Starting phenix.real_space_refine on Sat Aug 23 00:46:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlj_36399/08_2025/8jlj_36399_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlj_36399/08_2025/8jlj_36399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jlj_36399/08_2025/8jlj_36399_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlj_36399/08_2025/8jlj_36399_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jlj_36399/08_2025/8jlj_36399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlj_36399/08_2025/8jlj_36399.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.120 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 63 5.16 5 C 5676 2.51 5 N 1525 2.21 5 O 1653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8918 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1928 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 1 Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2596 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2147 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1784 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.01, per 1000 atoms: 0.23 Number of scatterers: 8918 At special positions: 0 Unit cell: (90.95, 125.8, 128.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 63 16.00 O 1653 8.00 N 1525 7.00 C 5676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 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: 3.13 Conformation dependent library (CDL) restraints added in 208.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 13 sheets defined 38.8% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.610A pdb=" N GLN A 24 " --> pdb=" O GLU A 20 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYS A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASP A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 27 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 210 through 216 removed outlier: 3.903A pdb=" N GLN A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 215 " --> pdb=" O ILE A 212 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASN A 216 " --> pdb=" O GLN A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 260 through 270 removed outlier: 3.785A pdb=" N LEU A 264 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA A 270 " --> pdb=" O GLU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 283 removed outlier: 3.998A pdb=" N ALA A 283 " --> pdb=" O PRO A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 removed outlier: 3.593A pdb=" N PHE A 312 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 358 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.536A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'R' and resid 24 through 49 removed outlier: 4.023A pdb=" N ILE R 32 " --> pdb=" O LEU R 28 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE R 33 " --> pdb=" O MET R 29 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 37 " --> pdb=" O ILE R 33 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL R 38 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY R 39 " --> pdb=" O ALA R 35 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER R 48 " --> pdb=" O ILE R 44 " (cutoff:3.500A) Processing helix chain 'R' and resid 55 through 86 removed outlier: 3.696A pdb=" N TRP R 59 " --> pdb=" O THR R 55 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU R 60 " --> pdb=" O PRO R 56 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU R 61 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET R 76 " --> pdb=" O GLY R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 94 through 126 Processing helix chain 'R' and resid 129 through 134 Processing helix chain 'R' and resid 135 through 161 removed outlier: 3.849A pdb=" N VAL R 141 " --> pdb=" O SER R 137 " (cutoff:3.500A) Proline residue: R 150 - end of helix removed outlier: 3.642A pdb=" N TYR R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE R 155 " --> pdb=" O ALA R 151 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY R 156 " --> pdb=" O VAL R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 176 Processing helix chain 'R' and resid 186 through 198 Processing helix chain 'R' and resid 198 through 225 removed outlier: 3.977A pdb=" N VAL R 204 " --> pdb=" O ILE R 200 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET R 205 " --> pdb=" O PRO R 201 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU R 206 " --> pdb=" O GLY R 202 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA R 216 " --> pdb=" O ILE R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 275 removed outlier: 3.805A pdb=" N GLY R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) Proline residue: R 263 - end of helix removed outlier: 3.528A pdb=" N THR R 268 " --> pdb=" O PHE R 264 " (cutoff:3.500A) Proline residue: R 272 - end of helix Processing helix chain 'R' and resid 279 through 297 removed outlier: 3.918A pdb=" N PHE R 289 " --> pdb=" O ALA R 285 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY R 290 " --> pdb=" O LEU R 286 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR R 291 " --> pdb=" O TYR R 287 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU R 292 " --> pdb=" O TRP R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 302 Processing helix chain 'R' and resid 305 through 310 Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.500A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 3.941A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 removed outlier: 3.544A pdb=" N MET Y 21 " --> pdb=" O GLU Y 17 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU Y 22 " --> pdb=" O GLN Y 18 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN Y 24 " --> pdb=" O LYS Y 20 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 44 removed outlier: 3.711A pdb=" N ALA Y 35 " --> pdb=" O SER Y 31 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR Y 40 " --> pdb=" O ASP Y 36 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS Y 41 " --> pdb=" O LEU Y 37 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N GLU Y 42 " --> pdb=" O MET Y 38 " (cutoff:3.500A) Processing helix chain 'Y' and resid 45 through 48 removed outlier: 3.851A pdb=" N ASP Y 48 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 45 through 48' Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 3.644A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N VAL A 201 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE A 221 " --> pdb=" O ILE A 255 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N PHE A 257 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE A 223 " --> pdb=" O PHE A 257 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ASN A 259 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL A 225 " --> pdb=" O ASN A 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.761A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.161A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.087A 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: 6.925A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 6.580A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.065A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.861A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.067A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.533A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.984A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR S 94 " --> pdb=" O THR S 115 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU S 117 " --> pdb=" O ALA S 92 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA S 92 " --> pdb=" O LEU S 117 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 140 through 141 Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 148 removed outlier: 3.618A pdb=" N VAL S 147 " --> pdb=" O LYS S 244 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU S 246 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 194 through 195 removed outlier: 3.726A pdb=" N ILE S 189 " --> pdb=" O TRP S 176 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1137 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.18 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.36: 2902 1.36 - 1.54: 6050 1.54 - 1.73: 69 1.73 - 1.91: 93 1.91 - 2.10: 1 Bond restraints: 9115 Sorted by residual: bond pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 1.526 1.608 -0.082 1.37e-02 5.33e+03 3.59e+01 bond pdb=" N THR A 33 " pdb=" CA THR A 33 " ideal model delta sigma weight residual 1.453 1.530 -0.077 1.31e-02 5.83e+03 3.42e+01 bond pdb=" C VAL R 204 " pdb=" N MET R 205 " ideal model delta sigma weight residual 1.335 1.262 0.072 1.25e-02 6.40e+03 3.33e+01 bond pdb=" C SER R 79 " pdb=" O SER R 79 " ideal model delta sigma weight residual 1.236 1.169 0.068 1.18e-02 7.18e+03 3.29e+01 bond pdb=" N MET R 205 " pdb=" CA MET R 205 " ideal model delta sigma weight residual 1.459 1.392 0.067 1.20e-02 6.94e+03 3.11e+01 ... (remaining 9110 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 11917 2.56 - 5.13: 340 5.13 - 7.69: 77 7.69 - 10.25: 8 10.25 - 12.82: 3 Bond angle restraints: 12345 Sorted by residual: angle pdb=" N THR A 33 " pdb=" CA THR A 33 " pdb=" C THR A 33 " ideal model delta sigma weight residual 110.55 123.37 -12.82 1.35e+00 5.49e-01 9.01e+01 angle pdb=" N LEU A 360 " pdb=" CA LEU A 360 " pdb=" C LEU A 360 " ideal model delta sigma weight residual 114.12 103.86 10.26 1.39e+00 5.18e-01 5.45e+01 angle pdb=" N CYS R 260 " pdb=" CA CYS R 260 " pdb=" C CYS R 260 " ideal model delta sigma weight residual 113.01 121.35 -8.34 1.20e+00 6.94e-01 4.83e+01 angle pdb=" N THR R 83 " pdb=" CA THR R 83 " pdb=" C THR R 83 " ideal model delta sigma weight residual 111.28 104.31 6.97 1.09e+00 8.42e-01 4.09e+01 angle pdb=" N THR R 99 " pdb=" CA THR R 99 " pdb=" C THR R 99 " ideal model delta sigma weight residual 111.28 104.50 6.78 1.09e+00 8.42e-01 3.87e+01 ... (remaining 12340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 4936 17.85 - 35.69: 379 35.69 - 53.54: 64 53.54 - 71.38: 22 71.38 - 89.23: 7 Dihedral angle restraints: 5408 sinusoidal: 2121 harmonic: 3287 Sorted by residual: dihedral pdb=" C ASN R 40 " pdb=" N ASN R 40 " pdb=" CA ASN R 40 " pdb=" CB ASN R 40 " ideal model delta harmonic sigma weight residual -122.60 -135.35 12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" C THR A 33 " pdb=" N THR A 33 " pdb=" CA THR A 33 " pdb=" CB THR A 33 " ideal model delta harmonic sigma weight residual -122.00 -134.42 12.42 0 2.50e+00 1.60e-01 2.47e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 5405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1181 0.077 - 0.155: 160 0.155 - 0.232: 28 0.232 - 0.310: 6 0.310 - 0.387: 3 Chirality restraints: 1378 Sorted by residual: chirality pdb=" CB VAL R 208 " pdb=" CA VAL R 208 " pdb=" CG1 VAL R 208 " pdb=" CG2 VAL R 208 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.75e+00 chirality pdb=" CA ASN R 40 " pdb=" N ASN R 40 " pdb=" C ASN R 40 " pdb=" CB ASN R 40 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA THR A 33 " pdb=" N THR A 33 " pdb=" C THR A 33 " pdb=" CB THR A 33 " both_signs ideal model delta sigma weight residual False 2.53 2.17 0.36 2.00e-01 2.50e+01 3.16e+00 ... (remaining 1375 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 20 " 0.024 2.00e-02 2.50e+03 4.61e-02 2.13e+01 pdb=" C GLU A 20 " -0.080 2.00e-02 2.50e+03 pdb=" O GLU A 20 " 0.028 2.00e-02 2.50e+03 pdb=" N LYS A 21 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 251 " -0.022 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C GLY R 251 " 0.074 2.00e-02 2.50e+03 pdb=" O GLY R 251 " -0.028 2.00e-02 2.50e+03 pdb=" N ILE R 252 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 293 " 0.022 2.00e-02 2.50e+03 4.10e-02 1.68e+01 pdb=" C ASN R 293 " -0.071 2.00e-02 2.50e+03 pdb=" O ASN R 293 " 0.026 2.00e-02 2.50e+03 pdb=" N SER R 294 " 0.024 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.80: 2201 2.80 - 3.34: 8232 3.34 - 3.88: 14524 3.88 - 4.42: 17322 4.42 - 4.96: 30277 Nonbonded interactions: 72556 Sorted by model distance: nonbonded pdb=" OE1 GLU A 311 " pdb=" NH2 ARG A 314 " model vdw 2.256 3.120 nonbonded pdb=" ND2 ASN R 163 " pdb=" O PHE R 184 " model vdw 2.266 3.120 nonbonded pdb=" OG SER S 17 " pdb=" O MET S 83 " model vdw 2.324 3.040 nonbonded pdb=" OD1 ASP A 226 " pdb=" OG SER A 228 " model vdw 2.340 3.040 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP Y 48 " model vdw 2.361 3.040 ... (remaining 72551 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.480 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.008 0.082 9118 Z= 0.604 Angle : 0.997 12.817 12351 Z= 0.680 Chirality : 0.059 0.387 1378 Planarity : 0.006 0.061 1565 Dihedral : 13.597 89.229 3281 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.82 % Allowed : 3.09 % Favored : 96.08 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.26), residues: 1116 helix: -0.23 (0.28), residues: 376 sheet: 1.34 (0.35), residues: 262 loop : -1.19 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 310 TYR 0.018 0.001 TYR R 213 PHE 0.039 0.002 PHE R 304 TRP 0.033 0.002 TRP R 147 HIS 0.011 0.001 HIS A 324 Details of bonding type rmsd covalent geometry : bond 0.00823 ( 9115) covalent geometry : angle 0.99321 (12345) SS BOND : bond 0.00864 ( 3) SS BOND : angle 4.02418 ( 6) hydrogen bonds : bond 0.24832 ( 398) hydrogen bonds : angle 7.42060 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 169 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.8363 (pt0) cc_final: 0.8120 (pt0) REVERT: B 186 ASP cc_start: 0.7640 (p0) cc_final: 0.7246 (p0) REVERT: R 165 LYS cc_start: 0.6515 (mttm) cc_final: 0.6295 (ptmt) REVERT: R 195 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7238 (mtm) REVERT: S 7 SER cc_start: 0.7338 (t) cc_final: 0.7018 (p) REVERT: S 20 LEU cc_start: 0.7457 (mt) cc_final: 0.7238 (mp) REVERT: S 70 ILE cc_start: 0.8041 (pt) cc_final: 0.7616 (tt) REVERT: S 89 GLU cc_start: 0.6802 (tm-30) cc_final: 0.6414 (mp0) outliers start: 8 outliers final: 4 residues processed: 174 average time/residue: 0.0915 time to fit residues: 20.6774 Evaluate side-chains 129 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 124 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 195 MET Chi-restraints excluded: chain R residue 219 GLN Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 286 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.0470 overall best weight: 1.7282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 GLN A 197 HIS A 261 GLN B 75 GLN B 268 ASN B 293 ASN R 40 ASN S 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.160532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.127172 restraints weight = 8278.728| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.21 r_work: 0.2896 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9118 Z= 0.173 Angle : 0.660 8.897 12351 Z= 0.348 Chirality : 0.046 0.226 1378 Planarity : 0.005 0.045 1565 Dihedral : 5.622 68.773 1254 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.44 % Allowed : 8.56 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.13 (0.26), residues: 1116 helix: 1.01 (0.28), residues: 388 sheet: 1.15 (0.35), residues: 257 loop : -1.33 (0.27), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 225 TYR 0.026 0.002 TYR S 235 PHE 0.018 0.002 PHE B 234 TRP 0.013 0.002 TRP B 82 HIS 0.008 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9115) covalent geometry : angle 0.65901 (12345) SS BOND : bond 0.01131 ( 3) SS BOND : angle 1.98382 ( 6) hydrogen bonds : bond 0.06502 ( 398) hydrogen bonds : angle 5.03386 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.202 Fit side-chains REVERT: B 186 ASP cc_start: 0.8125 (p0) cc_final: 0.7317 (p0) REVERT: B 217 MET cc_start: 0.8624 (ppp) cc_final: 0.8134 (ppp) REVERT: R 81 VAL cc_start: 0.7578 (p) cc_final: 0.7334 (t) REVERT: R 217 LYS cc_start: 0.7921 (OUTLIER) cc_final: 0.7504 (mmtm) REVERT: S 89 GLU cc_start: 0.7713 (tm-30) cc_final: 0.6990 (mp0) outliers start: 14 outliers final: 9 residues processed: 148 average time/residue: 0.0878 time to fit residues: 17.4501 Evaluate side-chains 133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 85 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 29 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.158293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.125708 restraints weight = 7292.446| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 0.94 r_work: 0.2930 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9118 Z= 0.135 Angle : 0.567 11.023 12351 Z= 0.299 Chirality : 0.043 0.140 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.406 77.501 1244 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.86 % Allowed : 11.24 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.26), residues: 1116 helix: 1.54 (0.28), residues: 388 sheet: 1.23 (0.33), residues: 270 loop : -1.43 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 303 TYR 0.024 0.001 TYR S 235 PHE 0.014 0.001 PHE B 199 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 9115) covalent geometry : angle 0.56579 (12345) SS BOND : bond 0.00763 ( 3) SS BOND : angle 1.55851 ( 6) hydrogen bonds : bond 0.05825 ( 398) hydrogen bonds : angle 4.66097 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.317 Fit side-chains REVERT: A 247 ARG cc_start: 0.8186 (ptm160) cc_final: 0.7978 (ptm160) REVERT: B 186 ASP cc_start: 0.8264 (p0) cc_final: 0.7447 (p0) REVERT: B 217 MET cc_start: 0.8740 (ppp) cc_final: 0.8221 (ppp) REVERT: B 234 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.6884 (t80) REVERT: R 217 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7496 (mmtm) outliers start: 18 outliers final: 13 residues processed: 144 average time/residue: 0.0876 time to fit residues: 16.8405 Evaluate side-chains 142 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 127 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLU Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 45 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 108 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.158686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.125078 restraints weight = 7779.133| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.04 r_work: 0.2946 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9118 Z= 0.116 Angle : 0.529 9.038 12351 Z= 0.281 Chirality : 0.042 0.141 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.381 80.385 1244 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.75 % Allowed : 11.55 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.26), residues: 1116 helix: 1.91 (0.28), residues: 383 sheet: 1.11 (0.32), residues: 285 loop : -1.35 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 18 TYR 0.019 0.001 TYR S 235 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 9115) covalent geometry : angle 0.52804 (12345) SS BOND : bond 0.00733 ( 3) SS BOND : angle 1.62226 ( 6) hydrogen bonds : bond 0.04889 ( 398) hydrogen bonds : angle 4.39867 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.221 Fit side-chains REVERT: A 247 ARG cc_start: 0.8030 (ptm160) cc_final: 0.7792 (ptm160) REVERT: A 314 ARG cc_start: 0.7776 (ptp-170) cc_final: 0.7523 (ttp-170) REVERT: B 186 ASP cc_start: 0.8174 (p0) cc_final: 0.7357 (p0) REVERT: B 234 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.6961 (t80) REVERT: R 200 ILE cc_start: 0.8463 (mm) cc_final: 0.8096 (mt) REVERT: R 217 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7405 (mmtm) REVERT: S 235 TYR cc_start: 0.6427 (OUTLIER) cc_final: 0.5765 (t80) outliers start: 17 outliers final: 10 residues processed: 145 average time/residue: 0.0865 time to fit residues: 16.8879 Evaluate side-chains 143 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 82 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.153006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.117694 restraints weight = 8168.816| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.31 r_work: 0.2830 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9118 Z= 0.189 Angle : 0.652 10.737 12351 Z= 0.345 Chirality : 0.046 0.146 1378 Planarity : 0.005 0.053 1565 Dihedral : 5.833 85.489 1243 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.16 % Allowed : 14.02 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.52 (0.26), residues: 1116 helix: 1.68 (0.27), residues: 389 sheet: 1.23 (0.33), residues: 265 loop : -1.43 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 22 TYR 0.032 0.002 TYR S 235 PHE 0.019 0.002 PHE B 151 TRP 0.017 0.002 TRP B 82 HIS 0.006 0.002 HIS S 232 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 9115) covalent geometry : angle 0.64994 (12345) SS BOND : bond 0.01301 ( 3) SS BOND : angle 2.45197 ( 6) hydrogen bonds : bond 0.06712 ( 398) hydrogen bonds : angle 4.71731 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.314 Fit side-chains REVERT: A 277 ASP cc_start: 0.6704 (m-30) cc_final: 0.6414 (m-30) REVERT: B 186 ASP cc_start: 0.8435 (p0) cc_final: 0.7189 (p0) REVERT: B 234 PHE cc_start: 0.8807 (OUTLIER) cc_final: 0.6962 (t80) REVERT: R 81 VAL cc_start: 0.7679 (p) cc_final: 0.7466 (t) REVERT: R 200 ILE cc_start: 0.8555 (mm) cc_final: 0.8215 (mt) REVERT: R 217 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7451 (mmtm) REVERT: S 235 TYR cc_start: 0.6994 (OUTLIER) cc_final: 0.5894 (t80) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.0903 time to fit residues: 17.4681 Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 33 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 71 optimal weight: 30.0000 chunk 98 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.155199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.119454 restraints weight = 8142.195| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.35 r_work: 0.2861 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9118 Z= 0.135 Angle : 0.566 9.929 12351 Z= 0.299 Chirality : 0.043 0.144 1378 Planarity : 0.004 0.045 1565 Dihedral : 5.694 85.442 1243 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.27 % Allowed : 14.95 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.26), residues: 1116 helix: 1.82 (0.27), residues: 389 sheet: 1.17 (0.32), residues: 286 loop : -1.46 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.023 0.001 TYR S 235 PHE 0.014 0.001 PHE A 189 TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 9115) covalent geometry : angle 0.56435 (12345) SS BOND : bond 0.00878 ( 3) SS BOND : angle 1.82267 ( 6) hydrogen bonds : bond 0.05525 ( 398) hydrogen bonds : angle 4.53077 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.310 Fit side-chains REVERT: A 277 ASP cc_start: 0.6717 (m-30) cc_final: 0.6408 (m-30) REVERT: B 234 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.6968 (t80) REVERT: R 200 ILE cc_start: 0.8569 (mm) cc_final: 0.8240 (mt) REVERT: R 217 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7353 (mmtm) REVERT: S 7 SER cc_start: 0.7813 (t) cc_final: 0.7366 (p) REVERT: S 235 TYR cc_start: 0.6774 (OUTLIER) cc_final: 0.5919 (t80) outliers start: 22 outliers final: 17 residues processed: 138 average time/residue: 0.0890 time to fit residues: 16.6906 Evaluate side-chains 141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain R residue 252 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 96 optimal weight: 0.0870 chunk 15 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 106 optimal weight: 0.0030 chunk 11 optimal weight: 0.1980 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 89 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.3970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.160983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.128231 restraints weight = 8187.082| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.10 r_work: 0.2960 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9118 Z= 0.094 Angle : 0.480 8.210 12351 Z= 0.253 Chirality : 0.041 0.131 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.361 84.676 1243 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.34 % Allowed : 16.08 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.26), residues: 1116 helix: 2.22 (0.28), residues: 383 sheet: 1.20 (0.32), residues: 287 loop : -1.25 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG S 72 TYR 0.011 0.001 TYR S 190 PHE 0.012 0.001 PHE B 199 TRP 0.009 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00178 ( 9115) covalent geometry : angle 0.47905 (12345) SS BOND : bond 0.00452 ( 3) SS BOND : angle 1.16100 ( 6) hydrogen bonds : bond 0.03798 ( 398) hydrogen bonds : angle 4.16477 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.355 Fit side-chains REVERT: A 277 ASP cc_start: 0.6701 (m-30) cc_final: 0.6365 (m-30) REVERT: B 219 ARG cc_start: 0.8071 (mtm110) cc_final: 0.7749 (mmm160) REVERT: B 234 PHE cc_start: 0.8731 (OUTLIER) cc_final: 0.6931 (t80) REVERT: R 80 MET cc_start: 0.6947 (ttt) cc_final: 0.6641 (ttp) REVERT: R 119 ASP cc_start: 0.8918 (t70) cc_final: 0.8630 (t0) REVERT: R 200 ILE cc_start: 0.8522 (mm) cc_final: 0.8192 (mt) REVERT: R 217 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7256 (mmtm) REVERT: S 7 SER cc_start: 0.7717 (t) cc_final: 0.7256 (p) REVERT: S 235 TYR cc_start: 0.6295 (OUTLIER) cc_final: 0.5836 (t80) outliers start: 13 outliers final: 9 residues processed: 139 average time/residue: 0.0808 time to fit residues: 15.4648 Evaluate side-chains 139 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 127 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 0.7980 chunk 88 optimal weight: 0.3980 chunk 46 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.160440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.127525 restraints weight = 8064.898| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.06 r_work: 0.2933 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9118 Z= 0.102 Angle : 0.501 8.239 12351 Z= 0.263 Chirality : 0.042 0.136 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.394 86.413 1243 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.44 % Allowed : 16.19 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.94 (0.26), residues: 1116 helix: 2.22 (0.28), residues: 383 sheet: 1.15 (0.32), residues: 289 loop : -1.25 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 303 TYR 0.016 0.001 TYR S 235 PHE 0.012 0.001 PHE B 199 TRP 0.012 0.001 TRP R 261 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 9115) covalent geometry : angle 0.50038 (12345) SS BOND : bond 0.00681 ( 3) SS BOND : angle 1.49059 ( 6) hydrogen bonds : bond 0.04150 ( 398) hydrogen bonds : angle 4.17243 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.330 Fit side-chains REVERT: A 277 ASP cc_start: 0.6710 (m-30) cc_final: 0.6387 (m-30) REVERT: B 186 ASP cc_start: 0.8121 (p0) cc_final: 0.7332 (p0) REVERT: B 219 ARG cc_start: 0.8123 (mtm110) cc_final: 0.7786 (mmm160) REVERT: B 234 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.6977 (t80) REVERT: R 80 MET cc_start: 0.7049 (ttt) cc_final: 0.6705 (ttp) REVERT: R 200 ILE cc_start: 0.8537 (mm) cc_final: 0.8229 (mt) REVERT: R 217 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7319 (mmtm) REVERT: S 7 SER cc_start: 0.7768 (t) cc_final: 0.7360 (p) REVERT: S 235 TYR cc_start: 0.6461 (OUTLIER) cc_final: 0.5943 (t80) outliers start: 14 outliers final: 11 residues processed: 136 average time/residue: 0.0863 time to fit residues: 16.0241 Evaluate side-chains 143 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.0870 chunk 12 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 329 HIS B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.152812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.118360 restraints weight = 7985.044| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 1.26 r_work: 0.2835 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9118 Z= 0.186 Angle : 0.650 11.825 12351 Z= 0.342 Chirality : 0.046 0.148 1378 Planarity : 0.005 0.047 1565 Dihedral : 5.945 89.565 1243 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.86 % Allowed : 16.19 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.26), residues: 1116 helix: 1.85 (0.27), residues: 389 sheet: 1.01 (0.33), residues: 280 loop : -1.27 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 304 TYR 0.034 0.002 TYR S 235 PHE 0.018 0.002 PHE B 151 TRP 0.016 0.002 TRP B 82 HIS 0.007 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 9115) covalent geometry : angle 0.64838 (12345) SS BOND : bond 0.01254 ( 3) SS BOND : angle 2.43965 ( 6) hydrogen bonds : bond 0.06492 ( 398) hydrogen bonds : angle 4.62998 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.217 Fit side-chains REVERT: A 277 ASP cc_start: 0.6784 (m-30) cc_final: 0.6480 (m-30) REVERT: A 359 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8725 (mm-30) REVERT: B 186 ASP cc_start: 0.8418 (p0) cc_final: 0.7168 (p0) REVERT: B 234 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.6935 (t80) REVERT: R 200 ILE cc_start: 0.8652 (mm) cc_final: 0.8380 (mt) REVERT: R 217 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7358 (mmtm) REVERT: S 7 SER cc_start: 0.7891 (t) cc_final: 0.7466 (p) REVERT: S 235 TYR cc_start: 0.7151 (OUTLIER) cc_final: 0.6034 (t80) outliers start: 18 outliers final: 14 residues processed: 140 average time/residue: 0.0918 time to fit residues: 17.2133 Evaluate side-chains 145 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.156738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.123760 restraints weight = 8046.336| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.06 r_work: 0.2884 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9118 Z= 0.112 Angle : 0.531 10.054 12351 Z= 0.278 Chirality : 0.042 0.140 1378 Planarity : 0.004 0.041 1565 Dihedral : 5.654 88.332 1243 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.75 % Allowed : 16.80 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1116 helix: 2.14 (0.28), residues: 379 sheet: 1.17 (0.32), residues: 287 loop : -1.33 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.018 0.001 TYR S 235 PHE 0.013 0.001 PHE B 199 TRP 0.012 0.001 TRP R 261 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 9115) covalent geometry : angle 0.53021 (12345) SS BOND : bond 0.00733 ( 3) SS BOND : angle 1.47191 ( 6) hydrogen bonds : bond 0.04701 ( 398) hydrogen bonds : angle 4.35811 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2232 Ramachandran restraints generated. 1116 Oldfield, 0 Emsley, 1116 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.405 Fit side-chains REVERT: A 277 ASP cc_start: 0.6854 (m-30) cc_final: 0.6495 (m-30) REVERT: A 359 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8623 (mm-30) REVERT: B 234 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.6941 (t80) REVERT: R 200 ILE cc_start: 0.8626 (mm) cc_final: 0.8333 (mt) REVERT: R 217 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7301 (mmtm) REVERT: S 7 SER cc_start: 0.7808 (t) cc_final: 0.7449 (p) REVERT: S 235 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6091 (t80) outliers start: 17 outliers final: 14 residues processed: 144 average time/residue: 0.0856 time to fit residues: 16.6881 Evaluate side-chains 148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain R residue 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 137 ASP Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 183 GLN Chi-restraints excluded: chain S residue 210 THR Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 47 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 109 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.155241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.118947 restraints weight = 7368.630| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.05 r_work: 0.2880 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9118 Z= 0.139 Angle : 0.578 10.661 12351 Z= 0.303 Chirality : 0.044 0.143 1378 Planarity : 0.004 0.045 1565 Dihedral : 5.751 89.090 1243 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.86 % Allowed : 16.80 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.26), residues: 1116 helix: 2.10 (0.28), residues: 379 sheet: 1.09 (0.32), residues: 293 loop : -1.25 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 314 TYR 0.027 0.002 TYR S 235 PHE 0.014 0.002 PHE B 199 TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 9115) covalent geometry : angle 0.57672 (12345) SS BOND : bond 0.00984 ( 3) SS BOND : angle 2.01125 ( 6) hydrogen bonds : bond 0.05408 ( 398) hydrogen bonds : angle 4.43807 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1828.31 seconds wall clock time: 31 minutes 56.66 seconds (1916.66 seconds total)