Starting phenix.real_space_refine on Sat Sep 12 04:24:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtf_24681/09_2026/7rtf_24681.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtf_24681/09_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_24681/09_2026/7rtf_24681.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtf_24681/09_2026/7rtf_24681.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7rtf_24681/09_2026/7rtf_24681.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtf_24681/09_2026/7rtf_24681.cif" model { file = "/net/cci-nas-00/data/ceres_data/7rtf_24681/09_2026/7rtf_24681.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtf_24681/09_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: {'RNAv2': 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: 3.13, per 1000 atoms: 0.23 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: 1.04 Conformation dependent library (CDL) restraints added in 440.3 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: 0.47 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: 1.51 Time building geometry restraints manager: 1.41 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: 17993 3.44 - 6.88: 335 6.88 - 10.32: 40 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: 32 99.08 - 132.11: 16 132.11 - 165.13: 4 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: 1649 0.060 - 0.119: 372 0.119 - 0.179: 83 0.179 - 0.238: 4 0.238 - 0.298: 8 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: 0.04 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: 1.020 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.790 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.280 ------------------------------------------------------------------------------- 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= 0.461 Angle : 1.386 17.206 18416 Z= 0.556 Chirality : 0.055 0.298 2116 Planarity : 0.013 0.162 2212 Dihedral : 18.699 165.133 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 0.00921 / 0.46 (13712) covalent geometry : angle 1.38579 / 0.56 (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 : 0.456 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: 0.5990 time to fit residues: 97.2914 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 : 0.496 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.182613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.140123 restraints weight = 12882.907| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 1.35 r_work: 0.3084 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 13712 Z= 0.179 Angle : 0.776 10.460 18416 Z= 0.356 Chirality : 0.048 0.195 2116 Planarity : 0.005 0.048 2212 Dihedral : 16.017 130.945 2404 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.26 % Allowed : 12.98 % Favored : 85.76 % 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: 0.02 (0.22), residues: 1564 helix: 0.65 (0.18), residues: 956 sheet: -0.08 (0.59), residues: 88 loop : -1.04 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 399 TYR 0.009 0.002 TYR B 175 PHE 0.006 0.001 PHE C 366 TRP 0.010 0.002 TRP D 176 HIS 0.003 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00454 / 0.18 (13712) covalent geometry : angle 0.77622 / 0.36 (18416) hydrogen bonds : bond 0.05937 / 3.83 ( 725) hydrogen bonds : angle 4.25486 / 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 145 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.396 Fit side-chains REVERT: A 382 ARG cc_start: 0.7910 (mmm160) cc_final: 0.7646 (mmm160) REVERT: C 382 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7660 (mmm160) outliers start: 17 outliers final: 12 residues processed: 131 average time/residue: 0.7117 time to fit residues: 101.1883 Evaluate side-chains 138 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 0.8980 chunk 73 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 109 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3968 r_free = 0.3968 target = 0.184246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.139810 restraints weight = 12965.793| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 1.40 r_work: 0.3050 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 13712 Z= 0.136 Angle : 0.681 8.308 18416 Z= 0.311 Chirality : 0.045 0.198 2116 Planarity : 0.004 0.043 2212 Dihedral : 14.604 130.600 2404 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.60 % Allowed : 13.43 % Favored : 83.98 % 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: 0.49 (0.22), residues: 1564 helix: 1.11 (0.18), residues: 952 sheet: 0.02 (0.58), residues: 88 loop : -1.02 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 254 TYR 0.013 0.001 TYR A 199 PHE 0.006 0.001 PHE A 366 TRP 0.008 0.001 TRP A 176 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (13712) covalent geometry : angle 0.68091 / 0.31 (18416) hydrogen bonds : bond 0.04972 / 3.20 ( 725) hydrogen bonds : angle 4.00393 / 2.90 ( 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: 35 poor density : 135 time to evaluate : 0.502 Fit side-chains REVERT: A 391 ARG cc_start: 0.8633 (ptm-80) cc_final: 0.8399 (ptt-90) REVERT: A 414 LEU cc_start: 0.4453 (OUTLIER) cc_final: 0.4019 (tm) REVERT: B 414 LEU cc_start: 0.4619 (OUTLIER) cc_final: 0.4174 (tm) REVERT: C 414 LEU cc_start: 0.4637 (OUTLIER) cc_final: 0.4200 (tm) REVERT: D 391 ARG cc_start: 0.8599 (ptm-80) cc_final: 0.8378 (ptt-90) REVERT: D 414 LEU cc_start: 0.4652 (OUTLIER) cc_final: 0.4221 (tm) outliers start: 35 outliers final: 17 residues processed: 163 average time/residue: 0.7060 time to fit residues: 124.7155 Evaluate side-chains 148 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.498 ------------------------------------------------------------------------------- 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 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 414 LEU Chi-restraints excluded: chain C residue 46 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 144 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 92 optimal weight: 0.0010 overall best weight: 0.8790 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.184396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.143174 restraints weight = 12956.220| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 1.31 r_work: 0.3122 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13712 Z= 0.130 Angle : 0.657 8.370 18416 Z= 0.300 Chirality : 0.044 0.205 2116 Planarity : 0.004 0.040 2212 Dihedral : 13.731 133.633 2404 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.12 % Allowed : 14.84 % Favored : 82.05 % 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: 0.78 (0.22), residues: 1564 helix: 1.33 (0.18), residues: 952 sheet: 0.11 (0.58), residues: 88 loop : -0.87 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 391 TYR 0.013 0.001 TYR D 199 PHE 0.006 0.001 PHE D 366 TRP 0.007 0.001 TRP A 176 HIS 0.002 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (13712) covalent geometry : angle 0.65653 / 0.30 (18416) hydrogen bonds : bond 0.04727 / 3.03 ( 725) hydrogen bonds : angle 3.85873 / 2.79 ( 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 183 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 141 time to evaluate : 0.501 Fit side-chains REVERT: A 273 ARG cc_start: 0.8215 (mtt-85) cc_final: 0.7972 (mtt-85) REVERT: A 388 ASP cc_start: 0.8040 (t70) cc_final: 0.7632 (t0) REVERT: A 391 ARG cc_start: 0.8620 (ptm-80) cc_final: 0.8398 (ptt-90) REVERT: A 414 LEU cc_start: 0.4582 (OUTLIER) cc_final: 0.4152 (tm) REVERT: B 382 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7627 (ttt90) REVERT: B 414 LEU cc_start: 0.4748 (OUTLIER) cc_final: 0.4293 (tm) REVERT: C 382 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7625 (mmm160) REVERT: C 414 LEU cc_start: 0.4765 (OUTLIER) cc_final: 0.4312 (tm) REVERT: D 382 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7638 (ttt90) REVERT: D 414 LEU cc_start: 0.4793 (OUTLIER) cc_final: 0.4316 (tm) outliers start: 42 outliers final: 20 residues processed: 175 average time/residue: 0.5682 time to fit residues: 109.2874 Evaluate side-chains 158 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 34 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 65 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 152 optimal weight: 0.0270 chunk 29 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 127 optimal weight: 0.0020 chunk 6 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 32 optimal weight: 0.9980 overall best weight: 0.4246 ------------------------------------------------------------------------------- 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 = 0.3994 r_free = 0.3994 target = 0.186655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.147245 restraints weight = 12969.457| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 1.31 r_work: 0.3159 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 13712 Z= 0.111 Angle : 0.637 9.710 18416 Z= 0.284 Chirality : 0.043 0.210 2116 Planarity : 0.004 0.036 2212 Dihedral : 12.596 127.911 2404 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.30 % Allowed : 16.99 % Favored : 80.71 % 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: 1.04 (0.23), residues: 1564 helix: 1.52 (0.18), residues: 956 sheet: 0.22 (0.57), residues: 88 loop : -0.76 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 391 TYR 0.017 0.001 TYR C 199 PHE 0.005 0.001 PHE A 366 TRP 0.005 0.001 TRP A 176 HIS 0.001 0.000 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (13712) covalent geometry : angle 0.63735 / 0.28 (18416) hydrogen bonds : bond 0.03990 / 2.55 ( 725) hydrogen bonds : angle 3.73810 / 2.70 ( 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 177 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.357 Fit side-chains REVERT: A 388 ASP cc_start: 0.7799 (t70) cc_final: 0.7567 (t0) REVERT: A 414 LEU cc_start: 0.4636 (OUTLIER) cc_final: 0.4185 (tm) REVERT: B 388 ASP cc_start: 0.8029 (t70) cc_final: 0.7620 (t0) REVERT: B 414 LEU cc_start: 0.4634 (OUTLIER) cc_final: 0.4427 (tm) REVERT: C 388 ASP cc_start: 0.7997 (t70) cc_final: 0.7596 (t0) REVERT: D 388 ASP cc_start: 0.7978 (t70) cc_final: 0.7638 (t0) REVERT: D 414 LEU cc_start: 0.4776 (OUTLIER) cc_final: 0.4425 (tm) outliers start: 31 outliers final: 19 residues processed: 170 average time/residue: 0.5483 time to fit residues: 102.2530 Evaluate side-chains 159 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 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 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 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: 0.6980 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 111 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.186280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.148080 restraints weight = 12972.515| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 1.39 r_work: 0.3211 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13712 Z= 0.114 Angle : 0.649 11.108 18416 Z= 0.287 Chirality : 0.044 0.220 2116 Planarity : 0.004 0.036 2212 Dihedral : 11.897 126.156 2404 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.52 % Allowed : 17.14 % Favored : 80.34 % 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: 1.20 (0.23), residues: 1564 helix: 1.64 (0.18), residues: 956 sheet: 0.39 (0.56), residues: 88 loop : -0.70 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 391 TYR 0.015 0.001 TYR B 199 PHE 0.006 0.001 PHE C 366 TRP 0.005 0.001 TRP C 176 HIS 0.001 0.001 HIS A 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 (13712) covalent geometry : angle 0.64880 / 0.29 (18416) hydrogen bonds : bond 0.04084 / 2.62 ( 725) hydrogen bonds : angle 3.64512 / 2.63 ( 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 172 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.533 Fit side-chains REVERT: A 414 LEU cc_start: 0.4628 (OUTLIER) cc_final: 0.4339 (tm) REVERT: B 388 ASP cc_start: 0.7936 (t70) cc_final: 0.7562 (t0) REVERT: C 388 ASP cc_start: 0.7881 (t70) cc_final: 0.7544 (t0) REVERT: D 388 ASP cc_start: 0.7908 (t70) cc_final: 0.7680 (t0) REVERT: D 414 LEU cc_start: 0.4621 (OUTLIER) cc_final: 0.4333 (tm) outliers start: 34 outliers final: 21 residues processed: 167 average time/residue: 0.5554 time to fit residues: 101.7167 Evaluate side-chains 156 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.476 ------------------------------------------------------------------------------- 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 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 46 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 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: 0.5980 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.183382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.139402 restraints weight = 12892.314| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.39 r_work: 0.3046 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 13712 Z= 0.149 Angle : 0.699 12.296 18416 Z= 0.313 Chirality : 0.046 0.222 2116 Planarity : 0.004 0.039 2212 Dihedral : 12.383 135.820 2404 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.15 % Allowed : 17.28 % Favored : 80.56 % 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 (0.22), residues: 1564 helix: 1.62 (0.18), residues: 952 sheet: 0.52 (0.58), residues: 88 loop : -0.73 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 391 TYR 0.010 0.001 TYR D 404 PHE 0.007 0.001 PHE B 366 TRP 0.009 0.002 TRP B 176 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (13712) covalent geometry : angle 0.69928 / 0.31 (18416) hydrogen bonds : bond 0.05051 / 3.24 ( 725) hydrogen bonds : angle 3.71064 / 2.69 ( 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 171 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.497 Fit side-chains REVERT: A 382 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7596 (mmm160) REVERT: A 414 LEU cc_start: 0.4667 (OUTLIER) cc_final: 0.4278 (tm) REVERT: B 273 ARG cc_start: 0.8024 (mtt-85) cc_final: 0.7814 (mtt90) REVERT: C 382 ARG cc_start: 0.7889 (mmm160) cc_final: 0.7680 (mmm160) REVERT: D 414 LEU cc_start: 0.4787 (OUTLIER) cc_final: 0.4358 (tm) outliers start: 29 outliers final: 21 residues processed: 165 average time/residue: 0.5922 time to fit residues: 106.9755 Evaluate side-chains 162 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 46 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 43 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 148 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 87 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 150 optimal weight: 0.0670 chunk 126 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.186154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.141522 restraints weight = 12880.856| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 1.40 r_work: 0.3129 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13712 Z= 0.114 Angle : 0.648 11.395 18416 Z= 0.286 Chirality : 0.043 0.228 2116 Planarity : 0.004 0.037 2212 Dihedral : 11.464 129.816 2404 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.08 % Allowed : 17.73 % 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: 1.41 (0.23), residues: 1564 helix: 1.82 (0.18), residues: 956 sheet: 0.54 (0.57), residues: 88 loop : -0.65 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.016 0.001 TYR C 199 PHE 0.006 0.001 PHE A 366 TRP 0.005 0.001 TRP D 176 HIS 0.001 0.000 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13712) covalent geometry : angle 0.64831 / 0.29 (18416) hydrogen bonds : bond 0.04037 / 2.58 ( 725) hydrogen bonds : angle 3.62581 / 2.62 ( 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 168 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.489 Fit side-chains REVERT: A 243 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7951 (mp) REVERT: A 312 ASP cc_start: 0.7744 (m-30) cc_final: 0.7494 (t0) REVERT: A 414 LEU cc_start: 0.4665 (OUTLIER) cc_final: 0.4440 (tm) REVERT: B 243 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7898 (mp) REVERT: B 274 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7637 (mp0) REVERT: B 388 ASP cc_start: 0.8066 (t70) cc_final: 0.7679 (t0) REVERT: C 243 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7910 (mp) REVERT: C 312 ASP cc_start: 0.7734 (m-30) cc_final: 0.7486 (t0) REVERT: C 388 ASP cc_start: 0.8058 (t70) cc_final: 0.7682 (t0) REVERT: D 243 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7938 (mp) REVERT: D 414 LEU cc_start: 0.4620 (OUTLIER) cc_final: 0.4381 (tm) outliers start: 28 outliers final: 14 residues processed: 163 average time/residue: 0.5503 time to fit residues: 98.9065 Evaluate side-chains 160 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.470 ------------------------------------------------------------------------------- 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 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 C residue 26 TYR 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 D residue 26 TYR Chi-restraints excluded: chain D residue 243 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 5 optimal weight: 0.0670 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 42 optimal weight: 0.0770 chunk 125 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 116 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.0570 chunk 11 optimal weight: 1.9990 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.187576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.148225 restraints weight = 12998.517| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.26 r_work: 0.3241 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13712 Z= 0.108 Angle : 0.641 11.785 18416 Z= 0.282 Chirality : 0.043 0.233 2116 Planarity : 0.004 0.036 2212 Dihedral : 10.710 120.646 2404 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.23 % Allowed : 17.21 % Favored : 80.56 % 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: 1.51 (0.23), residues: 1564 helix: 1.90 (0.18), residues: 956 sheet: 0.68 (0.57), residues: 88 loop : -0.63 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.018 0.001 TYR C 199 PHE 0.005 0.001 PHE A 366 TRP 0.004 0.001 TRP A 176 HIS 0.001 0.000 HIS A 316 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (13712) covalent geometry : angle 0.64126 / 0.28 (18416) hydrogen bonds : bond 0.03745 / 2.39 ( 725) hydrogen bonds : angle 3.53609 / 2.55 ( 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 184 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.505 Fit side-chains REVERT: A 311 ARG cc_start: 0.7769 (ttm170) cc_final: 0.7352 (ttm-80) REVERT: A 384 ARG cc_start: 0.8486 (mtm-85) cc_final: 0.8248 (mtp85) REVERT: B 243 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8055 (mp) REVERT: B 274 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7811 (mp0) REVERT: B 384 ARG cc_start: 0.8458 (mtm-85) cc_final: 0.8240 (mtp85) REVERT: C 243 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8070 (mp) REVERT: D 243 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8089 (mp) REVERT: D 384 ARG cc_start: 0.8476 (mtm-85) cc_final: 0.8260 (mtp85) outliers start: 30 outliers final: 14 residues processed: 175 average time/residue: 0.5998 time to fit residues: 115.0290 Evaluate side-chains 156 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 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 A residue 346 VAL 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 C residue 26 TYR 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 D residue 26 TYR Chi-restraints excluded: chain D residue 243 LEU 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: 0.5980 chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 121 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.185959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.143540 restraints weight = 12897.070| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.38 r_work: 0.3096 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2092 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= 0.126 Angle : 0.684 12.589 18416 Z= 0.303 Chirality : 0.044 0.230 2116 Planarity : 0.004 0.037 2212 Dihedral : 10.943 123.963 2404 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.56 % Allowed : 18.55 % Favored : 79.90 % 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: 1.58 (0.23), residues: 1564 helix: 1.97 (0.18), residues: 960 sheet: 0.66 (0.57), residues: 88 loop : -0.66 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 273 TYR 0.013 0.001 TYR A 199 PHE 0.006 0.001 PHE D 366 TRP 0.007 0.001 TRP D 176 HIS 0.002 0.001 HIS D 292 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (13712) covalent geometry : angle 0.68406 / 0.30 (18416) hydrogen bonds : bond 0.04240 / 2.72 ( 725) hydrogen bonds : angle 3.55974 / 2.57 ( 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 169 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.499 Fit side-chains REVERT: A 311 ARG cc_start: 0.7565 (ttm170) cc_final: 0.7096 (ttm-80) REVERT: A 384 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8184 (mtp85) REVERT: B 243 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7951 (mp) REVERT: B 274 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7618 (mp0) REVERT: C 243 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7957 (mp) REVERT: D 243 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7971 (mp) REVERT: D 384 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8186 (mtp85) outliers start: 21 outliers final: 15 residues processed: 164 average time/residue: 0.6241 time to fit residues: 111.4497 Evaluate side-chains 160 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 142 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 A residue 346 VAL 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 C residue 26 TYR 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 99 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 138 optimal weight: 0.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3964 r_free = 0.3964 target = 0.185173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.150886 restraints weight = 12935.607| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.13 r_work: 0.3237 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2128 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= 0.133 Angle : 0.697 12.759 18416 Z= 0.310 Chirality : 0.045 0.231 2116 Planarity : 0.004 0.037 2212 Dihedral : 11.384 132.370 2404 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.63 % Allowed : 18.47 % Favored : 79.90 % 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: 1.55 (0.23), residues: 1564 helix: 1.96 (0.18), residues: 956 sheet: 0.59 (0.56), residues: 88 loop : -0.65 (0.29), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.011 0.001 TYR D 199 PHE 0.007 0.001 PHE B 366 TRP 0.007 0.001 TRP B 176 HIS 0.002 0.001 HIS B 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 (13712) covalent geometry : angle 0.69677 / 0.31 (18416) hydrogen bonds : bond 0.04606 / 2.95 ( 725) hydrogen bonds : angle 3.60682 / 2.60 ( 2079) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3675.03 seconds wall clock time: 63 minutes 31.97 seconds (3811.97 seconds total)