Starting phenix.real_space_refine on Fri Dec 27 22:34:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1d_61972/12_2024/9k1d_61972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1d_61972/12_2024/9k1d_61972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k1d_61972/12_2024/9k1d_61972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1d_61972/12_2024/9k1d_61972.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1d_61972/12_2024/9k1d_61972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1d_61972/12_2024/9k1d_61972.cif" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4464 2.51 5 N 1151 2.21 5 O 1229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6892 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2130 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 14, 'TRANS': 251} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1756 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2513 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 322} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 347 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 4, 'TRANS': 40} Chain: "R" Number of atoms: 146 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 146 Unusual residues: {'BUA': 1, 'CLR': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 5.11, per 1000 atoms: 0.74 Number of scatterers: 6892 At special positions: 0 Unit cell: (77.112, 99.603, 127.449, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1229 8.00 N 1151 7.00 C 4464 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 82 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 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: 1.86 Conformation dependent library (CDL) restraints added in 997.6 milliseconds 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1624 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 8 sheets defined 46.2% alpha, 17.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'R' and resid 4 through 38 removed outlier: 3.563A pdb=" N MET R 12 " --> pdb=" O SER R 8 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR R 20 " --> pdb=" O ILE R 16 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU R 22 " --> pdb=" O PHE R 18 " (cutoff:3.500A) Proline residue: R 23 - end of helix removed outlier: 3.862A pdb=" N ARG R 30 " --> pdb=" O LEU R 26 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA R 31 " --> pdb=" O LEU R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 61 removed outlier: 3.907A pdb=" N ILE R 46 " --> pdb=" O ALA R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 71 removed outlier: 3.632A pdb=" N LYS R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER R 71 " --> pdb=" O ILE R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 113 removed outlier: 3.557A pdb=" N ILE R 105 " --> pdb=" O ALA R 101 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL R 111 " --> pdb=" O ARG R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 113 through 119 Processing helix chain 'R' and resid 122 through 139 removed outlier: 3.975A pdb=" N GLY R 126 " --> pdb=" O ARG R 122 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA R 129 " --> pdb=" O TYR R 125 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 150 removed outlier: 3.595A pdb=" N GLN R 148 " --> pdb=" O VAL R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 169 through 187 Proline residue: R 178 - end of helix removed outlier: 3.745A pdb=" N LEU R 181 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU R 182 " --> pdb=" O PRO R 178 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU R 187 " --> pdb=" O LEU R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 208 removed outlier: 3.517A pdb=" N SER R 208 " --> pdb=" O TRP R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 235 removed outlier: 3.957A pdb=" N PHE R 235 " --> pdb=" O PHE R 231 " (cutoff:3.500A) Processing helix chain 'R' and resid 235 through 249 removed outlier: 3.625A pdb=" N ASN R 239 " --> pdb=" O PHE R 235 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS R 242 " --> pdb=" O TYR R 238 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU R 243 " --> pdb=" O ASN R 239 " (cutoff:3.500A) Processing helix chain 'R' and resid 255 through 275 removed outlier: 3.516A pdb=" N LEU R 264 " --> pdb=" O VAL R 260 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN R 265 " --> pdb=" O PHE R 261 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA R 266 " --> pdb=" O SER R 262 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER R 267 " --> pdb=" O SER R 263 " (cutoff:3.500A) Proline residue: R 270 - end of helix Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.987A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.578A pdb=" N LYS A 46 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 226 through 230 removed outlier: 4.225A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 256 through 260 removed outlier: 3.845A pdb=" N THR A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 281 removed outlier: 3.545A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 327 through 352 removed outlier: 4.080A pdb=" N ASN A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 4.178A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N GLY A 40 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.635A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.981A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.794A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 160 removed outlier: 6.678A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.832A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 3.597A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.466A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 327 hydrogen bonds defined for protein. 948 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 2.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.36: 2196 1.36 - 1.48: 1744 1.48 - 1.61: 3006 1.61 - 1.74: 29 1.74 - 1.87: 76 Bond restraints: 7051 Sorted by residual: bond pdb=" C7 CLR R 403 " pdb=" C8 CLR R 403 " ideal model delta sigma weight residual 1.525 1.870 -0.345 2.00e-02 2.50e+03 2.97e+02 bond pdb=" C7 CLR R 405 " pdb=" C8 CLR R 405 " ideal model delta sigma weight residual 1.525 1.869 -0.344 2.00e-02 2.50e+03 2.96e+02 bond pdb=" C7 CLR R 402 " pdb=" C8 CLR R 402 " ideal model delta sigma weight residual 1.525 1.868 -0.343 2.00e-02 2.50e+03 2.94e+02 bond pdb=" C7 CLR R 404 " pdb=" C8 CLR R 404 " ideal model delta sigma weight residual 1.525 1.868 -0.343 2.00e-02 2.50e+03 2.94e+02 bond pdb=" C7 CLR R 406 " pdb=" C8 CLR R 406 " ideal model delta sigma weight residual 1.525 1.868 -0.343 2.00e-02 2.50e+03 2.93e+02 ... (remaining 7046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 9399 2.30 - 4.60: 139 4.60 - 6.90: 46 6.90 - 9.20: 8 9.20 - 11.50: 1 Bond angle restraints: 9593 Sorted by residual: angle pdb=" CB MET A 53 " pdb=" CG MET A 53 " pdb=" SD MET A 53 " ideal model delta sigma weight residual 112.70 124.20 -11.50 3.00e+00 1.11e-01 1.47e+01 angle pdb=" C14 CLR R 402 " pdb=" C13 CLR R 402 " pdb=" C18 CLR R 402 " ideal model delta sigma weight residual 112.24 103.76 8.48 3.00e+00 1.11e-01 8.00e+00 angle pdb=" C14 CLR R 403 " pdb=" C13 CLR R 403 " pdb=" C18 CLR R 403 " ideal model delta sigma weight residual 112.24 103.92 8.32 3.00e+00 1.11e-01 7.70e+00 angle pdb=" CA CYS B 121 " pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " ideal model delta sigma weight residual 114.40 120.78 -6.38 2.30e+00 1.89e-01 7.69e+00 angle pdb=" C12 CLR R 405 " pdb=" C13 CLR R 405 " pdb=" C14 CLR R 405 " ideal model delta sigma weight residual 106.64 114.49 -7.85 3.00e+00 1.11e-01 6.84e+00 ... (remaining 9588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 3754 17.93 - 35.87: 499 35.87 - 53.80: 130 53.80 - 71.74: 24 71.74 - 89.67: 7 Dihedral angle restraints: 4414 sinusoidal: 1911 harmonic: 2503 Sorted by residual: dihedral pdb=" CB CYS R 82 " pdb=" SG CYS R 82 " pdb=" SG CYS R 164 " pdb=" CB CYS R 164 " ideal model delta sinusoidal sigma weight residual 93.00 172.34 -79.34 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB GLU A 275 " pdb=" CG GLU A 275 " pdb=" CD GLU A 275 " pdb=" OE1 GLU A 275 " ideal model delta sinusoidal sigma weight residual 0.00 89.67 -89.67 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG B 137 " pdb=" CD ARG B 137 " pdb=" NE ARG B 137 " pdb=" CZ ARG B 137 " ideal model delta sinusoidal sigma weight residual -180.00 -137.42 -42.58 2 1.50e+01 4.44e-03 9.77e+00 ... (remaining 4411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 1095 0.163 - 0.325: 12 0.325 - 0.488: 4 0.488 - 0.650: 0 0.650 - 0.813: 5 Chirality restraints: 1116 Sorted by residual: chirality pdb=" C13 CLR R 405 " pdb=" C12 CLR R 405 " pdb=" C14 CLR R 405 " pdb=" C17 CLR R 405 " both_signs ideal model delta sigma weight residual False -2.93 -2.12 -0.81 2.00e-01 2.50e+01 1.65e+01 chirality pdb=" C13 CLR R 406 " pdb=" C12 CLR R 406 " pdb=" C14 CLR R 406 " pdb=" C17 CLR R 406 " both_signs ideal model delta sigma weight residual False -2.93 -2.12 -0.81 2.00e-01 2.50e+01 1.63e+01 chirality pdb=" C13 CLR R 404 " pdb=" C12 CLR R 404 " pdb=" C14 CLR R 404 " pdb=" C17 CLR R 404 " both_signs ideal model delta sigma weight residual False -2.93 -2.14 -0.79 2.00e-01 2.50e+01 1.55e+01 ... (remaining 1113 not shown) Planarity restraints: 1173 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 87 " -0.006 2.00e-02 2.50e+03 1.23e-02 1.50e+00 pdb=" C THR B 87 " 0.021 2.00e-02 2.50e+03 pdb=" O THR B 87 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN B 88 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA R 42 " 0.020 5.00e-02 4.00e+02 3.02e-02 1.46e+00 pdb=" N PRO R 43 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO R 43 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO R 43 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " 0.006 2.00e-02 2.50e+03 1.18e-02 1.40e+00 pdb=" C THR B 196 " -0.020 2.00e-02 2.50e+03 pdb=" O THR B 196 " 0.008 2.00e-02 2.50e+03 pdb=" N ARG B 197 " 0.007 2.00e-02 2.50e+03 ... (remaining 1170 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 313 2.73 - 3.27: 6723 3.27 - 3.81: 11339 3.81 - 4.36: 13464 4.36 - 4.90: 23625 Nonbonded interactions: 55464 Sorted by model distance: nonbonded pdb=" OD1 ASP B 153 " pdb=" N ASP B 154 " model vdw 2.183 3.120 nonbonded pdb=" OG1 THR B 159 " pdb=" NE1 TRP B 169 " model vdw 2.259 3.120 nonbonded pdb=" ND2 ASN B 230 " pdb=" OD1 ASP B 246 " model vdw 2.278 3.120 nonbonded pdb=" OG1 THR B 102 " pdb=" O SER B 147 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.296 3.040 ... (remaining 55459 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.210 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.940 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.020 0.345 7051 Z= 1.344 Angle : 0.718 11.504 9593 Z= 0.308 Chirality : 0.072 0.813 1116 Planarity : 0.003 0.030 1173 Dihedral : 16.966 89.670 2784 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.27 % Allowed : 29.20 % Favored : 70.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.30), residues: 844 helix: 1.50 (0.28), residues: 368 sheet: 0.96 (0.40), residues: 180 loop : -0.83 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 169 HIS 0.005 0.000 HIS A 188 PHE 0.012 0.001 PHE A 189 TYR 0.005 0.001 TYR R 14 ARG 0.007 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 1.624 Fit side-chains REVERT: R 73 PHE cc_start: 0.6920 (m-10) cc_final: 0.6553 (m-10) outliers start: 2 outliers final: 0 residues processed: 129 average time/residue: 0.2000 time to fit residues: 35.1418 Evaluate side-chains 119 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 chunk 48 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 148 GLN A 331 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7051 Z= 0.209 Angle : 0.569 8.872 9593 Z= 0.282 Chirality : 0.043 0.279 1116 Planarity : 0.004 0.034 1173 Dihedral : 5.880 48.165 1254 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.68 % Allowed : 24.56 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.29), residues: 844 helix: 1.65 (0.28), residues: 367 sheet: 0.78 (0.39), residues: 186 loop : -0.70 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.018 0.001 PHE B 199 TYR 0.009 0.001 TYR A 302 ARG 0.006 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.847 Fit side-chains REVERT: R 73 PHE cc_start: 0.6959 (m-10) cc_final: 0.6596 (m-10) REVERT: A 20 ASP cc_start: 0.7941 (m-30) cc_final: 0.7707 (m-30) REVERT: B 61 MET cc_start: 0.8883 (ppp) cc_final: 0.8338 (ptm) REVERT: B 127 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8181 (mmtm) outliers start: 27 outliers final: 18 residues processed: 136 average time/residue: 0.1880 time to fit residues: 34.6343 Evaluate side-chains 131 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7051 Z= 0.155 Angle : 0.505 7.265 9593 Z= 0.251 Chirality : 0.041 0.193 1116 Planarity : 0.003 0.030 1173 Dihedral : 5.369 44.098 1254 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.50 % Allowed : 25.24 % Favored : 70.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.30), residues: 844 helix: 1.70 (0.28), residues: 367 sheet: 0.82 (0.39), residues: 186 loop : -0.75 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE A 191 TYR 0.009 0.001 TYR A 296 ARG 0.004 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.749 Fit side-chains REVERT: R 73 PHE cc_start: 0.6855 (m-10) cc_final: 0.6557 (m-10) REVERT: R 138 PHE cc_start: 0.6078 (m-10) cc_final: 0.5847 (m-10) REVERT: A 20 ASP cc_start: 0.7992 (m-30) cc_final: 0.7620 (m-30) REVERT: B 75 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8150 (mp10) REVERT: B 88 ASN cc_start: 0.8322 (OUTLIER) cc_final: 0.8090 (m-40) REVERT: B 127 LYS cc_start: 0.8356 (mmtp) cc_final: 0.8122 (mmtm) REVERT: B 156 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7443 (mt0) outliers start: 33 outliers final: 18 residues processed: 136 average time/residue: 0.1834 time to fit residues: 33.6908 Evaluate side-chains 134 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 39 optimal weight: 0.5980 chunk 8 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 50 optimal weight: 2.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 71 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7051 Z= 0.158 Angle : 0.520 10.775 9593 Z= 0.255 Chirality : 0.042 0.318 1116 Planarity : 0.003 0.033 1173 Dihedral : 5.289 46.229 1254 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.64 % Allowed : 26.33 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.30), residues: 844 helix: 1.75 (0.28), residues: 367 sheet: 0.82 (0.39), residues: 186 loop : -0.72 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.013 0.001 PHE B 199 TYR 0.008 0.001 TYR R 76 ARG 0.003 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.785 Fit side-chains REVERT: R 73 PHE cc_start: 0.6824 (m-10) cc_final: 0.6520 (m-10) REVERT: R 75 TRP cc_start: 0.7221 (m-90) cc_final: 0.6944 (m-10) REVERT: R 138 PHE cc_start: 0.6098 (m-10) cc_final: 0.5838 (m-10) REVERT: A 20 ASP cc_start: 0.8001 (m-30) cc_final: 0.7534 (m-30) REVERT: B 75 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8166 (mp10) REVERT: B 88 ASN cc_start: 0.8345 (OUTLIER) cc_final: 0.8077 (m-40) REVERT: B 127 LYS cc_start: 0.8354 (mmtp) cc_final: 0.8109 (mmtm) REVERT: B 156 GLN cc_start: 0.7980 (OUTLIER) cc_final: 0.7466 (mt0) outliers start: 34 outliers final: 21 residues processed: 140 average time/residue: 0.1851 time to fit residues: 35.2992 Evaluate side-chains 140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 187 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 7051 Z= 0.398 Angle : 0.638 10.109 9593 Z= 0.321 Chirality : 0.046 0.221 1116 Planarity : 0.004 0.033 1173 Dihedral : 5.698 49.958 1254 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.91 % Allowed : 26.06 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.30), residues: 844 helix: 1.59 (0.28), residues: 367 sheet: 0.34 (0.37), residues: 194 loop : -0.75 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS B 311 PHE 0.021 0.002 PHE B 199 TYR 0.015 0.001 TYR R 94 ARG 0.005 0.000 ARG R 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 119 time to evaluate : 0.779 Fit side-chains REVERT: R 73 PHE cc_start: 0.6776 (m-10) cc_final: 0.6485 (m-10) REVERT: R 75 TRP cc_start: 0.7269 (m-90) cc_final: 0.7060 (m-10) REVERT: A 20 ASP cc_start: 0.7961 (m-30) cc_final: 0.7359 (m-30) REVERT: B 75 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.7936 (mp10) REVERT: B 127 LYS cc_start: 0.8359 (mmtp) cc_final: 0.8066 (mmtm) outliers start: 36 outliers final: 27 residues processed: 143 average time/residue: 0.1961 time to fit residues: 36.9082 Evaluate side-chains 143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 19 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 242 HIS ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 7051 Z= 0.251 Angle : 0.585 9.453 9593 Z= 0.291 Chirality : 0.044 0.213 1116 Planarity : 0.003 0.039 1173 Dihedral : 5.564 54.876 1254 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.73 % Allowed : 26.33 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.30), residues: 844 helix: 1.62 (0.28), residues: 365 sheet: 0.17 (0.37), residues: 192 loop : -0.72 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 254 HIS 0.003 0.001 HIS B 91 PHE 0.015 0.001 PHE B 199 TYR 0.021 0.001 TYR A 296 ARG 0.004 0.000 ARG R 107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 118 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: R 73 PHE cc_start: 0.6838 (m-10) cc_final: 0.6539 (m-10) REVERT: R 75 TRP cc_start: 0.7200 (m-90) cc_final: 0.6983 (m-10) REVERT: A 20 ASP cc_start: 0.8002 (m-30) cc_final: 0.7350 (m-30) REVERT: A 229 ASP cc_start: 0.7701 (OUTLIER) cc_final: 0.7481 (t0) REVERT: B 58 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8684 (pt) REVERT: B 127 LYS cc_start: 0.8298 (mmtp) cc_final: 0.7795 (mmtt) REVERT: B 156 GLN cc_start: 0.8107 (OUTLIER) cc_final: 0.7693 (mt0) outliers start: 42 outliers final: 28 residues processed: 150 average time/residue: 0.1954 time to fit residues: 38.9190 Evaluate side-chains 142 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 111 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 16 ILE Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 58 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 79 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7051 Z= 0.184 Angle : 0.572 9.954 9593 Z= 0.282 Chirality : 0.043 0.190 1116 Planarity : 0.003 0.037 1173 Dihedral : 5.441 59.988 1254 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 4.77 % Allowed : 27.69 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.30), residues: 844 helix: 1.61 (0.29), residues: 364 sheet: 0.16 (0.37), residues: 192 loop : -0.71 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.016 0.001 TYR A 296 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.815 Fit side-chains REVERT: R 73 PHE cc_start: 0.6790 (m-10) cc_final: 0.6483 (m-10) REVERT: A 20 ASP cc_start: 0.8017 (m-30) cc_final: 0.7336 (m-30) REVERT: B 58 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8504 (pt) REVERT: B 88 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8040 (m-40) REVERT: B 127 LYS cc_start: 0.8247 (mmtp) cc_final: 0.7759 (mmtt) REVERT: B 156 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7627 (mt0) outliers start: 35 outliers final: 24 residues processed: 144 average time/residue: 0.1780 time to fit residues: 34.5522 Evaluate side-chains 142 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 198 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 0.0670 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 39 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 overall best weight: 0.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7051 Z= 0.200 Angle : 0.596 12.289 9593 Z= 0.292 Chirality : 0.044 0.293 1116 Planarity : 0.003 0.035 1173 Dihedral : 5.248 50.388 1254 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.77 % Allowed : 27.69 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.30), residues: 844 helix: 1.56 (0.28), residues: 366 sheet: 0.11 (0.37), residues: 192 loop : -0.76 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 254 HIS 0.003 0.001 HIS R 45 PHE 0.013 0.001 PHE A 189 TYR 0.015 0.001 TYR A 296 ARG 0.004 0.000 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.776 Fit side-chains REVERT: R 14 TYR cc_start: 0.7756 (m-80) cc_final: 0.7510 (m-80) REVERT: R 73 PHE cc_start: 0.6816 (m-10) cc_final: 0.6484 (m-10) REVERT: A 20 ASP cc_start: 0.7984 (m-30) cc_final: 0.7290 (m-30) REVERT: B 58 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8551 (pt) REVERT: B 88 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8040 (m-40) REVERT: B 127 LYS cc_start: 0.8202 (mmtp) cc_final: 0.7762 (mmtt) REVERT: B 156 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7627 (mt0) outliers start: 35 outliers final: 24 residues processed: 142 average time/residue: 0.1975 time to fit residues: 37.0848 Evaluate side-chains 141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 114 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7051 Z= 0.265 Angle : 0.635 11.692 9593 Z= 0.315 Chirality : 0.045 0.279 1116 Planarity : 0.004 0.044 1173 Dihedral : 5.162 35.549 1254 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.37 % Allowed : 28.38 % Favored : 67.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.30), residues: 844 helix: 1.56 (0.29), residues: 364 sheet: -0.00 (0.37), residues: 192 loop : -0.69 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.014 0.001 PHE R 138 TYR 0.014 0.001 TYR A 296 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.783 Fit side-chains REVERT: R 14 TYR cc_start: 0.7776 (m-80) cc_final: 0.7549 (m-80) REVERT: R 73 PHE cc_start: 0.6844 (m-10) cc_final: 0.6545 (m-10) REVERT: A 20 ASP cc_start: 0.7987 (m-30) cc_final: 0.7281 (m-30) REVERT: B 58 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8730 (pt) REVERT: B 88 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8025 (m-40) REVERT: B 127 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7810 (mmtt) REVERT: B 156 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7752 (mt0) outliers start: 32 outliers final: 28 residues processed: 142 average time/residue: 0.1819 time to fit residues: 34.6707 Evaluate side-chains 146 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7051 Z= 0.211 Angle : 0.640 13.665 9593 Z= 0.315 Chirality : 0.044 0.313 1116 Planarity : 0.004 0.051 1173 Dihedral : 5.045 34.352 1254 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 4.23 % Allowed : 28.92 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.30), residues: 844 helix: 1.55 (0.28), residues: 363 sheet: -0.06 (0.37), residues: 194 loop : -0.74 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 254 HIS 0.003 0.001 HIS R 45 PHE 0.013 0.001 PHE A 189 TYR 0.023 0.001 TYR A 296 ARG 0.011 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1688 Ramachandran restraints generated. 844 Oldfield, 0 Emsley, 844 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.815 Fit side-chains REVERT: R 73 PHE cc_start: 0.6906 (m-10) cc_final: 0.6588 (m-10) REVERT: A 20 ASP cc_start: 0.7989 (m-30) cc_final: 0.7276 (m-30) REVERT: B 58 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8645 (pt) REVERT: B 88 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8022 (m-40) REVERT: B 127 LYS cc_start: 0.8230 (mmtp) cc_final: 0.7791 (mmtt) REVERT: B 156 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7589 (mt0) outliers start: 31 outliers final: 25 residues processed: 138 average time/residue: 0.1929 time to fit residues: 35.6300 Evaluate side-chains 140 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 104 SER Chi-restraints excluded: chain R residue 177 LEU Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 305 CYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 58 ILE Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.0170 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123527 restraints weight = 8951.494| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 1.75 r_work: 0.3266 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7051 Z= 0.208 Angle : 0.638 13.450 9593 Z= 0.313 Chirality : 0.044 0.312 1116 Planarity : 0.004 0.050 1173 Dihedral : 4.965 34.691 1254 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.09 % Allowed : 29.47 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.30), residues: 844 helix: 1.55 (0.29), residues: 365 sheet: -0.11 (0.37), residues: 194 loop : -0.80 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP R 254 HIS 0.002 0.001 HIS A 188 PHE 0.015 0.001 PHE R 138 TYR 0.021 0.001 TYR A 296 ARG 0.011 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1823.64 seconds wall clock time: 34 minutes 50.08 seconds (2090.08 seconds total)