle 3.65720 / 2.64 ( 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 179 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.533 Fit side-chains REVERT: A 414 LEU cc_start: 0.4645 (OUTLIER) cc_final: 0.4426 (tm) REVERT: B 243 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7983 (mp) REVERT: B 312 ASP cc_start: 0.7863 (m-30) cc_final: 0.7661 (t0) REVERT: B 414 LEU cc_start: 0.4816 (OUTLIER) cc_final: 0.4377 (tm) REVERT: C 243 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7960 (mp) REVERT: C 414 LEU cc_start: 0.4821 (OUTLIER) cc_final: 0.4410 (tm) REVERT: D 312 ASP cc_start: 0.7879 (m-30) cc_final: 0.7677 (t0) REVERT: D 414 LEU cc_start: 0.4824 (OUTLIER) cc_final: 0.4395 (tm) outliers start: 28 outliers final: 14 residues processed: 173 average time/residue: 0.5899 time to fit residues: 111.6702 Evaluate side-chains 153 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 243 LEU 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 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: 0.8980 chunk 48 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 42 optimal weight: 0.5980 chunk 125 optimal weight: 2.9990 chunk 121 optimal weight: 5.9990 chunk 116 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.185543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.142484 restraints weight = 12941.475| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.37 r_work: 0.3096 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13712 Z= 0.122 Angle : 0.633 12.117 18416 Z= 0.295 Chirality : 0.043 0.233 2116 Planarity : 0.004 0.037 2212 Dihedral : 12.909 133.407 2404 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.93 % Allowed : 18.84 % Favored : 79.23 % 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: 1.53 (0.23), residues: 1564 helix: 1.93 (0.18), residues: 952 sheet: 0.54 (0.57), residues: 88 loop : -0.61 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 391 TYR 0.008 0.001 TYR C 404 PHE 0.007 0.001 PHE D 366 TRP 0.006 0.001 TRP C 176 HIS 0.002 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13712) covalent geometry : angle 0.63342 / 0.30 (18416) hydrogen bonds : bond 0.04336 / 2.79 ( 725) hydrogen bonds : angle 3.63312 / 2.63 ( 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 162 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.491 Fit side-chains REVERT: A 414 LEU cc_start: 0.4693 (OUTLIER) cc_final: 0.4475 (tm) REVERT: B 243 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7998 (mp) REVERT: B 414 LEU cc_start: 0.4832 (OUTLIER) cc_final: 0.4395 (tm) REVERT: C 243 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7983 (mp) REVERT: C 414 LEU cc_start: 0.4779 (OUTLIER) cc_final: 0.4532 (tm) REVERT: D 414 LEU cc_start: 0.4841 (OUTLIER) cc_final: 0.4401 (tm) outliers start: 26 outliers final: 19 residues processed: 157 average time/residue: 0.6297 time to fit residues: 107.8767 Evaluate side-chains 159 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 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 46 LEU Chi-restraints excluded: chain B residue 243 LEU 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 121 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.4980 chunk 43 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.185461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.142417 restraints weight = 12892.778| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.36 r_work: 0.3095 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13712 Z= 0.122 Angle : 0.630 12.438 18416 Z= 0.293 Chirality : 0.043 0.230 2116 Planarity : 0.004 0.037 2212 Dihedral : 12.721 133.490 2404 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.08 % Allowed : 18.62 % Favored : 79.30 % 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: 1.50 (0.23), residues: 1564 helix: 1.91 (0.18), residues: 956 sheet: 0.61 (0.57), residues: 88 loop : -0.67 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 273 TYR 0.008 0.001 TYR D 404 PHE 0.006 0.001 PHE A 366 TRP 0.006 0.001 TRP C 176 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (13712) covalent geometry : angle 0.63035 / 0.29 (18416) hydrogen bonds : bond 0.04301 / 2.77 ( 725) hydrogen bonds : angle 3.60533 / 2.60 ( 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 166 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.790 Fit side-chains REVERT: A 414 LEU cc_start: 0.4649 (OUTLIER) cc_final: 0.4429 (tm) REVERT: B 243 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7947 (mp) REVERT: B 414 LEU cc_start: 0.4789 (OUTLIER) cc_final: 0.4512 (tm) REVERT: C 243 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7946 (mp) REVERT: C 414 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.4518 (tm) REVERT: D 312 ASP cc_start: 0.7833 (m-30) cc_final: 0.7590 (t0) REVERT: D 414 LEU cc_start: 0.4783 (OUTLIER) cc_final: 0.4497 (tm) outliers start: 28 outliers final: 20 residues processed: 161 average time/residue: 0.5265 time to fit residues: 93.3655 Evaluate side-chains 155 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 46 LEU 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 99 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 44 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.183563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.137049 restraints weight = 12889.846| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.38 r_work: 0.3089 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13712 Z= 0.139 Angle : 0.664 13.143 18416 Z= 0.310 Chirality : 0.045 0.233 2116 Planarity : 0.004 0.038 2212 Dihedral : 13.010 136.009 2404 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.00 % Allowed : 18.84 % Favored : 79.15 % 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: 1.41 (0.23), residues: 1564 helix: 1.84 (0.18), residues: 956 sheet: 0.61 (0.57), residues: 88 loop : -0.71 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 399 TYR 0.010 0.001 TYR A 404 PHE 0.007 0.001 PHE D 366 TRP 0.008 0.001 TRP C 176 HIS 0.002 0.001 HIS D 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13712) covalent geometry : angle 0.66426 / 0.31 (18416) hydrogen bonds : bond 0.04812 / 3.10 ( 725) hydrogen bonds : angle 3.63761 / 2.63 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3702.04 seconds wall clock time: 63 minutes 58.30 seconds (3838.30 seconds total)