Starting phenix.real_space_refine on Mon May 12 08:00:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlj_36399/05_2025/8jlj_36399_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlj_36399/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jlj_36399/05_2025/8jlj_36399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlj_36399/05_2025/8jlj_36399.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlj_36399/05_2025/8jlj_36399_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlj_36399/05_2025/8jlj_36399_neut.cif" } resolution = 3.1 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= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 5.53, per 1000 atoms: 0.62 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.21 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: 2.38 Time building geometry restraints manager: 2.78 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: 0.800 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: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 23.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.060 ------------------------------------------------------------------------------- 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 : 8.09 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 (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: -0.40 (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 TRP 0.033 0.002 TRP R 147 HIS 0.011 0.001 HIS A 324 PHE 0.039 0.002 PHE R 304 TYR 0.018 0.001 TYR R 213 ARG 0.003 0.000 ARG R 310 Details of bonding type rmsd hydrogen bonds : bond 0.24832 ( 398) hydrogen bonds : angle 7.42060 ( 1137) SS BOND : bond 0.00864 ( 3) SS BOND : angle 4.02418 ( 6) covalent geometry : bond 0.00823 ( 9115) covalent geometry : angle 0.99321 (12345) *********************** 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 : 0.985 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: 0.7245 (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: 0.2592 time to fit residues: 58.4829 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 : 0.925 ------------------------------------------------------------------------------- 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 93 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 = 0.3690 r_free = 0.3690 target = 0.162044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.129436 restraints weight = 7880.350| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.04 r_work: 0.2947 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9118 Z= 0.159 Angle : 0.639 8.513 12351 Z= 0.336 Chirality : 0.045 0.230 1378 Planarity : 0.005 0.040 1565 Dihedral : 5.573 69.174 1254 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.44 % Allowed : 8.45 % Favored : 90.10 % 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: 0.17 (0.26), residues: 1116 helix: 1.09 (0.28), residues: 382 sheet: 1.10 (0.35), residues: 258 loop : -1.29 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 82 HIS 0.008 0.002 HIS B 225 PHE 0.018 0.002 PHE A 189 TYR 0.022 0.002 TYR S 235 ARG 0.003 0.001 ARG R 225 Details of bonding type rmsd hydrogen bonds : bond 0.06085 ( 398) hydrogen bonds : angle 4.96991 ( 1137) SS BOND : bond 0.01087 ( 3) SS BOND : angle 1.92939 ( 6) covalent geometry : bond 0.00333 ( 9115) covalent geometry : angle 0.63795 (12345) *********************** 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 154 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.999 Fit side-chains REVERT: B 186 ASP cc_start: 0.8058 (p0) cc_final: 0.7242 (p0) REVERT: B 217 MET cc_start: 0.8544 (ppp) cc_final: 0.7974 (ppp) REVERT: R 165 LYS cc_start: 0.6691 (mttm) cc_final: 0.6264 (ptpt) REVERT: R 217 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7456 (mmtm) REVERT: S 89 GLU cc_start: 0.7506 (tm-30) cc_final: 0.6867 (mp0) outliers start: 14 outliers final: 10 residues processed: 146 average time/residue: 0.2561 time to fit residues: 49.4973 Evaluate side-chains 131 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 2 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 86 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.158354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.125240 restraints weight = 7768.631| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.05 r_work: 0.2904 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9118 Z= 0.133 Angle : 0.563 11.806 12351 Z= 0.296 Chirality : 0.043 0.139 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.353 77.381 1244 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.86 % Allowed : 11.13 % Favored : 87.01 % 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: 0.50 (0.26), residues: 1116 helix: 1.65 (0.28), residues: 382 sheet: 1.18 (0.33), residues: 269 loop : -1.38 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.001 PHE B 199 TYR 0.024 0.001 TYR S 235 ARG 0.005 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.05799 ( 398) hydrogen bonds : angle 4.62286 ( 1137) SS BOND : bond 0.00740 ( 3) SS BOND : angle 1.52679 ( 6) covalent geometry : bond 0.00277 ( 9115) covalent geometry : angle 0.56173 (12345) *********************** 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 148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 0.899 Fit side-chains REVERT: B 186 ASP cc_start: 0.8170 (p0) cc_final: 0.7354 (p0) REVERT: B 217 MET cc_start: 0.8617 (ppp) cc_final: 0.8089 (ppp) REVERT: B 234 PHE cc_start: 0.8759 (OUTLIER) cc_final: 0.6865 (t80) REVERT: R 157 MET cc_start: 0.7585 (ttp) cc_final: 0.7325 (ttp) REVERT: R 165 LYS cc_start: 0.6752 (mttm) cc_final: 0.6508 (mmtt) REVERT: R 217 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7487 (mmtm) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.2333 time to fit residues: 44.2572 Evaluate side-chains 139 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 47 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.0670 chunk 88 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 107 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.157745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.124046 restraints weight = 7760.600| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.12 r_work: 0.2924 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9118 Z= 0.126 Angle : 0.552 9.345 12351 Z= 0.292 Chirality : 0.043 0.145 1378 Planarity : 0.004 0.040 1565 Dihedral : 5.452 80.657 1244 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.75 % Allowed : 12.06 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.60 (0.26), residues: 1116 helix: 1.79 (0.28), residues: 389 sheet: 1.14 (0.32), residues: 280 loop : -1.42 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.005 0.001 HIS S 232 PHE 0.014 0.001 PHE B 199 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 398) hydrogen bonds : angle 4.47162 ( 1137) SS BOND : bond 0.00837 ( 3) SS BOND : angle 1.62791 ( 6) covalent geometry : bond 0.00260 ( 9115) covalent geometry : angle 0.55129 (12345) *********************** 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 151 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 1.011 Fit side-chains REVERT: A 314 ARG cc_start: 0.7815 (ptp-170) cc_final: 0.7571 (ttp-170) REVERT: B 186 ASP cc_start: 0.8261 (p0) cc_final: 0.7431 (p0) REVERT: B 234 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.6963 (t80) REVERT: R 200 ILE cc_start: 0.8468 (mm) cc_final: 0.8108 (mt) REVERT: R 217 LYS cc_start: 0.7803 (OUTLIER) cc_final: 0.7468 (mmtm) REVERT: S 235 TYR cc_start: 0.6489 (OUTLIER) cc_final: 0.5747 (t80) outliers start: 17 outliers final: 10 residues processed: 144 average time/residue: 0.2322 time to fit residues: 45.0341 Evaluate side-chains 138 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 65 THR Chi-restraints excluded: chain B residue 143 THR 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 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 235 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 0.0980 chunk 35 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 19 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.126858 restraints weight = 7427.662| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 0.97 r_work: 0.2963 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3223 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= 0.104 Angle : 0.502 8.622 12351 Z= 0.265 Chirality : 0.041 0.135 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.332 81.802 1244 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.65 % Allowed : 13.61 % Favored : 84.74 % 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 (0.26), residues: 1116 helix: 2.04 (0.28), residues: 383 sheet: 1.18 (0.32), residues: 283 loop : -1.31 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.015 0.001 TYR S 235 ARG 0.001 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04421 ( 398) hydrogen bonds : angle 4.29949 ( 1137) SS BOND : bond 0.00648 ( 3) SS BOND : angle 1.55377 ( 6) covalent geometry : bond 0.00203 ( 9115) covalent geometry : angle 0.50121 (12345) *********************** 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 144 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.900 Fit side-chains REVERT: B 186 ASP cc_start: 0.8204 (p0) cc_final: 0.7426 (p0) REVERT: B 234 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.6939 (t80) REVERT: R 200 ILE cc_start: 0.8544 (mm) cc_final: 0.8172 (mt) REVERT: R 217 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7378 (mmtm) REVERT: S 7 SER cc_start: 0.7763 (t) cc_final: 0.7278 (p) REVERT: S 160 ARG cc_start: 0.7744 (ttt180) cc_final: 0.7488 (ttt180) REVERT: S 235 TYR cc_start: 0.6605 (OUTLIER) cc_final: 0.5911 (t80) outliers start: 16 outliers final: 10 residues processed: 139 average time/residue: 0.2479 time to fit residues: 46.6097 Evaluate side-chains 138 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.893 ------------------------------------------------------------------------------- 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 183 HIS 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 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 9 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 72 optimal weight: 0.0030 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 16 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 23 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.159332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.126305 restraints weight = 7676.697| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.06 r_work: 0.2930 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9118 Z= 0.106 Angle : 0.506 9.606 12351 Z= 0.267 Chirality : 0.042 0.137 1378 Planarity : 0.004 0.037 1565 Dihedral : 5.338 84.335 1243 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.55 % Allowed : 14.95 % Favored : 83.51 % 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 (0.26), residues: 1116 helix: 2.17 (0.28), residues: 383 sheet: 1.13 (0.32), residues: 289 loop : -1.30 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS S 232 PHE 0.013 0.001 PHE B 199 TYR 0.018 0.001 TYR S 235 ARG 0.001 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 398) hydrogen bonds : angle 4.22421 ( 1137) SS BOND : bond 0.00727 ( 3) SS BOND : angle 1.47702 ( 6) covalent geometry : bond 0.00210 ( 9115) covalent geometry : angle 0.50533 (12345) *********************** 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 145 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.963 Fit side-chains REVERT: A 237 LEU cc_start: 0.8267 (mp) cc_final: 0.8022 (mm) REVERT: B 186 ASP cc_start: 0.8146 (p0) cc_final: 0.7362 (p0) REVERT: B 219 ARG cc_start: 0.8174 (mtm110) cc_final: 0.7777 (mmm160) REVERT: B 234 PHE cc_start: 0.8749 (OUTLIER) cc_final: 0.6921 (t80) REVERT: R 200 ILE cc_start: 0.8506 (mm) cc_final: 0.8164 (mt) REVERT: R 217 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7349 (mmtm) REVERT: S 7 SER cc_start: 0.7749 (t) cc_final: 0.7277 (p) REVERT: S 160 ARG cc_start: 0.7754 (ttt180) cc_final: 0.7466 (ttt180) REVERT: S 235 TYR cc_start: 0.6347 (OUTLIER) cc_final: 0.5851 (t80) outliers start: 15 outliers final: 10 residues processed: 138 average time/residue: 0.2363 time to fit residues: 44.1158 Evaluate side-chains 140 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 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 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 24 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 58 optimal weight: 9.9990 chunk 31 optimal weight: 0.0770 chunk 106 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 96 optimal weight: 0.0060 overall best weight: 1.6160 ------------------------------------------------------------------------------- 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 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 = 0.155303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.121984 restraints weight = 7949.048| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 1.04 r_work: 0.2860 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9118 Z= 0.146 Angle : 0.584 10.658 12351 Z= 0.309 Chirality : 0.044 0.146 1378 Planarity : 0.004 0.042 1565 Dihedral : 5.718 88.443 1243 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.96 % Allowed : 14.95 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.70 (0.26), residues: 1116 helix: 1.93 (0.28), residues: 389 sheet: 1.21 (0.32), residues: 281 loop : -1.46 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.005 0.001 HIS S 232 PHE 0.015 0.002 PHE B 199 TYR 0.028 0.002 TYR S 235 ARG 0.003 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.05702 ( 398) hydrogen bonds : angle 4.49072 ( 1137) SS BOND : bond 0.01045 ( 3) SS BOND : angle 2.09038 ( 6) covalent geometry : bond 0.00312 ( 9115) covalent geometry : angle 0.58253 (12345) *********************** 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 151 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 1.061 Fit side-chains REVERT: A 277 ASP cc_start: 0.6699 (m-30) cc_final: 0.6384 (m-30) REVERT: B 219 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7785 (mmm160) REVERT: B 234 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.6933 (t80) REVERT: R 200 ILE cc_start: 0.8592 (mm) cc_final: 0.8292 (mt) REVERT: R 217 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7372 (mmtm) REVERT: S 7 SER cc_start: 0.7875 (t) cc_final: 0.7458 (p) REVERT: S 235 TYR cc_start: 0.6908 (OUTLIER) cc_final: 0.6028 (t80) outliers start: 19 outliers final: 16 residues processed: 145 average time/residue: 0.2356 time to fit residues: 46.4635 Evaluate side-chains 145 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 0.970 ------------------------------------------------------------------------------- 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 227 SER 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 R residue 252 ILE Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR 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 31 SER 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 20 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 14 optimal weight: 7.9990 chunk 97 optimal weight: 0.3980 chunk 84 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.156172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.123595 restraints weight = 8251.569| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.15 r_work: 0.2856 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3602 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= 0.120 Angle : 0.536 9.631 12351 Z= 0.283 Chirality : 0.042 0.141 1378 Planarity : 0.004 0.041 1565 Dihedral : 5.601 87.413 1243 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.16 % Allowed : 14.74 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.75 (0.26), residues: 1116 helix: 2.02 (0.28), residues: 389 sheet: 1.16 (0.32), residues: 287 loop : -1.44 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE A 189 TYR 0.021 0.001 TYR S 235 ARG 0.002 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 398) hydrogen bonds : angle 4.33808 ( 1137) SS BOND : bond 0.00823 ( 3) SS BOND : angle 1.65079 ( 6) covalent geometry : bond 0.00247 ( 9115) covalent geometry : angle 0.53472 (12345) *********************** 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 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.000 Fit side-chains REVERT: A 277 ASP cc_start: 0.6728 (m-30) cc_final: 0.6391 (m-30) REVERT: B 219 ARG cc_start: 0.8200 (mtm110) cc_final: 0.7796 (mmm160) REVERT: B 234 PHE cc_start: 0.8737 (OUTLIER) cc_final: 0.6921 (t80) REVERT: R 200 ILE cc_start: 0.8599 (mm) cc_final: 0.8291 (mt) REVERT: R 217 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7350 (mmtm) REVERT: S 7 SER cc_start: 0.7865 (t) cc_final: 0.7432 (p) REVERT: S 235 TYR cc_start: 0.6790 (OUTLIER) cc_final: 0.5990 (t80) outliers start: 21 outliers final: 17 residues processed: 144 average time/residue: 0.2228 time to fit residues: 43.6672 Evaluate side-chains 147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 183 HIS 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 148 SER Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR 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 31 SER 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 49 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 71 optimal weight: 40.0000 chunk 8 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.156906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.123620 restraints weight = 8191.025| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.19 r_work: 0.2892 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3667 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= 0.119 Angle : 0.536 10.596 12351 Z= 0.283 Chirality : 0.042 0.139 1378 Planarity : 0.004 0.041 1565 Dihedral : 5.569 87.787 1243 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.96 % Allowed : 14.85 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.70 % 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: 0.84 (0.26), residues: 1116 helix: 2.13 (0.28), residues: 383 sheet: 1.16 (0.32), residues: 287 loop : -1.34 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.022 0.001 TYR S 235 ARG 0.002 0.000 ARG R 82 Details of bonding type rmsd hydrogen bonds : bond 0.04823 ( 398) hydrogen bonds : angle 4.31133 ( 1137) SS BOND : bond 0.00812 ( 3) SS BOND : angle 1.63157 ( 6) covalent geometry : bond 0.00245 ( 9115) covalent geometry : angle 0.53517 (12345) *********************** 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 150 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.026 Fit side-chains REVERT: A 277 ASP cc_start: 0.6740 (m-30) cc_final: 0.6449 (m-30) REVERT: B 234 PHE cc_start: 0.8782 (OUTLIER) cc_final: 0.6956 (t80) REVERT: R 80 MET cc_start: 0.7150 (ttt) cc_final: 0.6794 (ttp) REVERT: R 81 VAL cc_start: 0.7385 (p) cc_final: 0.7163 (t) REVERT: R 200 ILE cc_start: 0.8599 (mm) cc_final: 0.8316 (mt) REVERT: R 217 LYS cc_start: 0.7836 (OUTLIER) cc_final: 0.7411 (mmtm) REVERT: S 7 SER cc_start: 0.7794 (t) cc_final: 0.7415 (p) REVERT: S 235 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.5974 (t80) outliers start: 19 outliers final: 16 residues processed: 144 average time/residue: 0.2243 time to fit residues: 43.7745 Evaluate side-chains 148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 129 time to evaluate : 0.982 ------------------------------------------------------------------------------- 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 183 HIS 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 S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR 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 31 SER 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 3 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS S 13 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 = 0.155385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.122284 restraints weight = 8126.088| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.17 r_work: 0.2874 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3754 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 : 0.572 11.225 12351 Z= 0.302 Chirality : 0.043 0.144 1378 Planarity : 0.004 0.044 1565 Dihedral : 5.696 88.137 1243 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.96 % Allowed : 15.26 % 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 (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 (0.26), residues: 1116 helix: 2.06 (0.28), residues: 383 sheet: 1.07 (0.31), residues: 292 loop : -1.28 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.026 0.002 TYR S 235 ARG 0.002 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.05383 ( 398) hydrogen bonds : angle 4.42477 ( 1137) SS BOND : bond 0.00970 ( 3) SS BOND : angle 1.91766 ( 6) covalent geometry : bond 0.00297 ( 9115) covalent geometry : angle 0.57077 (12345) ********************** 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 149 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 1.023 Fit side-chains REVERT: A 277 ASP cc_start: 0.6777 (m-30) cc_final: 0.6463 (m-30) REVERT: B 186 ASP cc_start: 0.8350 (p0) cc_final: 0.7143 (p0) REVERT: B 234 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.6965 (t80) REVERT: R 200 ILE cc_start: 0.8634 (mm) cc_final: 0.8358 (mt) REVERT: R 217 LYS cc_start: 0.7792 (OUTLIER) cc_final: 0.7347 (mmtm) REVERT: S 7 SER cc_start: 0.7837 (t) cc_final: 0.7469 (p) REVERT: S 235 TYR cc_start: 0.6976 (OUTLIER) cc_final: 0.6042 (t80) outliers start: 19 outliers final: 16 residues processed: 142 average time/residue: 0.2320 time to fit residues: 44.2611 Evaluate side-chains 144 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 183 HIS 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 S residue 85 SER Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR 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 31 SER 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 43 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 57 optimal weight: 0.0050 chunk 64 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 53 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- 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 = 0.3627 r_free = 0.3627 target = 0.156816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 106)---------------| | r_work = 0.3128 r_free = 0.3128 target = 0.115174 restraints weight = 7568.348| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.31 r_work: 0.2887 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3754 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= 0.113 Angle : 0.526 10.109 12351 Z= 0.277 Chirality : 0.042 0.140 1378 Planarity : 0.004 0.040 1565 Dihedral : 5.579 87.939 1243 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.96 % Allowed : 15.26 % 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 (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: 0.86 (0.26), residues: 1116 helix: 2.17 (0.28), residues: 383 sheet: 1.15 (0.32), residues: 287 loop : -1.32 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.019 0.001 TYR S 235 ARG 0.002 0.000 ARG R 82 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 398) hydrogen bonds : angle 4.28668 ( 1137) SS BOND : bond 0.00774 ( 3) SS BOND : angle 1.57465 ( 6) covalent geometry : bond 0.00228 ( 9115) covalent geometry : angle 0.52477 (12345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4643.74 seconds wall clock time: 81 minutes 4.20 seconds (4864.20 seconds total)