Starting phenix.real_space_refine on Sat May 10 21:00:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k1d_61972/05_2025/9k1d_61972.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k1d_61972/05_2025/9k1d_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_61972/05_2025/9k1d_61972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k1d_61972/05_2025/9k1d_61972.map" model { file = "/net/cci-nas-00/data/ceres_data/9k1d_61972/05_2025/9k1d_61972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k1d_61972/05_2025/9k1d_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-5687/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: 4.65, per 1000 atoms: 0.67 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: 1.72 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.75 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: 2.01 Time building geometry restraints manager: 2.02 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: 6.020 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 18.280 Find NCS groups from input model: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.290 ------------------------------------------------------------------------------- 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 7053 Z= 0.997 Angle : 0.717 11.504 9597 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 Details of bonding type rmsd hydrogen bonds : bond 0.17346 ( 327) hydrogen bonds : angle 5.39912 ( 948) SS BOND : bond 0.00645 ( 2) SS BOND : angle 0.19827 ( 4) covalent geometry : bond 0.01995 ( 7051) covalent geometry : angle 0.71762 ( 9593) *********************** 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 : 0.738 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: 0.1939 time to fit residues: 33.3281 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 : 0.801 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.162586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.128601 restraints weight = 9180.737| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.87 r_work: 0.3321 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 7053 Z= 0.140 Angle : 0.569 8.872 9597 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 Details of bonding type rmsd hydrogen bonds : bond 0.03454 ( 327) hydrogen bonds : angle 4.11944 ( 948) SS BOND : bond 0.01418 ( 2) SS BOND : angle 0.39934 ( 4) covalent geometry : bond 0.00318 ( 7051) covalent geometry : angle 0.56913 ( 9593) *********************** 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 : 0.749 Fit side-chains REVERT: R 73 PHE cc_start: 0.6937 (m-10) cc_final: 0.6537 (m-10) REVERT: A 20 ASP cc_start: 0.7758 (m-30) cc_final: 0.7553 (m-30) REVERT: B 61 MET cc_start: 0.8655 (ppp) cc_final: 0.8147 (ptm) REVERT: B 127 LYS cc_start: 0.8406 (mmtp) cc_final: 0.8196 (mmtm) outliers start: 27 outliers final: 18 residues processed: 136 average time/residue: 0.1923 time to fit residues: 35.4248 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 : 0.825 ------------------------------------------------------------------------------- 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 51 optimal weight: 0.0770 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.160988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.127641 restraints weight = 9200.861| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.83 r_work: 0.3325 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7053 Z= 0.107 Angle : 0.506 7.562 9597 Z= 0.251 Chirality : 0.041 0.188 1116 Planarity : 0.003 0.029 1173 Dihedral : 5.394 43.664 1254 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.50 % Allowed : 25.38 % Favored : 70.12 % 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 0.014 0.001 PHE A 191 TYR 0.013 0.001 TYR R 76 ARG 0.003 0.000 ARG A 32 Details of bonding type rmsd hydrogen bonds : bond 0.03132 ( 327) hydrogen bonds : angle 3.93369 ( 948) SS BOND : bond 0.01102 ( 2) SS BOND : angle 0.25940 ( 4) covalent geometry : bond 0.00239 ( 7051) covalent geometry : angle 0.50577 ( 9593) *********************** 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 147 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 114 time to evaluate : 0.745 Fit side-chains REVERT: R 73 PHE cc_start: 0.6885 (m-10) cc_final: 0.6503 (m-10) REVERT: A 20 ASP cc_start: 0.8107 (m-30) cc_final: 0.7755 (m-30) REVERT: B 75 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8249 (mp10) REVERT: B 88 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (m-40) REVERT: B 127 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8252 (mmtm) REVERT: B 156 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7827 (mt0) outliers start: 33 outliers final: 18 residues processed: 135 average time/residue: 0.1728 time to fit residues: 31.5035 Evaluate side-chains 132 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 80 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119198 restraints weight = 9343.956| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 1.90 r_work: 0.3209 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 7053 Z= 0.230 Angle : 0.630 10.545 9597 Z= 0.316 Chirality : 0.046 0.259 1116 Planarity : 0.004 0.032 1173 Dihedral : 5.727 47.951 1254 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 5.73 % Allowed : 24.83 % Favored : 69.44 % 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: 0.76 (0.30), residues: 844 helix: 1.57 (0.28), residues: 367 sheet: 0.37 (0.37), residues: 194 loop : -0.74 (0.37), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS B 311 PHE 0.018 0.002 PHE B 199 TYR 0.015 0.001 TYR R 94 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 327) hydrogen bonds : angle 4.29782 ( 948) SS BOND : bond 0.02276 ( 2) SS BOND : angle 0.48140 ( 4) covalent geometry : bond 0.00551 ( 7051) covalent geometry : angle 0.63054 ( 9593) *********************** 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 167 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 125 time to evaluate : 0.738 Fit side-chains REVERT: R 73 PHE cc_start: 0.6923 (m-10) cc_final: 0.6596 (m-10) REVERT: R 75 TRP cc_start: 0.7302 (m-90) cc_final: 0.7008 (m-10) REVERT: R 138 PHE cc_start: 0.7166 (m-10) cc_final: 0.6629 (m-80) REVERT: A 20 ASP cc_start: 0.8105 (m-30) cc_final: 0.7588 (m-30) REVERT: B 75 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8075 (mp10) REVERT: B 127 LYS cc_start: 0.8495 (mmtp) cc_final: 0.8208 (mmtm) REVERT: B 156 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8110 (mt0) REVERT: B 307 VAL cc_start: 0.8785 (t) cc_final: 0.8504 (p) outliers start: 42 outliers final: 28 residues processed: 153 average time/residue: 0.1893 time to fit residues: 38.3393 Evaluate side-chains 146 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 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 294 ASN Chi-restraints excluded: chain A residue 295 THR 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 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 Chi-restraints excluded: chain C residue 37 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 53 optimal weight: 0.5980 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 12 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 14 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.122308 restraints weight = 9064.401| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.82 r_work: 0.3255 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7053 Z= 0.118 Angle : 0.549 8.122 9597 Z= 0.274 Chirality : 0.042 0.191 1116 Planarity : 0.003 0.034 1173 Dihedral : 5.425 51.313 1254 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.37 % Allowed : 27.15 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.80 (0.30), residues: 844 helix: 1.66 (0.28), residues: 367 sheet: 0.35 (0.38), residues: 192 loop : -0.77 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR A 296 ARG 0.004 0.000 ARG R 107 Details of bonding type rmsd hydrogen bonds : bond 0.03189 ( 327) hydrogen bonds : angle 4.04333 ( 948) SS BOND : bond 0.01231 ( 2) SS BOND : angle 0.19610 ( 4) covalent geometry : bond 0.00264 ( 7051) covalent geometry : angle 0.54958 ( 9593) *********************** 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 152 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: R 73 PHE cc_start: 0.6920 (m-10) cc_final: 0.6585 (m-10) REVERT: R 75 TRP cc_start: 0.7329 (m-90) cc_final: 0.6998 (m-10) REVERT: R 138 PHE cc_start: 0.6734 (m-10) cc_final: 0.6015 (m-10) REVERT: A 20 ASP cc_start: 0.8183 (m-30) cc_final: 0.7578 (m-30) REVERT: B 88 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8108 (m-40) REVERT: B 127 LYS cc_start: 0.8434 (mmtp) cc_final: 0.7891 (mmtt) REVERT: B 156 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7914 (mt0) REVERT: B 307 VAL cc_start: 0.8761 (t) cc_final: 0.8467 (p) outliers start: 32 outliers final: 20 residues processed: 143 average time/residue: 0.1843 time to fit residues: 35.2978 Evaluate side-chains 129 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 0.754 ------------------------------------------------------------------------------- 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 295 THR 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 79 LEU Chi-restraints excluded: chain B residue 88 ASN 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 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 52 optimal weight: 0.2980 chunk 50 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 41 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** A 304 GLN B 16 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.156652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.122501 restraints weight = 9102.582| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.83 r_work: 0.3260 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7053 Z= 0.121 Angle : 0.554 8.340 9597 Z= 0.276 Chirality : 0.042 0.190 1116 Planarity : 0.003 0.034 1173 Dihedral : 5.362 53.986 1254 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.18 % Allowed : 26.60 % Favored : 68.21 % 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: 0.79 (0.30), residues: 844 helix: 1.68 (0.28), residues: 367 sheet: 0.29 (0.38), residues: 192 loop : -0.77 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 254 HIS 0.003 0.001 HIS B 142 PHE 0.013 0.001 PHE A 189 TYR 0.014 0.001 TYR A 296 ARG 0.004 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 327) hydrogen bonds : angle 4.00398 ( 948) SS BOND : bond 0.01295 ( 2) SS BOND : angle 0.25691 ( 4) covalent geometry : bond 0.00277 ( 7051) covalent geometry : angle 0.55391 ( 9593) *********************** 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 155 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 117 time to evaluate : 0.767 Fit side-chains REVERT: R 73 PHE cc_start: 0.6835 (m-10) cc_final: 0.6512 (m-10) REVERT: R 75 TRP cc_start: 0.7313 (m-90) cc_final: 0.7020 (m-10) REVERT: R 138 PHE cc_start: 0.6672 (m-10) cc_final: 0.6195 (m-80) REVERT: A 20 ASP cc_start: 0.8157 (m-30) cc_final: 0.7521 (m-30) REVERT: B 58 ILE cc_start: 0.8836 (OUTLIER) cc_final: 0.8395 (pt) REVERT: B 75 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8661 (mm-40) REVERT: B 88 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8128 (m-40) REVERT: B 127 LYS cc_start: 0.8407 (mmtp) cc_final: 0.7873 (mmtt) REVERT: B 156 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7879 (mt0) REVERT: B 307 VAL cc_start: 0.8782 (t) cc_final: 0.8486 (p) outliers start: 38 outliers final: 26 residues processed: 143 average time/residue: 0.1856 time to fit residues: 35.1872 Evaluate side-chains 141 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU 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 295 THR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain B residue 16 ASN 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 75 GLN 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.156243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123283 restraints weight = 9055.688| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.74 r_work: 0.3274 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7053 Z= 0.160 Angle : 0.602 11.048 9597 Z= 0.296 Chirality : 0.044 0.291 1116 Planarity : 0.003 0.036 1173 Dihedral : 5.463 58.134 1254 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.87 % Allowed : 26.60 % 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: 0.74 (0.30), residues: 844 helix: 1.64 (0.28), residues: 367 sheet: 0.20 (0.37), residues: 192 loop : -0.76 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 254 HIS 0.003 0.001 HIS A 188 PHE 0.013 0.001 PHE A 189 TYR 0.013 0.001 TYR R 94 ARG 0.010 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03332 ( 327) hydrogen bonds : angle 4.08055 ( 948) SS BOND : bond 0.01568 ( 2) SS BOND : angle 0.36514 ( 4) covalent geometry : bond 0.00379 ( 7051) covalent geometry : angle 0.60189 ( 9593) *********************** 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: 43 poor density : 111 time to evaluate : 0.818 Fit side-chains REVERT: R 73 PHE cc_start: 0.6811 (m-10) cc_final: 0.6542 (m-10) REVERT: R 75 TRP cc_start: 0.7249 (m-90) cc_final: 0.6956 (m-10) REVERT: R 138 PHE cc_start: 0.6721 (m-10) cc_final: 0.6291 (m-80) REVERT: A 20 ASP cc_start: 0.8184 (m-30) cc_final: 0.7537 (m-30) REVERT: B 58 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8616 (pt) REVERT: B 75 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.8666 (mm-40) REVERT: B 127 LYS cc_start: 0.8434 (mmtp) cc_final: 0.7902 (mmtt) REVERT: B 156 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7881 (mt0) REVERT: B 307 VAL cc_start: 0.8810 (t) cc_final: 0.8519 (p) outliers start: 43 outliers final: 30 residues processed: 141 average time/residue: 0.1875 time to fit residues: 35.1172 Evaluate side-chains 143 residues out of total 740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU 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 295 THR 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 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 C residue 37 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 68.2579 > 50: distance: 19 - 35: 14.107 distance: 32 - 35: 11.576 distance: 35 - 36: 26.530 distance: 36 - 37: 9.211 distance: 36 - 39: 27.118 distance: 37 - 38: 22.742 distance: 37 - 46: 13.959 distance: 38 - 69: 35.814 distance: 39 - 40: 10.344 distance: 40 - 41: 6.385 distance: 40 - 42: 4.654 distance: 41 - 43: 13.271 distance: 42 - 44: 10.464 distance: 43 - 45: 4.748 distance: 44 - 45: 6.287 distance: 46 - 47: 11.643 distance: 46 - 52: 29.630 distance: 47 - 48: 12.987 distance: 47 - 50: 15.849 distance: 48 - 49: 10.470 distance: 48 - 53: 18.087 distance: 49 - 81: 11.384 distance: 50 - 51: 35.118 distance: 51 - 52: 11.151 distance: 54 - 55: 7.116 distance: 55 - 56: 24.204 distance: 55 - 60: 9.294 distance: 56 - 90: 17.521 distance: 57 - 58: 18.493 distance: 57 - 59: 21.278 distance: 60 - 61: 24.314 distance: 61 - 62: 6.881 distance: 61 - 64: 21.181 distance: 62 - 63: 17.643 distance: 62 - 69: 10.942 distance: 64 - 65: 23.578 distance: 65 - 66: 17.562 distance: 66 - 67: 29.716 distance: 66 - 68: 11.894 distance: 69 - 70: 13.358 distance: 70 - 71: 23.139 distance: 70 - 73: 9.732 distance: 71 - 81: 35.376 distance: 74 - 75: 13.186 distance: 74 - 76: 10.731 distance: 75 - 77: 12.682 distance: 76 - 78: 11.115 distance: 77 - 79: 13.716 distance: 78 - 79: 12.101 distance: 79 - 80: 7.097 distance: 81 - 82: 21.494 distance: 82 - 83: 14.976 distance: 82 - 85: 17.119 distance: 83 - 90: 3.965 distance: 85 - 86: 21.517 distance: 86 - 87: 21.400 distance: 87 - 88: 9.438 distance: 88 - 89: 35.602 distance: 90 - 91: 30.770 distance: 91 - 92: 23.901 distance: 91 - 94: 11.810 distance: 92 - 93: 16.863 distance: 92 - 98: 33.716 distance: 94 - 95: 13.082 distance: 95 - 96: 16.493 distance: 95 - 97: 35.330 distance: 98 - 99: 22.371 distance: 99 - 100: 10.707 distance: 99 - 102: 8.016 distance: 100 - 101: 22.334 distance: 100 - 104: 11.661 distance: 102 - 103: 7.563 distance: 104 - 105: 14.024 distance: 105 - 106: 4.919 distance: 105 - 108: 16.644 distance: 106 - 107: 11.639 distance: 106 - 115: 11.471 distance: 108 - 109: 11.719 distance: 109 - 110: 11.770 distance: 110 - 111: 13.013 distance: 115 - 116: 8.024 distance: 116 - 117: 4.659 distance: 116 - 119: 6.103 distance: 117 - 118: 15.392 distance: 119 - 120: 8.862 distance: 120 - 121: 6.797 distance: 121 - 122: 5.988 distance: 122 - 123: 10.459 distance: 123 - 124: 7.867 distance: 123 - 125: 11.499