Starting phenix.real_space_refine on Tue Apr 29 18:03:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jlj_36399/04_2025/8jlj_36399_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jlj_36399/04_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_36399/04_2025/8jlj_36399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jlj_36399/04_2025/8jlj_36399.map" model { file = "/net/cci-nas-00/data/ceres_data/8jlj_36399/04_2025/8jlj_36399_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jlj_36399/04_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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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: 5.21, per 1000 atoms: 0.58 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: 2.12 Conformation dependent library (CDL) restraints added in 956.6 milliseconds 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: 0.94 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: 2.30 Time building geometry restraints manager: 2.51 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: 0.760 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: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.690 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.760 ------------------------------------------------------------------------------- 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 : 1.014 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: 0.2649 time to fit residues: 60.2535 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 : 0.918 ------------------------------------------------------------------------------- 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 = 0.129438 restraints weight = 7880.351| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.04 r_work: 0.2938 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 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 0.06084 ( 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 : 0.901 Fit side-chains REVERT: B 186 ASP cc_start: 0.8056 (p0) cc_final: 0.7241 (p0) REVERT: B 217 MET cc_start: 0.8526 (ppp) cc_final: 0.7945 (ppp) REVERT: R 165 LYS cc_start: 0.6695 (mttm) cc_final: 0.6284 (ptpt) REVERT: R 217 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7456 (mmtm) REVERT: S 89 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6881 (mp0) outliers start: 14 outliers final: 10 residues processed: 146 average time/residue: 0.2596 time to fit residues: 50.3535 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 : 0.997 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 261 GLN R 98 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.155853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.121546 restraints weight = 8002.501| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.29 r_work: 0.2902 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9118 Z= 0.150 Angle : 0.596 11.734 12351 Z= 0.315 Chirality : 0.044 0.143 1378 Planarity : 0.004 0.042 1565 Dihedral : 5.564 80.196 1244 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.16 % Allowed : 11.13 % Favored : 86.70 % 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: 0.45 (0.26), residues: 1116 helix: 1.57 (0.28), residues: 388 sheet: 1.20 (0.32), residues: 272 loop : -1.45 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.007 0.001 HIS B 225 PHE 0.014 0.002 PHE B 199 TYR 0.031 0.002 TYR S 235 ARG 0.005 0.000 ARG A 303 Details of bonding type rmsd hydrogen bonds : bond 0.06313 ( 398) hydrogen bonds : angle 4.68677 ( 1137) SS BOND : bond 0.00840 ( 3) SS BOND : angle 1.70008 ( 6) covalent geometry : bond 0.00320 ( 9115) covalent geometry : angle 0.59522 (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 155 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.329 Fit side-chains REVERT: A 314 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7539 (ttp-170) REVERT: B 234 PHE cc_start: 0.8772 (OUTLIER) cc_final: 0.6907 (t80) REVERT: R 157 MET cc_start: 0.7617 (ttp) cc_final: 0.7369 (ttp) REVERT: R 165 LYS cc_start: 0.6778 (mttm) cc_final: 0.6546 (mmtt) REVERT: R 217 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7424 (mmtm) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 0.2441 time to fit residues: 48.3147 Evaluate side-chains 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 130 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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: 3.9990 chunk 14 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 chunk 107 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.160121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.127793 restraints weight = 7671.230| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.01 r_work: 0.2933 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3144 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 : 0.523 9.230 12351 Z= 0.277 Chirality : 0.042 0.140 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.438 80.868 1244 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.34 % Allowed : 12.99 % Favored : 85.67 % 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: 0.63 (0.26), residues: 1116 helix: 1.83 (0.27), residues: 389 sheet: 1.10 (0.32), residues: 285 loop : -1.39 (0.27), residues: 442 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 0.017 0.001 TYR S 235 ARG 0.003 0.000 ARG S 160 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 398) hydrogen bonds : angle 4.42910 ( 1137) SS BOND : bond 0.00699 ( 3) SS BOND : angle 1.59412 ( 6) covalent geometry : bond 0.00220 ( 9115) covalent geometry : angle 0.52170 (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 146 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 1.075 Fit side-chains REVERT: A 311 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7208 (mm-30) REVERT: A 314 ARG cc_start: 0.7846 (ptp-170) cc_final: 0.7593 (ttp-170) REVERT: B 234 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.6948 (t80) REVERT: R 200 ILE cc_start: 0.8482 (mm) cc_final: 0.8118 (mt) REVERT: R 217 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7478 (mmtm) REVERT: S 235 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.5745 (t80) outliers start: 13 outliers final: 8 residues processed: 144 average time/residue: 0.2383 time to fit residues: 46.3398 Evaluate side-chains 139 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 R residue 259 VAL Chi-restraints excluded: chain S residue 235 TYR Chi-restraints excluded: chain Y residue 31 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 25 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 99 optimal weight: 0.9990 chunk 6 optimal weight: 0.0570 chunk 72 optimal weight: 0.0270 chunk 19 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.4162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.156064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.123018 restraints weight = 7706.857| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.03 r_work: 0.2873 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9118 Z= 0.138 Angle : 0.571 10.217 12351 Z= 0.302 Chirality : 0.043 0.144 1378 Planarity : 0.004 0.042 1565 Dihedral : 5.643 85.260 1244 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.16 % Allowed : 14.33 % Favored : 83.51 % 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: 0.65 (0.26), residues: 1116 helix: 1.86 (0.28), residues: 389 sheet: 1.17 (0.32), residues: 285 loop : -1.44 (0.27), residues: 442 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 0.014 0.002 PHE B 199 TYR 0.025 0.002 TYR S 235 ARG 0.002 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.05539 ( 398) hydrogen bonds : angle 4.49903 ( 1137) SS BOND : bond 0.01037 ( 3) SS BOND : angle 1.94596 ( 6) covalent geometry : bond 0.00292 ( 9115) covalent geometry : angle 0.56939 (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 148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.933 Fit side-chains REVERT: A 277 ASP cc_start: 0.6719 (m-30) cc_final: 0.6383 (m-30) REVERT: B 234 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.6912 (t80) REVERT: R 157 MET cc_start: 0.7277 (ttm) cc_final: 0.6990 (ttp) REVERT: R 200 ILE cc_start: 0.8541 (mm) cc_final: 0.8186 (mt) REVERT: R 217 LYS cc_start: 0.7747 (OUTLIER) cc_final: 0.7356 (mmtm) REVERT: S 235 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.6024 (t80) outliers start: 21 outliers final: 17 residues processed: 141 average time/residue: 0.2320 time to fit residues: 44.4713 Evaluate side-chains 145 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 9 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 73 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 16 optimal weight: 0.0020 chunk 77 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.125546 restraints weight = 7671.294| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.01 r_work: 0.2940 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3444 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= 0.111 Angle : 0.519 8.965 12351 Z= 0.275 Chirality : 0.042 0.140 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.508 85.596 1243 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.96 % Allowed : 14.74 % Favored : 83.30 % 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: 0.76 (0.26), residues: 1116 helix: 2.02 (0.28), residues: 389 sheet: 1.11 (0.32), residues: 289 loop : -1.39 (0.27), residues: 438 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 A 189 TYR 0.017 0.001 TYR S 235 ARG 0.002 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.04713 ( 398) hydrogen bonds : angle 4.33894 ( 1137) SS BOND : bond 0.00715 ( 3) SS BOND : angle 1.56327 ( 6) covalent geometry : bond 0.00221 ( 9115) covalent geometry : angle 0.51769 (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 147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 1.044 Fit side-chains REVERT: A 277 ASP cc_start: 0.6672 (m-30) cc_final: 0.6362 (m-30) REVERT: B 219 ARG cc_start: 0.8122 (mtm110) cc_final: 0.7764 (mmm160) REVERT: B 234 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.6953 (t80) REVERT: R 200 ILE cc_start: 0.8518 (mm) cc_final: 0.8186 (mt) REVERT: R 217 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7367 (mmtm) REVERT: S 7 SER cc_start: 0.7726 (t) cc_final: 0.7312 (p) REVERT: S 235 TYR cc_start: 0.6624 (OUTLIER) cc_final: 0.5936 (t80) outliers start: 19 outliers final: 13 residues processed: 139 average time/residue: 0.2590 time to fit residues: 49.0394 Evaluate side-chains 141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 1.483 ------------------------------------------------------------------------------- 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 143 THR 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 24 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 58 optimal weight: 0.0270 chunk 31 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 96 optimal weight: 0.0980 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.162962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.130609 restraints weight = 8055.817| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 1.06 r_work: 0.2988 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9118 Z= 0.089 Angle : 0.462 8.058 12351 Z= 0.244 Chirality : 0.041 0.128 1378 Planarity : 0.003 0.038 1565 Dihedral : 5.222 84.685 1243 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.55 % Allowed : 15.26 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1116 helix: 2.24 (0.28), residues: 383 sheet: 1.22 (0.32), residues: 286 loop : -1.22 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 211 HIS 0.003 0.001 HIS A 197 PHE 0.011 0.001 PHE A 189 TYR 0.011 0.001 TYR S 190 ARG 0.002 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 398) hydrogen bonds : angle 4.04341 ( 1137) SS BOND : bond 0.00402 ( 3) SS BOND : angle 1.03937 ( 6) covalent geometry : bond 0.00169 ( 9115) covalent geometry : angle 0.46130 (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 147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.925 Fit side-chains REVERT: B 186 ASP cc_start: 0.8015 (p0) cc_final: 0.7320 (p0) REVERT: B 219 ARG cc_start: 0.8129 (mtm110) cc_final: 0.7754 (mmm160) REVERT: B 333 ASP cc_start: 0.8134 (p0) cc_final: 0.7843 (p0) REVERT: R 80 MET cc_start: 0.7052 (ttt) cc_final: 0.6725 (ttp) REVERT: R 119 ASP cc_start: 0.8911 (t70) cc_final: 0.8620 (t0) REVERT: R 200 ILE cc_start: 0.8479 (mm) cc_final: 0.8155 (mt) REVERT: R 217 LYS cc_start: 0.7619 (OUTLIER) cc_final: 0.7250 (mmtm) REVERT: S 7 SER cc_start: 0.7696 (t) cc_final: 0.7252 (p) REVERT: S 235 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5811 (t80) outliers start: 15 outliers final: 10 residues processed: 142 average time/residue: 0.2324 time to fit residues: 44.5430 Evaluate side-chains 133 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 121 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 GLU 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 322 ASP Chi-restraints excluded: chain R residue 217 LYS Chi-restraints excluded: chain S residue 91 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 20 optimal weight: 0.1980 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 62 optimal weight: 0.0970 chunk 100 optimal weight: 0.0970 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3670 r_free = 0.3670 target = 0.160559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.128114 restraints weight = 8297.036| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.14 r_work: 0.2957 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9118 Z= 0.100 Angle : 0.494 9.447 12351 Z= 0.259 Chirality : 0.041 0.134 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.299 86.679 1243 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.75 % Allowed : 15.57 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1116 helix: 2.28 (0.28), residues: 383 sheet: 1.22 (0.32), residues: 287 loop : -1.18 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 261 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE B 199 TYR 0.014 0.001 TYR S 235 ARG 0.002 0.000 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 398) hydrogen bonds : angle 4.07738 ( 1137) SS BOND : bond 0.00672 ( 3) SS BOND : angle 1.45202 ( 6) covalent geometry : bond 0.00197 ( 9115) covalent geometry : angle 0.49306 (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 148 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 1.146 Fit side-chains REVERT: A 277 ASP cc_start: 0.6678 (m-30) cc_final: 0.6345 (m-30) REVERT: A 359 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8547 (mm-30) REVERT: B 186 ASP cc_start: 0.8104 (p0) cc_final: 0.7380 (p0) REVERT: B 219 ARG cc_start: 0.8143 (mtm110) cc_final: 0.7783 (mmm160) REVERT: B 234 PHE cc_start: 0.8723 (OUTLIER) cc_final: 0.6915 (t80) REVERT: R 80 MET cc_start: 0.6960 (ttt) cc_final: 0.6632 (ttp) REVERT: R 200 ILE cc_start: 0.8484 (mm) cc_final: 0.8196 (mt) REVERT: R 217 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7308 (mmtm) REVERT: S 7 SER cc_start: 0.7717 (t) cc_final: 0.7300 (p) REVERT: S 235 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.5957 (t80) outliers start: 17 outliers final: 13 residues processed: 143 average time/residue: 0.2664 time to fit residues: 52.0946 Evaluate side-chains 147 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 1.105 ------------------------------------------------------------------------------- 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 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 91 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 49 optimal weight: 0.8980 chunk 74 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 42 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3673 r_free = 0.3673 target = 0.160893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.122317 restraints weight = 8243.507| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.07 r_work: 0.2912 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 9118 Z= 0.097 Angle : 0.486 9.582 12351 Z= 0.255 Chirality : 0.041 0.133 1378 Planarity : 0.004 0.038 1565 Dihedral : 5.319 87.810 1243 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.65 % Allowed : 15.88 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1116 helix: 2.29 (0.28), residues: 383 sheet: 1.24 (0.32), residues: 287 loop : -1.16 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE B 199 TYR 0.012 0.001 TYR S 235 ARG 0.003 0.000 ARG R 82 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 398) hydrogen bonds : angle 4.06554 ( 1137) SS BOND : bond 0.00611 ( 3) SS BOND : angle 1.30904 ( 6) covalent geometry : bond 0.00189 ( 9115) covalent geometry : angle 0.48485 (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 144 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 128 time to evaluate : 0.995 Fit side-chains REVERT: A 277 ASP cc_start: 0.6767 (m-30) cc_final: 0.6362 (m-30) REVERT: B 186 ASP cc_start: 0.8125 (p0) cc_final: 0.7361 (p0) REVERT: B 219 ARG cc_start: 0.8115 (mtm110) cc_final: 0.7674 (mmm160) REVERT: R 80 MET cc_start: 0.7002 (ttt) cc_final: 0.6693 (ttp) REVERT: R 200 ILE cc_start: 0.8531 (mm) cc_final: 0.8237 (mt) REVERT: R 217 LYS cc_start: 0.7604 (OUTLIER) cc_final: 0.7148 (mmtm) REVERT: S 7 SER cc_start: 0.7756 (t) cc_final: 0.7298 (p) REVERT: S 235 TYR cc_start: 0.6301 (OUTLIER) cc_final: 0.5936 (t80) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.2350 time to fit residues: 44.2521 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 : 0.915 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 61 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 75 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 83 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3608 r_free = 0.3608 target = 0.155144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.118538 restraints weight = 8171.705| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.38 r_work: 0.2842 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9118 Z= 0.153 Angle : 0.591 11.572 12351 Z= 0.311 Chirality : 0.044 0.146 1378 Planarity : 0.004 0.039 1565 Dihedral : 5.726 89.351 1243 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.75 % Allowed : 15.57 % Favored : 82.68 % 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: 0.85 (0.26), residues: 1116 helix: 2.11 (0.28), residues: 383 sheet: 1.17 (0.33), residues: 276 loop : -1.24 (0.27), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS S 232 PHE 0.015 0.002 PHE B 199 TYR 0.027 0.002 TYR S 235 ARG 0.003 0.000 ARG R 82 Details of bonding type rmsd hydrogen bonds : bond 0.05603 ( 398) hydrogen bonds : angle 4.42725 ( 1137) SS BOND : bond 0.01097 ( 3) SS BOND : angle 2.05082 ( 6) covalent geometry : bond 0.00335 ( 9115) covalent geometry : angle 0.58948 (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 141 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.923 Fit side-chains REVERT: A 277 ASP cc_start: 0.6765 (m-30) cc_final: 0.6471 (m-30) REVERT: B 234 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.6926 (t80) REVERT: R 200 ILE cc_start: 0.8654 (mm) cc_final: 0.8386 (mt) REVERT: R 217 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7428 (mmtm) REVERT: S 7 SER cc_start: 0.7861 (t) cc_final: 0.7512 (p) REVERT: S 235 TYR cc_start: 0.7160 (OUTLIER) cc_final: 0.6229 (t80) outliers start: 17 outliers final: 14 residues processed: 134 average time/residue: 0.2370 time to fit residues: 42.9517 Evaluate side-chains 139 residues out of total 975 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 122 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 0.0370 chunk 57 optimal weight: 0.0970 chunk 64 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 65 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.3980 chunk 53 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 overall best weight: 0.3456 ------------------------------------------------------------------------------- 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 = 0.3677 r_free = 0.3677 target = 0.161268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.128958 restraints weight = 8146.977| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.05 r_work: 0.2959 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3689 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 : 0.478 8.975 12351 Z= 0.251 Chirality : 0.041 0.131 1378 Planarity : 0.003 0.039 1565 Dihedral : 5.392 88.016 1243 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.34 % Allowed : 16.39 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1116 helix: 2.26 (0.28), residues: 383 sheet: 1.24 (0.32), residues: 287 loop : -1.18 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 261 HIS 0.003 0.001 HIS B 225 PHE 0.012 0.001 PHE A 189 TYR 0.011 0.001 TYR S 190 ARG 0.005 0.000 ARG R 82 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 398) hydrogen bonds : angle 4.09081 ( 1137) SS BOND : bond 0.00471 ( 3) SS BOND : angle 1.05000 ( 6) covalent geometry : bond 0.00181 ( 9115) covalent geometry : angle 0.47737 (12345) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4763.06 seconds wall clock time: 82 minutes 34.65 seconds (4954.65 seconds total)