Starting phenix.real_space_refine on Sat Oct 24 21:51:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0l_32243/10_2026/7w0l_32243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0l_32243/10_2026/7w0l_32243.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w0l_32243/10_2026/7w0l_32243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0l_32243/10_2026/7w0l_32243.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0l_32243/10_2026/7w0l_32243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0l_32243/10_2026/7w0l_32243.map" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4236 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 7396 2.51 5 N 1932 2.21 5 O 2108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11526 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1819 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 2607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2607 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "C" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 56} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "Q" Number of atoms: 2376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2376 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain: "R" Number of atoms: 2393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2393 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 11, 'TRANS': 286} Chain: "S" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1800 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 10, 'TRANS': 223} Chain breaks: 1 Chain: "Q" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'8EH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.38, per 1000 atoms: 0.21 Number of scatterers: 11526 At special positions: 0 Unit cell: (125.8, 106.25, 136.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 2108 8.00 N 1932 7.00 C 7396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS Q 102 " - pdb=" SG CYS Q 181 " distance=2.04 Simple disulfide: pdb=" SG CYS R 102 " - pdb=" SG CYS R 181 " distance=2.05 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.01 Conformation dependent library (CDL) restraints added in 661.5 milliseconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2732 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 14 sheets defined 47.2% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.657A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.040A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE A 55 " --> pdb=" O LYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 4.355A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.739A pdb=" N GLU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 3.564A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.562A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 3.730A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.758A pdb=" N ALA B 21 " --> pdb=" O GLN B 17 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 280 through 282 No H-bonds generated for 'chain 'B' and resid 280 through 282' Processing helix chain 'C' and resid 35 through 55 removed outlier: 3.966A pdb=" N ALA C 41 " --> pdb=" O THR C 37 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU C 50 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET C 52 " --> pdb=" O GLU C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 75 removed outlier: 3.686A pdb=" N ALA C 64 " --> pdb=" O LYS C 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 56 Proline residue: Q 32 - end of helix removed outlier: 3.542A pdb=" N SER Q 56 " --> pdb=" O THR Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 61 Processing helix chain 'Q' and resid 62 through 81 removed outlier: 4.033A pdb=" N SER Q 70 " --> pdb=" O ILE Q 66 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR Q 81 " --> pdb=" O THR Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 91 removed outlier: 3.711A pdb=" N TYR Q 88 " --> pdb=" O LEU Q 84 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 137 removed outlier: 4.042A pdb=" N CYS Q 102 " --> pdb=" O GLY Q 98 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS Q 103 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE Q 131 " --> pdb=" O ARG Q 127 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL Q 132 " --> pdb=" O TYR Q 128 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Proline residue: Q 134 - end of helix Processing helix chain 'Q' and resid 145 through 161 removed outlier: 3.518A pdb=" N ALA Q 161 " --> pdb=" O ALA Q 157 " (cutoff:3.500A) Processing helix chain 'Q' and resid 162 through 167 Processing helix chain 'Q' and resid 190 through 192 No H-bonds generated for 'chain 'Q' and resid 190 through 192' Processing helix chain 'Q' and resid 193 through 232 removed outlier: 3.957A pdb=" N TRP Q 197 " --> pdb=" O SER Q 193 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU Q 198 " --> pdb=" O GLU Q 194 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 208 " (cutoff:3.500A) Proline residue: Q 213 - end of helix removed outlier: 3.670A pdb=" N ILE Q 224 " --> pdb=" O CYS Q 220 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE Q 232 " --> pdb=" O ILE Q 228 " (cutoff:3.500A) Processing helix chain 'Q' and resid 238 through 278 removed outlier: 3.820A pdb=" N LYS Q 242 " --> pdb=" O GLU Q 238 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE Q 249 " --> pdb=" O ARG Q 245 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE Q 250 " --> pdb=" O LEU Q 246 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL Q 251 " --> pdb=" O LEU Q 247 " (cutoff:3.500A) Proline residue: Q 263 - end of helix removed outlier: 4.135A pdb=" N SER Q 275 " --> pdb=" O TYR Q 271 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU Q 276 " --> pdb=" O MET Q 272 " (cutoff:3.500A) Processing helix chain 'Q' and resid 280 through 299 Proline residue: Q 292 - end of helix removed outlier: 4.119A pdb=" N TYR Q 299 " --> pdb=" O THR Q 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 311 Proline residue: Q 306 - end of helix Processing helix chain 'Q' and resid 312 through 322 Processing helix chain 'R' and resid 30 through 61 removed outlier: 3.790A pdb=" N ILE R 34 " --> pdb=" O LEU R 30 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL R 49 " --> pdb=" O GLY R 45 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N ARG R 58 " --> pdb=" O PHE R 54 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N GLU R 59 " --> pdb=" O ARG R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 81 removed outlier: 4.005A pdb=" N ILE R 68 " --> pdb=" O ALA R 64 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR R 81 " --> pdb=" O THR R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 81 through 91 removed outlier: 4.560A pdb=" N TRP R 85 " --> pdb=" O THR R 81 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG R 91 " --> pdb=" O THR R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 132 removed outlier: 3.728A pdb=" N LYS R 103 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 139 No H-bonds generated for 'chain 'R' and resid 137 through 139' Processing helix chain 'R' and resid 140 through 145 removed outlier: 3.922A pdb=" N VAL R 144 " --> pdb=" O LEU R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 167 removed outlier: 3.841A pdb=" N THR R 150 " --> pdb=" O GLY R 146 " (cutoff:3.500A) Proline residue: R 163 - end of helix Processing helix chain 'R' and resid 184 through 188 removed outlier: 4.105A pdb=" N MET R 187 " --> pdb=" O ASP R 184 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 232 removed outlier: 3.905A pdb=" N VAL R 208 " --> pdb=" O SER R 204 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N VAL R 212 " --> pdb=" O VAL R 208 " (cutoff:3.500A) Proline residue: R 213 - end of helix removed outlier: 3.946A pdb=" N PHE R 232 " --> pdb=" O ILE R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 275 removed outlier: 3.558A pdb=" N LYS R 242 " --> pdb=" O GLU R 238 " (cutoff:3.500A) Proline residue: R 263 - end of helix Processing helix chain 'R' and resid 281 through 298 Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 299 through 311 Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 321 Processing helix chain 'S' and resid 220 through 224 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190 removed outlier: 7.096A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 225 " --> pdb=" O PHE A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.941A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.743A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP B 83 " --> pdb=" O ASN B 88 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 3.701A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 3.599A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.834A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.623A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.069A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 285 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'S' and resid 4 through 7 removed outlier: 3.527A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR S 78 " --> pdb=" O ASP S 73 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 45 through 51 removed outlier: 3.614A pdb=" N GLU S 46 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 146 through 147 removed outlier: 3.909A pdb=" N GLY S 225 " --> pdb=" O LEU S 245 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 155 through 160 removed outlier: 3.758A pdb=" N VAL S 155 " --> pdb=" O ILE S 216 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER S 208 " --> pdb=" O ALA S 211 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'S' and resid 186 through 189 removed outlier: 6.878A pdb=" N TRP S 176 " --> pdb=" O LEU S 188 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1602 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3635 1.34 - 1.47: 3155 1.47 - 1.60: 4872 1.60 - 1.72: 2 1.72 - 1.85: 131 Bond restraints: 11795 Sorted by residual: bond pdb=" C30 8EH R 401 " pdb=" C31 8EH R 401 " ideal model delta sigma weight residual 1.472 1.567 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C30 8EH Q 401 " pdb=" C31 8EH Q 401 " ideal model delta sigma weight residual 1.472 1.564 -0.092 2.00e-02 2.50e+03 2.12e+01 bond pdb=" C30 8EH R 401 " pdb=" N29 8EH R 401 " ideal model delta sigma weight residual 1.313 1.404 -0.091 2.00e-02 2.50e+03 2.08e+01 bond pdb=" C30 8EH Q 401 " pdb=" N29 8EH Q 401 " ideal model delta sigma weight residual 1.313 1.403 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C12 8EH R 401 " pdb=" N28 8EH R 401 " ideal model delta sigma weight residual 1.307 1.393 -0.086 2.00e-02 2.50e+03 1.83e+01 ... (remaining 11790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 15578 2.45 - 4.91: 369 4.91 - 7.36: 56 7.36 - 9.81: 7 9.81 - 12.27: 2 Bond angle restraints: 16012 Sorted by residual: angle pdb=" C ALA B 257 " pdb=" N ASP B 258 " pdb=" CA ASP B 258 " ideal model delta sigma weight residual 122.40 130.46 -8.06 1.45e+00 4.76e-01 3.09e+01 angle pdb=" CA TYR S 235 " pdb=" CB TYR S 235 " pdb=" CG TYR S 235 " ideal model delta sigma weight residual 113.90 105.20 8.70 1.80e+00 3.09e-01 2.34e+01 angle pdb=" C GLY B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta sigma weight residual 121.71 115.94 5.77 1.39e+00 5.18e-01 1.72e+01 angle pdb=" O15 8EH Q 401 " pdb=" S14 8EH Q 401 " pdb=" O16 8EH Q 401 " ideal model delta sigma weight residual 119.97 107.70 12.27 3.00e+00 1.11e-01 1.67e+01 angle pdb=" O15 8EH R 401 " pdb=" S14 8EH R 401 " pdb=" O16 8EH R 401 " ideal model delta sigma weight residual 119.97 107.73 12.24 3.00e+00 1.11e-01 1.66e+01 ... (remaining 16007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.86: 6721 30.86 - 61.71: 219 61.71 - 92.57: 12 92.57 - 123.43: 0 123.43 - 154.28: 2 Dihedral angle restraints: 6954 sinusoidal: 2716 harmonic: 4238 Sorted by residual: dihedral pdb=" CA GLU Q 174 " pdb=" C GLU Q 174 " pdb=" N ASN Q 175 " pdb=" CA ASN Q 175 " ideal model delta harmonic sigma weight residual -180.00 -150.69 -29.31 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA GLY A 352 " pdb=" C GLY A 352 " pdb=" N LEU A 353 " pdb=" CA LEU A 353 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual 180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 6951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1560 0.069 - 0.139: 232 0.139 - 0.208: 18 0.208 - 0.278: 2 0.278 - 0.347: 2 Chirality restraints: 1814 Sorted by residual: chirality pdb=" C19 8EH Q 401 " pdb=" C17 8EH Q 401 " pdb=" C21 8EH Q 401 " pdb=" O20 8EH Q 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.78 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" C19 8EH R 401 " pdb=" C17 8EH R 401 " pdb=" C21 8EH R 401 " pdb=" O20 8EH R 401 " both_signs ideal model delta sigma weight residual False -2.43 -2.77 0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 1811 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE R 291 " 0.032 2.00e-02 2.50e+03 2.56e-02 1.15e+01 pdb=" CG PHE R 291 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE R 291 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 291 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE R 291 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 PHE R 291 " 0.012 2.00e-02 2.50e+03 pdb=" CZ PHE R 291 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 289 " 0.016 2.00e-02 2.50e+03 3.22e-02 1.04e+01 pdb=" C ASN R 289 " -0.056 2.00e-02 2.50e+03 pdb=" O ASN R 289 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE R 290 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 190 " 0.028 2.00e-02 2.50e+03 1.87e-02 7.02e+00 pdb=" CG TYR S 190 " -0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR S 190 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR S 190 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR S 190 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR S 190 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR S 190 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR S 190 " 0.004 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 72 2.49 - 3.09: 8734 3.09 - 3.70: 17063 3.70 - 4.30: 23276 4.30 - 4.90: 38672 Nonbonded interactions: 87817 Sorted by model distance: nonbonded pdb=" O ALA B 257 " pdb=" OD1 ASP B 258 " model vdw 1.891 3.040 nonbonded pdb=" O ILE B 37 " pdb=" NZ LYS B 301 " model vdw 2.207 3.120 nonbonded pdb=" O LYS B 280 " pdb=" OG SER B 281 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLN S 142 " pdb=" OG1 THR S 243 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR B 102 " pdb=" O SER B 147 " model vdw 2.214 3.040 ... (remaining 87812 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 Found NCS groups: ncs_group { reference = (chain 'Q' and (resid 26 through 321 or resid 401)) selection = (chain 'R' and resid 26 through 401) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.220 Find NCS groups from input model: 0.150 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:1.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 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 : 0.010 0.095 11798 Z= 0.457 Angle : 0.942 12.266 16018 Z= 0.527 Chirality : 0.051 0.347 1814 Planarity : 0.005 0.056 1995 Dihedral : 15.214 154.284 4213 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.62 % Favored : 91.31 % Rotamer: Outliers : 0.08 % Allowed : 9.37 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.27 (0.19), residues: 1439 helix: -1.17 (0.18), residues: 622 sheet: -2.12 (0.29), residues: 278 loop : -3.30 (0.21), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 205 TYR 0.044 0.003 TYR S 190 PHE 0.057 0.003 PHE R 291 TRP 0.019 0.002 TRP A 211 HIS 0.008 0.002 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00974 / 0.46 (11795) covalent geometry : angle 0.93912 / 0.53 (16012) SS BOND : bond 0.01496 / 0.74 ( 3) SS BOND : angle 3.67820 / 1.67 ( 6) hydrogen bonds : bond 0.18111 / 11.98 ( 550) hydrogen bonds : angle 6.41359 / 4.39 ( 1602) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 374 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8259 (mttp) cc_final: 0.8039 (mttp) REVERT: A 197 LYS cc_start: 0.8250 (mtpp) cc_final: 0.7851 (mttp) REVERT: A 209 LYS cc_start: 0.8482 (mtpt) cc_final: 0.8217 (mtpt) REVERT: A 231 ASP cc_start: 0.7473 (t70) cc_final: 0.7239 (t70) REVERT: A 242 ARG cc_start: 0.7781 (mtt90) cc_final: 0.7536 (mtt90) REVERT: A 247 MET cc_start: 0.7829 (mtm) cc_final: 0.7557 (mtm) REVERT: A 289 GLU cc_start: 0.7175 (pm20) cc_final: 0.6616 (pm20) REVERT: A 308 GLU cc_start: 0.7565 (tt0) cc_final: 0.7187 (tt0) REVERT: A 341 ASP cc_start: 0.8326 (t70) cc_final: 0.8056 (t70) REVERT: A 345 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7880 (mtpp) REVERT: B 14 LEU cc_start: 0.9095 (mp) cc_final: 0.8622 (mp) REVERT: B 34 THR cc_start: 0.7617 (p) cc_final: 0.7381 (t) REVERT: B 59 TYR cc_start: 0.8437 (m-10) cc_final: 0.8209 (m-80) REVERT: B 61 MET cc_start: 0.7405 (tmm) cc_final: 0.6946 (tmm) REVERT: B 79 LEU cc_start: 0.7931 (tp) cc_final: 0.7485 (tt) REVERT: B 98 SER cc_start: 0.8326 (m) cc_final: 0.7828 (t) REVERT: B 179 THR cc_start: 0.8609 (t) cc_final: 0.8348 (p) REVERT: B 195 ASP cc_start: 0.7773 (t70) cc_final: 0.7525 (t0) REVERT: B 291 ASP cc_start: 0.7635 (t70) cc_final: 0.7325 (t70) REVERT: B 300 LEU cc_start: 0.8370 (mt) cc_final: 0.8161 (mt) REVERT: B 308 LEU cc_start: 0.8160 (mt) cc_final: 0.7955 (mp) REVERT: B 338 ILE cc_start: 0.8370 (mt) cc_final: 0.8110 (mm) REVERT: C 42 GLN cc_start: 0.8148 (tp40) cc_final: 0.7904 (tp40) REVERT: Q 36 MET cc_start: 0.8180 (mmm) cc_final: 0.7468 (mpp) REVERT: Q 71 LEU cc_start: 0.8823 (tt) cc_final: 0.8606 (tt) REVERT: Q 88 TYR cc_start: 0.8528 (t80) cc_final: 0.8316 (t80) REVERT: Q 107 TYR cc_start: 0.8173 (t80) cc_final: 0.7897 (t80) REVERT: Q 201 LEU cc_start: 0.7888 (tp) cc_final: 0.7630 (tp) REVERT: Q 262 MET cc_start: 0.6484 (tmm) cc_final: 0.6230 (tmm) REVERT: Q 295 THR cc_start: 0.8152 (t) cc_final: 0.7828 (p) REVERT: Q 301 ASN cc_start: 0.8480 (t0) cc_final: 0.8218 (t0) REVERT: Q 308 LEU cc_start: 0.7691 (mm) cc_final: 0.7487 (mm) REVERT: R 46 ASN cc_start: 0.8696 (m-40) cc_final: 0.8361 (m-40) REVERT: R 165 MET cc_start: 0.8275 (tpt) cc_final: 0.7811 (tpp) REVERT: R 216 ILE cc_start: 0.8335 (mt) cc_final: 0.8135 (mt) REVERT: R 222 PHE cc_start: 0.7931 (t80) cc_final: 0.7700 (t80) REVERT: R 228 ILE cc_start: 0.8542 (tp) cc_final: 0.8166 (tt) REVERT: R 245 ARG cc_start: 0.7743 (ttt90) cc_final: 0.7478 (ttt90) REVERT: R 288 MET cc_start: 0.7108 (mmm) cc_final: 0.6832 (mmm) REVERT: S 3 GLN cc_start: 0.7457 (tm-30) cc_final: 0.6869 (tm-30) REVERT: S 140 MET cc_start: 0.7912 (mtp) cc_final: 0.7693 (mtp) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.0994 time to fit residues: 52.6568 Evaluate side-chains 348 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55] chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 331 ASN B 259 GLN Q 318 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.103381 restraints weight = 19291.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.106895 restraints weight = 9246.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109183 restraints weight = 5820.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110659 restraints weight = 4302.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111423 restraints weight = 3516.221| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11798 Z= 0.146 Angle : 0.680 8.793 16018 Z= 0.351 Chirality : 0.043 0.196 1814 Planarity : 0.004 0.060 1995 Dihedral : 7.747 99.611 1646 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 1.84 % Allowed : 16.17 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.21), residues: 1439 helix: 0.37 (0.20), residues: 619 sheet: -1.59 (0.31), residues: 280 loop : -2.83 (0.22), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 219 TYR 0.027 0.001 TYR S 235 PHE 0.019 0.002 PHE A 196 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (11795) covalent geometry : angle 0.67908 / 0.35 (16012) SS BOND : bond 0.01317 / 0.68 ( 3) SS BOND : angle 1.89542 / 0.94 ( 6) hydrogen bonds : bond 0.05086 / 3.30 ( 550) hydrogen bonds : angle 4.75918 / 3.23 ( 1602) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 341 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7853 (ptt-90) cc_final: 0.7617 (ptt-90) REVERT: A 46 LYS cc_start: 0.8671 (ptmt) cc_final: 0.8427 (ptpp) REVERT: A 209 LYS cc_start: 0.8411 (mtpt) cc_final: 0.8149 (mtpt) REVERT: A 231 ASP cc_start: 0.7351 (t70) cc_final: 0.7060 (t70) REVERT: A 242 ARG cc_start: 0.7689 (mtt90) cc_final: 0.7095 (mtt90) REVERT: A 247 MET cc_start: 0.7757 (mtm) cc_final: 0.7464 (mtm) REVERT: A 289 GLU cc_start: 0.7008 (pm20) cc_final: 0.6614 (pm20) REVERT: A 308 GLU cc_start: 0.7573 (tt0) cc_final: 0.7265 (tt0) REVERT: A 345 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7859 (mtpp) REVERT: B 19 ARG cc_start: 0.7714 (ttp-110) cc_final: 0.7398 (ttp-110) REVERT: B 61 MET cc_start: 0.7503 (tmm) cc_final: 0.6904 (tmm) REVERT: B 98 SER cc_start: 0.8298 (m) cc_final: 0.7725 (t) REVERT: B 111 TYR cc_start: 0.8563 (m-80) cc_final: 0.8111 (m-80) REVERT: B 120 ILE cc_start: 0.8336 (pt) cc_final: 0.7782 (mt) REVERT: B 173 THR cc_start: 0.8435 (t) cc_final: 0.8134 (p) REVERT: B 195 ASP cc_start: 0.7680 (t70) cc_final: 0.7356 (t0) REVERT: B 291 ASP cc_start: 0.7558 (t70) cc_final: 0.7188 (t70) REVERT: B 300 LEU cc_start: 0.8227 (mt) cc_final: 0.7820 (mt) REVERT: B 308 LEU cc_start: 0.8124 (mt) cc_final: 0.7923 (mp) REVERT: B 325 MET cc_start: 0.7852 (mtt) cc_final: 0.7631 (mtm) REVERT: B 338 ILE cc_start: 0.8186 (mt) cc_final: 0.7909 (mm) REVERT: C 55 ASN cc_start: 0.7720 (m-40) cc_final: 0.7354 (m-40) REVERT: Q 71 LEU cc_start: 0.8805 (tt) cc_final: 0.8556 (tp) REVERT: Q 107 TYR cc_start: 0.7994 (t80) cc_final: 0.7504 (t80) REVERT: Q 162 MET cc_start: 0.7712 (tpp) cc_final: 0.7203 (mpp) REVERT: Q 179 VAL cc_start: 0.7012 (OUTLIER) cc_final: 0.6583 (t) REVERT: Q 201 LEU cc_start: 0.7911 (tp) cc_final: 0.7676 (tp) REVERT: Q 262 MET cc_start: 0.6271 (tmm) cc_final: 0.6000 (tmm) REVERT: Q 283 PHE cc_start: 0.7135 (t80) cc_final: 0.6651 (t80) REVERT: Q 295 THR cc_start: 0.8392 (t) cc_final: 0.8145 (p) REVERT: Q 304 LEU cc_start: 0.8432 (pp) cc_final: 0.8181 (pp) REVERT: R 46 ASN cc_start: 0.8473 (m-40) cc_final: 0.8254 (m-40) REVERT: R 228 ILE cc_start: 0.8467 (tp) cc_final: 0.8101 (tt) REVERT: R 245 ARG cc_start: 0.7708 (ttt90) cc_final: 0.7462 (ttt90) REVERT: S 3 GLN cc_start: 0.7507 (tm-30) cc_final: 0.6907 (tm-30) REVERT: S 5 VAL cc_start: 0.8301 (OUTLIER) cc_final: 0.8097 (t) REVERT: S 42 GLU cc_start: 0.7096 (mp0) cc_final: 0.6857 (mp0) REVERT: S 213 THR cc_start: 0.8361 (t) cc_final: 0.8042 (p) REVERT: S 230 MET cc_start: 0.7840 (ttp) cc_final: 0.7632 (ttm) outliers start: 23 outliers final: 13 residues processed: 349 average time/residue: 0.1041 time to fit residues: 51.5027 Evaluate side-chains 339 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 324 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 153 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [82, 29, 40, 84, 76, 135, 28, 139, 34, 87, 105] chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 135 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 105 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 176 GLN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103022 restraints weight = 19379.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.106554 restraints weight = 9325.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108853 restraints weight = 5865.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110290 restraints weight = 4329.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111113 restraints weight = 3565.643| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11798 Z= 0.154 Angle : 0.654 7.345 16018 Z= 0.337 Chirality : 0.042 0.197 1814 Planarity : 0.004 0.064 1995 Dihedral : 6.848 65.900 1646 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.25 % Favored : 93.68 % Rotamer: Outliers : 2.96 % Allowed : 19.62 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.22), residues: 1439 helix: 0.73 (0.20), residues: 622 sheet: -1.34 (0.31), residues: 288 loop : -2.57 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 219 TYR 0.025 0.001 TYR S 235 PHE 0.019 0.001 PHE R 78 TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (11795) covalent geometry : angle 0.65278 / 0.34 (16012) SS BOND : bond 0.00815 / 0.40 ( 3) SS BOND : angle 2.09403 / 1.06 ( 6) hydrogen bonds : bond 0.04888 / 3.15 ( 550) hydrogen bonds : angle 4.54871 / 3.08 ( 1602) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7815 (ptt-90) cc_final: 0.7589 (ptt-90) REVERT: A 209 LYS cc_start: 0.8441 (mtpt) cc_final: 0.8202 (mtpt) REVERT: A 231 ASP cc_start: 0.7367 (t70) cc_final: 0.7053 (t0) REVERT: A 242 ARG cc_start: 0.7888 (mtt90) cc_final: 0.7260 (mtt90) REVERT: A 247 MET cc_start: 0.7696 (mtm) cc_final: 0.7440 (mtm) REVERT: A 289 GLU cc_start: 0.7012 (pm20) cc_final: 0.6674 (pm20) REVERT: A 303 ILE cc_start: 0.8017 (tp) cc_final: 0.7769 (tp) REVERT: A 308 GLU cc_start: 0.7618 (tt0) cc_final: 0.7299 (tt0) REVERT: A 345 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7851 (mtpp) REVERT: B 61 MET cc_start: 0.7301 (tmm) cc_final: 0.6816 (tmm) REVERT: B 98 SER cc_start: 0.8303 (m) cc_final: 0.7688 (t) REVERT: B 111 TYR cc_start: 0.8579 (m-80) cc_final: 0.8071 (m-80) REVERT: B 120 ILE cc_start: 0.8336 (pt) cc_final: 0.7749 (mt) REVERT: B 188 MET cc_start: 0.7871 (mmm) cc_final: 0.7408 (mmm) REVERT: B 195 ASP cc_start: 0.7611 (t70) cc_final: 0.7324 (t0) REVERT: B 237 ASN cc_start: 0.7665 (t0) cc_final: 0.7254 (t0) REVERT: B 239 ASN cc_start: 0.8368 (m-40) cc_final: 0.7801 (m-40) REVERT: B 291 ASP cc_start: 0.7684 (t70) cc_final: 0.7258 (t70) REVERT: B 300 LEU cc_start: 0.8201 (mt) cc_final: 0.7727 (mt) REVERT: B 338 ILE cc_start: 0.8129 (mt) cc_final: 0.7877 (mm) REVERT: C 55 ASN cc_start: 0.7686 (m-40) cc_final: 0.7352 (m-40) REVERT: Q 107 TYR cc_start: 0.8004 (t80) cc_final: 0.7540 (t80) REVERT: Q 179 VAL cc_start: 0.7001 (OUTLIER) cc_final: 0.6702 (m) REVERT: Q 201 LEU cc_start: 0.7934 (tp) cc_final: 0.7694 (tp) REVERT: Q 253 LEU cc_start: 0.8519 (mm) cc_final: 0.8300 (mm) REVERT: Q 262 MET cc_start: 0.6328 (tmm) cc_final: 0.5996 (tmm) REVERT: Q 283 PHE cc_start: 0.7171 (t80) cc_final: 0.6658 (t80) REVERT: R 46 ASN cc_start: 0.8471 (m-40) cc_final: 0.8269 (m-40) REVERT: R 55 ARG cc_start: 0.7806 (ttm110) cc_final: 0.6998 (ttm110) REVERT: R 228 ILE cc_start: 0.8492 (tp) cc_final: 0.8179 (tt) REVERT: R 245 ARG cc_start: 0.7698 (ttt90) cc_final: 0.7484 (ttt90) REVERT: S 3 GLN cc_start: 0.7482 (tm-30) cc_final: 0.6821 (tm-30) REVERT: S 42 GLU cc_start: 0.7119 (mp0) cc_final: 0.6876 (mp0) REVERT: S 77 ASN cc_start: 0.8897 (m-40) cc_final: 0.8653 (m-40) REVERT: S 230 MET cc_start: 0.7814 (ttp) cc_final: 0.7590 (ttm) outliers start: 37 outliers final: 22 residues processed: 359 average time/residue: 0.0989 time to fit residues: 50.6554 Evaluate side-chains 354 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 331 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [16, 47, 98, 12, 44, 112, 125, 25, 82, 38, 31] chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 112 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.4452 > 50:) chunk 125 optimal weight: 0.2980 chunk 25 optimal weight: 0.0670 chunk 82 optimal weight: 0.0770 chunk 38 optimal weight: 0.7980 chunk 31 optimal weight: 0.0670 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN ** R 301 ASN ** 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 = 0.3647 r_free = 0.3647 target = 0.131076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.107164 restraints weight = 19261.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110709 restraints weight = 9196.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113030 restraints weight = 5777.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.114466 restraints weight = 4259.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.115474 restraints weight = 3508.662| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11798 Z= 0.116 Angle : 0.619 7.104 16018 Z= 0.312 Chirality : 0.041 0.179 1814 Planarity : 0.004 0.062 1995 Dihedral : 5.674 51.450 1646 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 3.04 % Allowed : 22.50 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.22), residues: 1439 helix: 1.03 (0.21), residues: 624 sheet: -1.00 (0.32), residues: 275 loop : -2.41 (0.24), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 219 TYR 0.024 0.001 TYR S 235 PHE 0.014 0.001 PHE Q 291 TRP 0.010 0.001 TRP S 47 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (11795) covalent geometry : angle 0.61841 / 0.31 (16012) SS BOND : bond 0.00567 / 0.28 ( 3) SS BOND : angle 1.36789 / 0.68 ( 6) hydrogen bonds : bond 0.03877 / 2.50 ( 550) hydrogen bonds : angle 4.27166 / 2.91 ( 1602) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 335 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8381 (mtpt) cc_final: 0.8100 (mtpt) REVERT: A 218 VAL cc_start: 0.7306 (m) cc_final: 0.7053 (t) REVERT: A 231 ASP cc_start: 0.7233 (t70) cc_final: 0.6886 (t0) REVERT: A 247 MET cc_start: 0.7577 (mtm) cc_final: 0.7339 (mtm) REVERT: A 250 PHE cc_start: 0.8551 (t80) cc_final: 0.8347 (t80) REVERT: A 308 GLU cc_start: 0.7549 (tt0) cc_final: 0.7239 (tt0) REVERT: A 345 LYS cc_start: 0.8197 (mtpt) cc_final: 0.7807 (mtpp) REVERT: B 61 MET cc_start: 0.7242 (tmm) cc_final: 0.6773 (tmm) REVERT: B 98 SER cc_start: 0.8268 (m) cc_final: 0.7671 (t) REVERT: B 111 TYR cc_start: 0.8586 (m-80) cc_final: 0.8156 (m-80) REVERT: B 173 THR cc_start: 0.8551 (t) cc_final: 0.8202 (p) REVERT: B 195 ASP cc_start: 0.7618 (t70) cc_final: 0.7278 (t0) REVERT: B 237 ASN cc_start: 0.7640 (t0) cc_final: 0.7056 (t0) REVERT: B 239 ASN cc_start: 0.8345 (m-40) cc_final: 0.7696 (m110) REVERT: B 291 ASP cc_start: 0.7724 (t70) cc_final: 0.7339 (t70) REVERT: B 300 LEU cc_start: 0.8179 (mt) cc_final: 0.7757 (mt) REVERT: C 55 ASN cc_start: 0.7645 (m-40) cc_final: 0.7309 (m-40) REVERT: Q 179 VAL cc_start: 0.6941 (OUTLIER) cc_final: 0.6552 (t) REVERT: Q 201 LEU cc_start: 0.7935 (tp) cc_final: 0.7721 (tp) REVERT: Q 262 MET cc_start: 0.6286 (tmm) cc_final: 0.5856 (tmm) REVERT: Q 268 LYS cc_start: 0.8728 (tttm) cc_final: 0.8463 (ttmt) REVERT: Q 283 PHE cc_start: 0.7229 (t80) cc_final: 0.6689 (t80) REVERT: R 35 TYR cc_start: 0.8210 (m-80) cc_final: 0.7915 (m-80) REVERT: R 79 VAL cc_start: 0.8558 (t) cc_final: 0.8235 (p) REVERT: R 160 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8241 (mp) REVERT: R 165 MET cc_start: 0.7972 (tpt) cc_final: 0.7580 (tpp) REVERT: R 166 VAL cc_start: 0.8476 (m) cc_final: 0.8247 (p) REVERT: R 201 LEU cc_start: 0.8423 (mt) cc_final: 0.7983 (mt) REVERT: R 220 CYS cc_start: 0.8091 (m) cc_final: 0.7611 (m) REVERT: R 317 ARG cc_start: 0.7187 (mtm-85) cc_final: 0.6868 (mtm-85) REVERT: S 3 GLN cc_start: 0.7594 (tm-30) cc_final: 0.6875 (tm-30) REVERT: S 42 GLU cc_start: 0.7038 (mp0) cc_final: 0.6807 (mp0) REVERT: S 65 LYS cc_start: 0.8561 (tmtt) cc_final: 0.8197 (tmtt) REVERT: S 77 ASN cc_start: 0.8854 (m-40) cc_final: 0.8639 (m-40) outliers start: 38 outliers final: 21 residues processed: 355 average time/residue: 0.1006 time to fit residues: 50.9655 Evaluate side-chains 342 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 319 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [86, 95, 59, 20, 64, 81, 78, 84, 0, 12, 137] chunk 86 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 137 optimal weight: 0.0270 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 301 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.130507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.106503 restraints weight = 19208.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.110045 restraints weight = 9196.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112371 restraints weight = 5784.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.113674 restraints weight = 4288.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114684 restraints weight = 3572.313| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11798 Z= 0.123 Angle : 0.624 9.221 16018 Z= 0.314 Chirality : 0.041 0.159 1814 Planarity : 0.004 0.064 1995 Dihedral : 5.589 47.512 1646 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 3.36 % Allowed : 23.54 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.22), residues: 1439 helix: 1.10 (0.21), residues: 622 sheet: -0.93 (0.32), residues: 295 loop : -2.31 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 219 TYR 0.022 0.001 TYR S 235 PHE 0.018 0.001 PHE R 222 TRP 0.011 0.001 TRP Q 154 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (11795) covalent geometry : angle 0.62290 / 0.31 (16012) SS BOND : bond 0.00521 / 0.26 ( 3) SS BOND : angle 1.63559 / 0.85 ( 6) hydrogen bonds : bond 0.04060 / 2.61 ( 550) hydrogen bonds : angle 4.24872 / 2.89 ( 1602) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 338 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8145 (mtpt) REVERT: A 231 ASP cc_start: 0.7244 (t70) cc_final: 0.6916 (t0) REVERT: A 247 MET cc_start: 0.7595 (mtm) cc_final: 0.7351 (mtm) REVERT: A 308 GLU cc_start: 0.7547 (tt0) cc_final: 0.7227 (tt0) REVERT: A 345 LYS cc_start: 0.8183 (mtpt) cc_final: 0.7843 (mtpp) REVERT: B 17 GLN cc_start: 0.8006 (tm-30) cc_final: 0.7544 (tm-30) REVERT: B 34 THR cc_start: 0.7731 (t) cc_final: 0.7442 (t) REVERT: B 61 MET cc_start: 0.7304 (tmm) cc_final: 0.6728 (tmm) REVERT: B 98 SER cc_start: 0.8266 (m) cc_final: 0.7673 (t) REVERT: B 111 TYR cc_start: 0.8582 (m-80) cc_final: 0.8153 (m-80) REVERT: B 173 THR cc_start: 0.8563 (t) cc_final: 0.8227 (p) REVERT: B 188 MET cc_start: 0.7862 (mmm) cc_final: 0.7424 (mmm) REVERT: B 195 ASP cc_start: 0.7638 (t70) cc_final: 0.7281 (t0) REVERT: B 291 ASP cc_start: 0.7775 (t70) cc_final: 0.7315 (t70) REVERT: B 300 LEU cc_start: 0.8078 (mt) cc_final: 0.7720 (mt) REVERT: C 55 ASN cc_start: 0.7597 (m-40) cc_final: 0.7210 (m-40) REVERT: Q 107 TYR cc_start: 0.7951 (t80) cc_final: 0.7482 (t80) REVERT: Q 162 MET cc_start: 0.7715 (tpp) cc_final: 0.7273 (mpp) REVERT: Q 179 VAL cc_start: 0.6964 (OUTLIER) cc_final: 0.6599 (m) REVERT: Q 262 MET cc_start: 0.6287 (tmm) cc_final: 0.5862 (tmm) REVERT: Q 268 LYS cc_start: 0.8733 (tttm) cc_final: 0.8473 (ttmt) REVERT: Q 283 PHE cc_start: 0.7120 (t80) cc_final: 0.6543 (t80) REVERT: Q 288 MET cc_start: 0.8015 (mmt) cc_final: 0.7777 (mmm) REVERT: R 79 VAL cc_start: 0.8552 (t) cc_final: 0.8279 (p) REVERT: R 160 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8272 (mp) REVERT: R 165 MET cc_start: 0.7938 (tpt) cc_final: 0.7545 (tpp) REVERT: R 166 VAL cc_start: 0.8499 (m) cc_final: 0.8268 (p) REVERT: R 220 CYS cc_start: 0.8070 (m) cc_final: 0.7608 (m) REVERT: S 3 GLN cc_start: 0.7574 (tm-30) cc_final: 0.6851 (tm-30) REVERT: S 42 GLU cc_start: 0.7095 (mp0) cc_final: 0.6844 (mp0) REVERT: S 65 LYS cc_start: 0.8560 (tmtt) cc_final: 0.8198 (tmtt) REVERT: S 87 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7209 (mtt90) outliers start: 42 outliers final: 30 residues processed: 362 average time/residue: 0.0966 time to fit residues: 50.1826 Evaluate side-chains 370 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 338 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 34 ILE Chi-restraints excluded: chain Q residue 40 LEU Chi-restraints excluded: chain Q residue 67 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [38, 47, 62, 49, 35, 136, 63, 11, 28, 42, 92] chunk 38 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.3980 chunk 35 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 88 ASN B 259 GLN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.125229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101474 restraints weight = 19700.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.104911 restraints weight = 9412.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107160 restraints weight = 5919.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.108649 restraints weight = 4395.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109520 restraints weight = 3590.327| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11798 Z= 0.144 Angle : 0.637 10.391 16018 Z= 0.323 Chirality : 0.042 0.169 1814 Planarity : 0.004 0.064 1995 Dihedral : 5.781 48.332 1646 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 3.20 % Allowed : 24.34 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.22), residues: 1439 helix: 1.12 (0.21), residues: 620 sheet: -0.77 (0.32), residues: 289 loop : -2.30 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 219 TYR 0.025 0.001 TYR S 235 PHE 0.031 0.001 PHE R 222 TRP 0.011 0.001 TRP Q 154 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (11795) covalent geometry : angle 0.63568 / 0.32 (16012) SS BOND : bond 0.00727 / 0.36 ( 3) SS BOND : angle 1.90213 / 0.98 ( 6) hydrogen bonds : bond 0.04376 / 2.80 ( 550) hydrogen bonds : angle 4.33905 / 2.95 ( 1602) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 342 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 37 LEU cc_start: 0.8242 (tp) cc_final: 0.8019 (tt) REVERT: A 46 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8389 (mtmm) REVERT: A 209 LYS cc_start: 0.8398 (mtpt) cc_final: 0.8169 (mtpt) REVERT: A 231 ASP cc_start: 0.7275 (t70) cc_final: 0.6945 (t0) REVERT: A 247 MET cc_start: 0.7605 (mtm) cc_final: 0.7323 (mtm) REVERT: A 250 PHE cc_start: 0.8576 (t80) cc_final: 0.8374 (t80) REVERT: A 289 GLU cc_start: 0.7017 (pm20) cc_final: 0.6787 (pm20) REVERT: A 308 GLU cc_start: 0.7561 (tt0) cc_final: 0.7266 (tt0) REVERT: A 345 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7827 (mtpp) REVERT: B 17 GLN cc_start: 0.7998 (tm-30) cc_final: 0.7546 (tm-30) REVERT: B 34 THR cc_start: 0.7751 (t) cc_final: 0.7466 (t) REVERT: B 61 MET cc_start: 0.7321 (tmm) cc_final: 0.6729 (tmm) REVERT: B 98 SER cc_start: 0.8270 (m) cc_final: 0.7681 (t) REVERT: B 111 TYR cc_start: 0.8591 (m-80) cc_final: 0.8123 (m-80) REVERT: B 173 THR cc_start: 0.8570 (t) cc_final: 0.8251 (p) REVERT: B 188 MET cc_start: 0.7923 (mmm) cc_final: 0.7493 (mmm) REVERT: B 195 ASP cc_start: 0.7644 (t70) cc_final: 0.7287 (t0) REVERT: B 237 ASN cc_start: 0.7667 (t0) cc_final: 0.7223 (t0) REVERT: B 291 ASP cc_start: 0.7810 (t70) cc_final: 0.7345 (t70) REVERT: B 300 LEU cc_start: 0.8149 (mt) cc_final: 0.7756 (mt) REVERT: C 55 ASN cc_start: 0.7590 (m-40) cc_final: 0.7212 (m-40) REVERT: Q 107 TYR cc_start: 0.7995 (t80) cc_final: 0.7526 (t80) REVERT: Q 162 MET cc_start: 0.7734 (tpp) cc_final: 0.7322 (mpp) REVERT: Q 179 VAL cc_start: 0.6964 (OUTLIER) cc_final: 0.6602 (m) REVERT: Q 262 MET cc_start: 0.6374 (tmm) cc_final: 0.5956 (tmm) REVERT: Q 268 LYS cc_start: 0.8733 (tttm) cc_final: 0.8458 (ttmt) REVERT: Q 283 PHE cc_start: 0.7126 (t80) cc_final: 0.6607 (t80) REVERT: Q 288 MET cc_start: 0.8025 (mmt) cc_final: 0.7783 (mmt) REVERT: R 79 VAL cc_start: 0.8565 (t) cc_final: 0.8233 (p) REVERT: R 82 LEU cc_start: 0.8600 (mt) cc_final: 0.8240 (mm) REVERT: R 91 ARG cc_start: 0.8400 (ttp80) cc_final: 0.8174 (tmm-80) REVERT: R 160 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8320 (mp) REVERT: R 165 MET cc_start: 0.7950 (tpt) cc_final: 0.7574 (tpp) REVERT: R 166 VAL cc_start: 0.8506 (m) cc_final: 0.8243 (p) REVERT: R 201 LEU cc_start: 0.8461 (mt) cc_final: 0.8029 (mt) REVERT: R 220 CYS cc_start: 0.8103 (m) cc_final: 0.7673 (m) REVERT: R 317 ARG cc_start: 0.7172 (mtm-85) cc_final: 0.6868 (mtm-85) REVERT: S 3 GLN cc_start: 0.7470 (tm-30) cc_final: 0.6732 (tm-30) REVERT: S 42 GLU cc_start: 0.7088 (mp0) cc_final: 0.6848 (mp0) REVERT: S 65 LYS cc_start: 0.8607 (tmtt) cc_final: 0.8247 (tmtt) REVERT: S 230 MET cc_start: 0.7794 (ttp) cc_final: 0.7491 (ttm) outliers start: 40 outliers final: 31 residues processed: 361 average time/residue: 0.0964 time to fit residues: 49.7730 Evaluate side-chains 369 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 336 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain Q residue 290 ILE Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 174 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [35, 33, 76, 125, 17, 30, 126, 12, 71, 80, 60] chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 125 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 80 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.124877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.101054 restraints weight = 19458.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.104485 restraints weight = 9362.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106734 restraints weight = 5897.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108235 restraints weight = 4393.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.109120 restraints weight = 3585.729| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11798 Z= 0.155 Angle : 0.653 9.733 16018 Z= 0.331 Chirality : 0.043 0.199 1814 Planarity : 0.004 0.066 1995 Dihedral : 5.856 49.227 1646 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 3.04 % Allowed : 25.22 % Favored : 71.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.22), residues: 1439 helix: 1.12 (0.21), residues: 620 sheet: -0.89 (0.32), residues: 297 loop : -2.33 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 219 TYR 0.025 0.001 TYR S 235 PHE 0.017 0.001 PHE R 78 TRP 0.013 0.001 TRP R 261 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (11795) covalent geometry : angle 0.65161 / 0.33 (16012) SS BOND : bond 0.00686 / 0.34 ( 3) SS BOND : angle 1.98748 / 1.03 ( 6) hydrogen bonds : bond 0.04503 / 2.88 ( 550) hydrogen bonds : angle 4.35389 / 2.96 ( 1602) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 342 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7245 (mt-10) REVERT: A 46 LYS cc_start: 0.8603 (mtmm) cc_final: 0.8277 (mttm) REVERT: A 209 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8205 (mtpt) REVERT: A 231 ASP cc_start: 0.7311 (t70) cc_final: 0.7002 (t0) REVERT: A 247 MET cc_start: 0.7598 (mtm) cc_final: 0.7336 (mtm) REVERT: A 289 GLU cc_start: 0.7009 (pm20) cc_final: 0.6807 (pm20) REVERT: A 308 GLU cc_start: 0.7531 (tt0) cc_final: 0.7240 (tt0) REVERT: A 345 LYS cc_start: 0.8151 (mtpt) cc_final: 0.7803 (mtpp) REVERT: A 348 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8238 (mt) REVERT: B 17 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7549 (tm-30) REVERT: B 34 THR cc_start: 0.7729 (t) cc_final: 0.7456 (t) REVERT: B 61 MET cc_start: 0.7309 (tmm) cc_final: 0.6673 (tmm) REVERT: B 98 SER cc_start: 0.8285 (m) cc_final: 0.7696 (t) REVERT: B 173 THR cc_start: 0.8569 (t) cc_final: 0.8269 (p) REVERT: B 188 MET cc_start: 0.7975 (mmm) cc_final: 0.7496 (mmm) REVERT: B 195 ASP cc_start: 0.7645 (t70) cc_final: 0.7305 (t0) REVERT: B 237 ASN cc_start: 0.7672 (t0) cc_final: 0.7228 (t0) REVERT: B 291 ASP cc_start: 0.7816 (t70) cc_final: 0.7347 (t70) REVERT: B 300 LEU cc_start: 0.8186 (mt) cc_final: 0.7750 (mt) REVERT: C 55 ASN cc_start: 0.7619 (m-40) cc_final: 0.7260 (m-40) REVERT: Q 107 TYR cc_start: 0.8010 (t80) cc_final: 0.7540 (t80) REVERT: Q 179 VAL cc_start: 0.6998 (OUTLIER) cc_final: 0.6634 (m) REVERT: Q 262 MET cc_start: 0.6421 (tmm) cc_final: 0.5968 (tmm) REVERT: Q 268 LYS cc_start: 0.8720 (tttm) cc_final: 0.8443 (ttmt) REVERT: Q 283 PHE cc_start: 0.7134 (t80) cc_final: 0.6634 (t80) REVERT: Q 288 MET cc_start: 0.8033 (mmt) cc_final: 0.7793 (mmt) REVERT: R 79 VAL cc_start: 0.8597 (t) cc_final: 0.8256 (p) REVERT: R 82 LEU cc_start: 0.8606 (mt) cc_final: 0.8253 (mm) REVERT: R 160 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8329 (mp) REVERT: R 165 MET cc_start: 0.7950 (tpt) cc_final: 0.7583 (tpp) REVERT: R 166 VAL cc_start: 0.8505 (m) cc_final: 0.8231 (p) REVERT: R 220 CYS cc_start: 0.8090 (m) cc_final: 0.7650 (m) REVERT: R 317 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6881 (mtm-85) REVERT: S 3 GLN cc_start: 0.7436 (tm-30) cc_final: 0.6723 (tm-30) REVERT: S 42 GLU cc_start: 0.7114 (mp0) cc_final: 0.6890 (mp0) REVERT: S 65 LYS cc_start: 0.8601 (tmtt) cc_final: 0.8242 (tmtt) REVERT: S 245 LEU cc_start: 0.8382 (mt) cc_final: 0.8130 (mt) outliers start: 38 outliers final: 33 residues processed: 361 average time/residue: 0.0959 time to fit residues: 49.5905 Evaluate side-chains 375 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 339 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [119, 135, 101, 61, 7, 72, 88, 4, 67, 94, 108] chunk 119 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 61 optimal weight: 0.4980 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 0.4980 chunk 88 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** R 46 ASN ** 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 = 0.3617 r_free = 0.3617 target = 0.128747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.104680 restraints weight = 19174.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108183 restraints weight = 9230.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.110502 restraints weight = 5821.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.111913 restraints weight = 4328.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.112846 restraints weight = 3581.300| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11798 Z= 0.142 Angle : 0.656 9.426 16018 Z= 0.330 Chirality : 0.042 0.192 1814 Planarity : 0.004 0.064 1995 Dihedral : 5.842 48.955 1646 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 3.68 % Allowed : 25.54 % Favored : 70.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.22), residues: 1439 helix: 1.16 (0.21), residues: 619 sheet: -0.80 (0.33), residues: 287 loop : -2.27 (0.25), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 219 TYR 0.025 0.001 TYR S 235 PHE 0.015 0.001 PHE A 250 TRP 0.021 0.001 TRP R 261 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11795) covalent geometry : angle 0.65563 / 0.33 (16012) SS BOND : bond 0.00703 / 0.35 ( 3) SS BOND : angle 1.80866 / 0.93 ( 6) hydrogen bonds : bond 0.04376 / 2.78 ( 550) hydrogen bonds : angle 4.33035 / 2.95 ( 1602) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8272 (mttm) REVERT: A 192 LYS cc_start: 0.8153 (mttp) cc_final: 0.7943 (mttp) REVERT: A 209 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8219 (mtpt) REVERT: A 231 ASP cc_start: 0.7321 (t70) cc_final: 0.7003 (t0) REVERT: A 247 MET cc_start: 0.7623 (mtm) cc_final: 0.7320 (mtm) REVERT: A 308 GLU cc_start: 0.7543 (tt0) cc_final: 0.7236 (tt0) REVERT: A 345 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7798 (mtpp) REVERT: A 348 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8192 (mt) REVERT: B 17 GLN cc_start: 0.8012 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 34 THR cc_start: 0.7719 (t) cc_final: 0.7503 (t) REVERT: B 61 MET cc_start: 0.7289 (tmm) cc_final: 0.6723 (tmm) REVERT: B 98 SER cc_start: 0.8282 (m) cc_final: 0.7679 (t) REVERT: B 173 THR cc_start: 0.8573 (t) cc_final: 0.8276 (p) REVERT: B 188 MET cc_start: 0.7926 (mmm) cc_final: 0.7498 (mmm) REVERT: B 195 ASP cc_start: 0.7650 (t70) cc_final: 0.7300 (t0) REVERT: B 237 ASN cc_start: 0.7694 (t0) cc_final: 0.7221 (t0) REVERT: B 291 ASP cc_start: 0.7817 (t70) cc_final: 0.7336 (t70) REVERT: B 300 LEU cc_start: 0.8214 (mt) cc_final: 0.7803 (mt) REVERT: C 55 ASN cc_start: 0.7577 (m-40) cc_final: 0.7204 (m-40) REVERT: Q 107 TYR cc_start: 0.7986 (t80) cc_final: 0.7553 (t80) REVERT: Q 140 LEU cc_start: -0.1292 (OUTLIER) cc_final: -0.1531 (pp) REVERT: Q 179 VAL cc_start: 0.6953 (OUTLIER) cc_final: 0.6592 (m) REVERT: Q 262 MET cc_start: 0.6419 (tmm) cc_final: 0.5958 (tmm) REVERT: Q 268 LYS cc_start: 0.8720 (tttm) cc_final: 0.8425 (ttmt) REVERT: Q 283 PHE cc_start: 0.7126 (t80) cc_final: 0.6632 (t80) REVERT: Q 288 MET cc_start: 0.8033 (mmt) cc_final: 0.7782 (mmt) REVERT: R 79 VAL cc_start: 0.8593 (t) cc_final: 0.8243 (p) REVERT: R 82 LEU cc_start: 0.8586 (mt) cc_final: 0.8226 (mm) REVERT: R 90 TYR cc_start: 0.7678 (t80) cc_final: 0.7463 (t80) REVERT: R 160 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8320 (mp) REVERT: R 165 MET cc_start: 0.7934 (tpt) cc_final: 0.7563 (tpp) REVERT: R 166 VAL cc_start: 0.8498 (m) cc_final: 0.8236 (p) REVERT: R 220 CYS cc_start: 0.8094 (m) cc_final: 0.7656 (m) REVERT: R 300 VAL cc_start: 0.8571 (OUTLIER) cc_final: 0.8291 (p) REVERT: R 317 ARG cc_start: 0.7160 (mtm-85) cc_final: 0.6899 (mtm-85) REVERT: S 3 GLN cc_start: 0.7437 (tm-30) cc_final: 0.6678 (tm-30) REVERT: S 5 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7942 (p) REVERT: S 42 GLU cc_start: 0.7080 (mp0) cc_final: 0.6851 (mp0) REVERT: S 65 LYS cc_start: 0.8612 (tmtt) cc_final: 0.8258 (tmtt) outliers start: 46 outliers final: 36 residues processed: 364 average time/residue: 0.0975 time to fit residues: 50.8537 Evaluate side-chains 380 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 338 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 153 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain Q residue 212 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [23, 76, 127, 134, 93, 13, 52, 68, 104, 79, 19] chunk 23 optimal weight: 0.9980 chunk 76 optimal weight: 0.1980 chunk 127 optimal weight: 3.9990 chunk 134 optimal weight: 0.1980 chunk 93 optimal weight: 0.0060 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN 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 = 0.128986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.104360 restraints weight = 19089.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.108027 restraints weight = 8807.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110512 restraints weight = 5441.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.111921 restraints weight = 3972.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112979 restraints weight = 3300.730| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11798 Z= 0.122 Angle : 0.649 10.070 16018 Z= 0.323 Chirality : 0.042 0.216 1814 Planarity : 0.004 0.063 1995 Dihedral : 5.625 46.167 1646 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 3.36 % Allowed : 26.10 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.22), residues: 1439 helix: 1.22 (0.21), residues: 620 sheet: -0.73 (0.33), residues: 278 loop : -2.31 (0.24), residues: 541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.023 0.001 TYR S 235 PHE 0.017 0.001 PHE A 250 TRP 0.025 0.001 TRP R 261 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11795) covalent geometry : angle 0.64813 / 0.32 (16012) SS BOND : bond 0.00618 / 0.31 ( 3) SS BOND : angle 1.44079 / 0.74 ( 6) hydrogen bonds : bond 0.04037 / 2.57 ( 550) hydrogen bonds : angle 4.24150 / 2.90 ( 1602) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 333 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8472 (mtmm) cc_final: 0.8188 (mttm) REVERT: A 192 LYS cc_start: 0.8149 (mttp) cc_final: 0.7893 (mttp) REVERT: A 209 LYS cc_start: 0.8473 (mtpt) cc_final: 0.8227 (mtpt) REVERT: A 231 ASP cc_start: 0.7314 (t70) cc_final: 0.6981 (t0) REVERT: A 247 MET cc_start: 0.7637 (mtm) cc_final: 0.7338 (mtm) REVERT: A 280 LYS cc_start: 0.8028 (tppt) cc_final: 0.7592 (tppt) REVERT: A 308 GLU cc_start: 0.7551 (tt0) cc_final: 0.7243 (tt0) REVERT: A 345 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7794 (mtpp) REVERT: A 348 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8133 (mt) REVERT: B 17 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 19 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7403 (ttp-110) REVERT: B 34 THR cc_start: 0.7724 (t) cc_final: 0.7450 (t) REVERT: B 61 MET cc_start: 0.7357 (tmm) cc_final: 0.6733 (tmm) REVERT: B 98 SER cc_start: 0.8259 (m) cc_final: 0.7649 (t) REVERT: B 173 THR cc_start: 0.8560 (t) cc_final: 0.8233 (p) REVERT: B 188 MET cc_start: 0.7918 (mmm) cc_final: 0.7458 (mmm) REVERT: B 195 ASP cc_start: 0.7691 (t70) cc_final: 0.7333 (t0) REVERT: B 237 ASN cc_start: 0.7662 (t0) cc_final: 0.7199 (t0) REVERT: B 273 ILE cc_start: 0.7820 (OUTLIER) cc_final: 0.7419 (pt) REVERT: B 291 ASP cc_start: 0.7842 (t70) cc_final: 0.7373 (t70) REVERT: B 300 LEU cc_start: 0.8097 (mt) cc_final: 0.7708 (mt) REVERT: Q 107 TYR cc_start: 0.7895 (t80) cc_final: 0.7574 (t80) REVERT: Q 140 LEU cc_start: -0.1302 (OUTLIER) cc_final: -0.1543 (pp) REVERT: Q 162 MET cc_start: 0.7605 (tpp) cc_final: 0.7172 (mpp) REVERT: Q 179 VAL cc_start: 0.6989 (OUTLIER) cc_final: 0.6626 (m) REVERT: Q 262 MET cc_start: 0.6371 (tmm) cc_final: 0.5892 (tmm) REVERT: Q 268 LYS cc_start: 0.8711 (tttm) cc_final: 0.8412 (ttmt) REVERT: Q 283 PHE cc_start: 0.7131 (t80) cc_final: 0.6647 (t80) REVERT: Q 288 MET cc_start: 0.8035 (mmt) cc_final: 0.7794 (mmt) REVERT: R 79 VAL cc_start: 0.8548 (t) cc_final: 0.8215 (p) REVERT: R 82 LEU cc_start: 0.8556 (mt) cc_final: 0.8210 (mm) REVERT: R 160 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8283 (mp) REVERT: R 165 MET cc_start: 0.7880 (tpt) cc_final: 0.7506 (tpp) REVERT: R 166 VAL cc_start: 0.8477 (m) cc_final: 0.8248 (p) REVERT: R 220 CYS cc_start: 0.8087 (m) cc_final: 0.7653 (m) REVERT: R 272 MET cc_start: 0.6739 (ptt) cc_final: 0.6533 (ptt) REVERT: R 300 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8234 (p) REVERT: R 317 ARG cc_start: 0.7162 (mtm-85) cc_final: 0.6927 (mtm-85) REVERT: S 3 GLN cc_start: 0.7454 (tm-30) cc_final: 0.6673 (tm-30) REVERT: S 42 GLU cc_start: 0.7090 (mp0) cc_final: 0.6848 (mp0) REVERT: S 65 LYS cc_start: 0.8588 (tmtt) cc_final: 0.8232 (tmtt) outliers start: 42 outliers final: 33 residues processed: 358 average time/residue: 0.0926 time to fit residues: 47.8550 Evaluate side-chains 363 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 324 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLU Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 11 LEU Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [122, 87, 130, 65, 58, 134, 33, 19, 105, 1, 118] chunk 122 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 130 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 134 optimal weight: 0.0170 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 105 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 142 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.128284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.103615 restraints weight = 19404.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.107255 restraints weight = 8891.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.109746 restraints weight = 5493.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.111185 restraints weight = 4007.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112230 restraints weight = 3320.312| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11798 Z= 0.126 Angle : 0.656 11.096 16018 Z= 0.327 Chirality : 0.042 0.214 1814 Planarity : 0.004 0.061 1995 Dihedral : 5.580 44.225 1646 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.84 % Favored : 94.09 % Rotamer: Outliers : 3.12 % Allowed : 26.50 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.22), residues: 1439 helix: 1.23 (0.21), residues: 623 sheet: -0.72 (0.33), residues: 278 loop : -2.26 (0.24), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 219 TYR 0.024 0.001 TYR S 235 PHE 0.016 0.001 PHE A 250 TRP 0.030 0.001 TRP R 261 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (11795) covalent geometry : angle 0.65534 / 0.33 (16012) SS BOND : bond 0.00672 / 0.33 ( 3) SS BOND : angle 1.57330 / 0.83 ( 6) hydrogen bonds : bond 0.04074 / 2.59 ( 550) hydrogen bonds : angle 4.23372 / 2.91 ( 1602) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 332 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8197 (mttm) REVERT: A 192 LYS cc_start: 0.8174 (mttp) cc_final: 0.7913 (mttp) REVERT: A 209 LYS cc_start: 0.8512 (mtpt) cc_final: 0.8267 (mtpt) REVERT: A 231 ASP cc_start: 0.7306 (t70) cc_final: 0.6983 (t0) REVERT: A 247 MET cc_start: 0.7719 (mtm) cc_final: 0.7380 (mtm) REVERT: A 280 LYS cc_start: 0.8061 (tppt) cc_final: 0.7597 (tppt) REVERT: A 308 GLU cc_start: 0.7544 (tt0) cc_final: 0.7240 (tt0) REVERT: A 345 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7788 (mtpp) REVERT: A 348 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8189 (mt) REVERT: B 17 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7634 (tm-30) REVERT: B 19 ARG cc_start: 0.7776 (ttp-110) cc_final: 0.7386 (ttp-110) REVERT: B 34 THR cc_start: 0.7718 (t) cc_final: 0.7448 (t) REVERT: B 61 MET cc_start: 0.7347 (tmm) cc_final: 0.6717 (tmm) REVERT: B 98 SER cc_start: 0.8252 (m) cc_final: 0.7640 (t) REVERT: B 173 THR cc_start: 0.8561 (t) cc_final: 0.8216 (p) REVERT: B 188 MET cc_start: 0.7944 (mmm) cc_final: 0.7544 (mmm) REVERT: B 195 ASP cc_start: 0.7698 (t70) cc_final: 0.7330 (t0) REVERT: B 237 ASN cc_start: 0.7662 (t0) cc_final: 0.7196 (t0) REVERT: B 273 ILE cc_start: 0.7828 (OUTLIER) cc_final: 0.7624 (pt) REVERT: B 291 ASP cc_start: 0.7859 (t70) cc_final: 0.7397 (t70) REVERT: B 300 LEU cc_start: 0.8156 (mt) cc_final: 0.7790 (mt) REVERT: Q 107 TYR cc_start: 0.7950 (t80) cc_final: 0.7584 (t80) REVERT: Q 140 LEU cc_start: -0.1278 (OUTLIER) cc_final: -0.1520 (pp) REVERT: Q 162 MET cc_start: 0.7670 (tpp) cc_final: 0.7280 (mpp) REVERT: Q 179 VAL cc_start: 0.6990 (OUTLIER) cc_final: 0.6605 (m) REVERT: Q 262 MET cc_start: 0.6485 (tmm) cc_final: 0.5982 (tmm) REVERT: Q 268 LYS cc_start: 0.8725 (tttm) cc_final: 0.8431 (ttmt) REVERT: Q 283 PHE cc_start: 0.7144 (t80) cc_final: 0.6637 (t80) REVERT: Q 288 MET cc_start: 0.8059 (mmt) cc_final: 0.7808 (mmt) REVERT: R 44 THR cc_start: 0.8424 (t) cc_final: 0.8180 (t) REVERT: R 79 VAL cc_start: 0.8562 (t) cc_final: 0.8225 (p) REVERT: R 82 LEU cc_start: 0.8562 (mt) cc_final: 0.8225 (mm) REVERT: R 91 ARG cc_start: 0.8306 (ttp80) cc_final: 0.8096 (tmm-80) REVERT: R 160 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8275 (mp) REVERT: R 165 MET cc_start: 0.7885 (tpt) cc_final: 0.7511 (tpp) REVERT: R 166 VAL cc_start: 0.8467 (m) cc_final: 0.8239 (p) REVERT: R 220 CYS cc_start: 0.8096 (m) cc_final: 0.7676 (m) REVERT: R 244 ARG cc_start: 0.7380 (tpp80) cc_final: 0.6728 (tpp80) REVERT: R 300 VAL cc_start: 0.8523 (OUTLIER) cc_final: 0.8240 (p) REVERT: R 317 ARG cc_start: 0.7176 (mtm-85) cc_final: 0.6920 (mtm-85) REVERT: S 3 GLN cc_start: 0.7497 (tm-30) cc_final: 0.6692 (tm-30) REVERT: S 42 GLU cc_start: 0.7090 (mp0) cc_final: 0.6833 (mp0) REVERT: S 65 LYS cc_start: 0.8581 (tmtt) cc_final: 0.8228 (tmtt) REVERT: S 230 MET cc_start: 0.7769 (ttp) cc_final: 0.7497 (ttm) outliers start: 39 outliers final: 28 residues processed: 354 average time/residue: 0.1001 time to fit residues: 50.6806 Evaluate side-chains 363 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 329 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain Q residue 71 LEU Chi-restraints excluded: chain Q residue 109 ILE Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 179 VAL Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain R residue 102 CYS Chi-restraints excluded: chain R residue 124 SER Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 167 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 300 VAL Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 168 SER Chi-restraints excluded: chain S residue 169 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: [119, 58, 59, 1, 100, 99, 96, 83, 11, 128, 92] chunk 119 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 119 ASN ** R 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.126162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.101411 restraints weight = 19462.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.105065 restraints weight = 8975.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.107484 restraints weight = 5540.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.109014 restraints weight = 4062.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.109935 restraints weight = 3322.193| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11798 Z= 0.159 Angle : 0.680 10.888 16018 Z= 0.342 Chirality : 0.043 0.213 1814 Planarity : 0.005 0.058 1995 Dihedral : 5.853 45.891 1646 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.82 % Rotamer: Outliers : 2.48 % Allowed : 27.22 % Favored : 70.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.22), residues: 1439 helix: 1.22 (0.21), residues: 620 sheet: -0.72 (0.33), residues: 289 loop : -2.31 (0.24), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 219 TYR 0.028 0.001 TYR S 235 PHE 0.017 0.001 PHE R 78 TRP 0.033 0.001 TRP R 261 HIS 0.004 0.001 HIS B 142 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.16 (11795) covalent geometry : angle 0.67949 / 0.34 (16012) SS BOND : bond 0.00793 / 0.39 ( 3) SS BOND : angle 1.96744 / 1.02 ( 6) hydrogen bonds : bond 0.04553 / 2.89 ( 550) hydrogen bonds : angle 4.34079 / 2.98 ( 1602) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2148.38 seconds wall clock time: 37 minutes 46.64 seconds (2266.64 seconds total)