Starting phenix.real_space_refine on Fri Jun 13 09:20:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0l_32243/06_2025/7w0l_32243.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0l_32243/06_2025/7w0l_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0l_32243/06_2025/7w0l_32243.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0l_32243/06_2025/7w0l_32243.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0l_32243/06_2025/7w0l_32243.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0l_32243/06_2025/7w0l_32243.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ARG: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: 8.39, per 1000 atoms: 0.73 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: 4.18 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 1.09 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: 3.59 Time building geometry restraints manager: 4.00 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 321 or resid 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: 31.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 5.350 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.260 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 13.94 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.019 0.002 TRP A 211 HIS 0.008 0.002 HIS B 183 PHE 0.057 0.003 PHE R 291 TYR 0.044 0.003 TYR S 190 ARG 0.006 0.001 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.18111 ( 550) hydrogen bonds : angle 6.41359 ( 1602) SS BOND : bond 0.01496 ( 3) SS BOND : angle 3.67820 ( 6) covalent geometry : bond 0.00974 (11795) covalent geometry : angle 0.93912 (16012) *********************** 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 : 1.298 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: 0.7240 (t70) REVERT: A 237 ASP cc_start: 0.8987 (t0) cc_final: 0.8771 (t0) 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: 0.6615 (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: 0.7903 (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: 0.8165 (tt) REVERT: R 245 ARG cc_start: 0.7743 (ttt90) cc_final: 0.7479 (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: 0.7695 (mtp) outliers start: 1 outliers final: 0 residues processed: 375 average time/residue: 0.2592 time to fit residues: 136.1982 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 : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.8980 chunk 107 optimal weight: 0.2980 chunk 59 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 72 optimal weight: 50.0000 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 128 optimal weight: 0.5980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 259 GLN Q 318 GLN ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.102953 restraints weight = 19107.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.106440 restraints weight = 9182.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.108772 restraints weight = 5793.764| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11798 Z= 0.143 Angle : 0.682 8.989 16018 Z= 0.352 Chirality : 0.043 0.200 1814 Planarity : 0.004 0.059 1995 Dihedral : 7.810 100.397 1646 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.35 % Favored : 94.58 % Rotamer: Outliers : 1.68 % Allowed : 16.57 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.21), residues: 1439 helix: 0.35 (0.20), residues: 619 sheet: -1.58 (0.31), residues: 281 loop : -2.82 (0.22), residues: 539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.018 0.002 PHE A 196 TYR 0.027 0.001 TYR S 235 ARG 0.009 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05160 ( 550) hydrogen bonds : angle 4.79143 ( 1602) SS BOND : bond 0.00774 ( 3) SS BOND : angle 2.01543 ( 6) covalent geometry : bond 0.00300 (11795) covalent geometry : angle 0.68118 (16012) *********************** 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 360 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 339 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7855 (ptt-90) cc_final: 0.7622 (ptt-90) REVERT: A 46 LYS cc_start: 0.8643 (ptmt) cc_final: 0.8405 (ptpp) REVERT: A 197 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7775 (mtpp) REVERT: A 209 LYS cc_start: 0.8446 (mtpt) cc_final: 0.8178 (mtpt) REVERT: A 231 ASP cc_start: 0.7390 (t70) cc_final: 0.7101 (t70) REVERT: A 242 ARG cc_start: 0.7687 (mtt90) cc_final: 0.7141 (mtt90) REVERT: A 247 MET cc_start: 0.7780 (mtm) cc_final: 0.7500 (mtm) REVERT: A 289 GLU cc_start: 0.7040 (pm20) cc_final: 0.6654 (pm20) REVERT: A 303 ILE cc_start: 0.8040 (mm) cc_final: 0.7748 (tp) REVERT: A 308 GLU cc_start: 0.7589 (tt0) cc_final: 0.7287 (tt0) REVERT: A 345 LYS cc_start: 0.8209 (mtpt) cc_final: 0.7849 (mtpp) REVERT: B 19 ARG cc_start: 0.7727 (ttp-110) cc_final: 0.7410 (ttp-110) REVERT: B 61 MET cc_start: 0.7502 (tmm) cc_final: 0.6914 (tmm) REVERT: B 98 SER cc_start: 0.8299 (m) cc_final: 0.7759 (t) REVERT: B 111 TYR cc_start: 0.8562 (m-80) cc_final: 0.8097 (m-80) REVERT: B 120 ILE cc_start: 0.8346 (pt) cc_final: 0.7817 (mt) REVERT: B 195 ASP cc_start: 0.7700 (t70) cc_final: 0.7379 (t0) REVERT: B 291 ASP cc_start: 0.7581 (t70) cc_final: 0.7224 (t70) REVERT: B 300 LEU cc_start: 0.8230 (mt) cc_final: 0.7829 (mt) REVERT: B 325 MET cc_start: 0.7849 (mtt) cc_final: 0.7621 (mtm) REVERT: B 338 ILE cc_start: 0.8173 (mt) cc_final: 0.7909 (mm) REVERT: C 55 ASN cc_start: 0.7709 (m-40) cc_final: 0.7344 (m-40) REVERT: Q 71 LEU cc_start: 0.8769 (tt) cc_final: 0.8521 (tp) REVERT: Q 107 TYR cc_start: 0.8010 (t80) cc_final: 0.7527 (t80) REVERT: Q 162 MET cc_start: 0.7681 (tpp) cc_final: 0.7174 (mpp) REVERT: Q 179 VAL cc_start: 0.7043 (OUTLIER) cc_final: 0.6607 (t) REVERT: Q 201 LEU cc_start: 0.7932 (tp) cc_final: 0.7681 (tp) REVERT: Q 262 MET cc_start: 0.6331 (tmm) cc_final: 0.6049 (tmm) REVERT: Q 283 PHE cc_start: 0.7191 (t80) cc_final: 0.6682 (t80) REVERT: Q 295 THR cc_start: 0.8383 (t) cc_final: 0.8127 (p) REVERT: Q 304 LEU cc_start: 0.8451 (pp) cc_final: 0.8202 (pp) REVERT: R 46 ASN cc_start: 0.8485 (m-40) cc_final: 0.8255 (m-40) REVERT: R 228 ILE cc_start: 0.8470 (tp) cc_final: 0.8120 (tt) REVERT: R 245 ARG cc_start: 0.7750 (ttt90) cc_final: 0.7487 (ttt90) REVERT: S 3 GLN cc_start: 0.7494 (tm-30) cc_final: 0.6896 (tm-30) REVERT: S 5 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.8076 (t) REVERT: S 42 GLU cc_start: 0.7105 (mp0) cc_final: 0.6864 (mp0) REVERT: S 80 PHE cc_start: 0.8317 (m-80) cc_final: 0.7963 (m-80) REVERT: S 213 THR cc_start: 0.8366 (t) cc_final: 0.8033 (p) outliers start: 21 outliers final: 12 residues processed: 347 average time/residue: 0.2647 time to fit residues: 129.7347 Evaluate side-chains 338 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 324 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 312 LYS 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 284 ASP Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 168 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: chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 128 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 0.0170 chunk 52 optimal weight: 4.9990 overall best weight: 1.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3579 r_free = 0.3579 target = 0.126056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102221 restraints weight = 19307.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.105728 restraints weight = 9317.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.108060 restraints weight = 5886.679| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11798 Z= 0.185 Angle : 0.674 7.743 16018 Z= 0.350 Chirality : 0.043 0.212 1814 Planarity : 0.005 0.065 1995 Dihedral : 7.107 69.386 1646 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.46 % Favored : 93.47 % Rotamer: Outliers : 2.96 % Allowed : 19.46 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.22), residues: 1439 helix: 0.69 (0.20), residues: 621 sheet: -1.36 (0.31), residues: 288 loop : -2.61 (0.23), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP S 47 HIS 0.005 0.001 HIS S 35 PHE 0.020 0.002 PHE R 78 TYR 0.026 0.002 TYR S 190 ARG 0.010 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.05235 ( 550) hydrogen bonds : angle 4.65346 ( 1602) SS BOND : bond 0.01031 ( 3) SS BOND : angle 2.42233 ( 6) covalent geometry : bond 0.00420 (11795) covalent geometry : angle 0.67233 (16012) *********************** 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 375 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 338 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7860 (ptt-90) cc_final: 0.7627 (ptt-90) REVERT: A 209 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8232 (mtpt) REVERT: A 231 ASP cc_start: 0.7450 (t70) cc_final: 0.7141 (t0) REVERT: A 242 ARG cc_start: 0.7868 (mtt90) cc_final: 0.7342 (mtt90) REVERT: A 247 MET cc_start: 0.7746 (mtm) cc_final: 0.7479 (mtm) REVERT: A 256 ASN cc_start: 0.8270 (t0) cc_final: 0.8054 (t0) REVERT: A 289 GLU cc_start: 0.7073 (pm20) cc_final: 0.6728 (pm20) REVERT: A 308 GLU cc_start: 0.7653 (tt0) cc_final: 0.7324 (tt0) REVERT: A 345 LYS cc_start: 0.8243 (mtpt) cc_final: 0.7854 (mtpp) REVERT: B 61 MET cc_start: 0.7284 (tmm) cc_final: 0.6769 (tmm) REVERT: B 98 SER cc_start: 0.8302 (m) cc_final: 0.7684 (t) REVERT: B 111 TYR cc_start: 0.8577 (m-80) cc_final: 0.8046 (m-80) REVERT: B 120 ILE cc_start: 0.8363 (pt) cc_final: 0.7792 (mt) REVERT: B 188 MET cc_start: 0.7931 (mmm) cc_final: 0.7493 (mmm) REVERT: B 195 ASP cc_start: 0.7645 (t70) cc_final: 0.7369 (t0) REVERT: B 237 ASN cc_start: 0.7720 (t0) cc_final: 0.7345 (t0) REVERT: B 239 ASN cc_start: 0.8385 (m-40) cc_final: 0.7845 (m-40) REVERT: B 291 ASP cc_start: 0.7648 (t70) cc_final: 0.7234 (t70) REVERT: B 300 LEU cc_start: 0.8214 (mt) cc_final: 0.7755 (mt) REVERT: B 338 ILE cc_start: 0.8167 (mt) cc_final: 0.7886 (mm) REVERT: C 55 ASN cc_start: 0.7682 (m-40) cc_final: 0.7330 (m-40) REVERT: Q 107 TYR cc_start: 0.8062 (t80) cc_final: 0.7618 (t80) REVERT: Q 179 VAL cc_start: 0.7029 (OUTLIER) cc_final: 0.6731 (m) REVERT: Q 201 LEU cc_start: 0.7980 (tp) cc_final: 0.7738 (tp) REVERT: Q 253 LEU cc_start: 0.8531 (mm) cc_final: 0.8308 (mm) REVERT: Q 262 MET cc_start: 0.6354 (tmm) cc_final: 0.6055 (tmm) REVERT: Q 283 PHE cc_start: 0.7272 (t80) cc_final: 0.6722 (t80) REVERT: R 46 ASN cc_start: 0.8500 (m-40) cc_final: 0.8278 (m-40) REVERT: R 55 ARG cc_start: 0.7882 (ttm110) cc_final: 0.7012 (ttm110) REVERT: R 228 ILE cc_start: 0.8531 (tp) cc_final: 0.8217 (tt) REVERT: R 245 ARG cc_start: 0.7761 (ttt90) cc_final: 0.7535 (ttt90) REVERT: R 317 ARG cc_start: 0.7224 (mtm-85) cc_final: 0.6917 (mtm-85) REVERT: S 3 GLN cc_start: 0.7485 (tm-30) cc_final: 0.6844 (tm-30) REVERT: S 42 GLU cc_start: 0.7148 (mp0) cc_final: 0.6904 (mp0) REVERT: S 77 ASN cc_start: 0.8925 (m-40) cc_final: 0.8687 (m-40) outliers start: 37 outliers final: 23 residues processed: 357 average time/residue: 0.2395 time to fit residues: 119.1997 Evaluate side-chains 359 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 335 time to evaluate : 1.424 ------------------------------------------------------------------------------- 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 278 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 112 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 232 ILE 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 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 169 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 43 optimal weight: 0.0970 chunk 0 optimal weight: 5.9990 chunk 76 optimal weight: 0.4980 chunk 96 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 41 optimal weight: 0.0570 chunk 15 optimal weight: 0.5980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3578 r_free = 0.3578 target = 0.126068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102431 restraints weight = 19403.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105915 restraints weight = 9309.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108214 restraints weight = 5838.781| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11798 Z= 0.123 Angle : 0.627 7.195 16018 Z= 0.321 Chirality : 0.041 0.168 1814 Planarity : 0.004 0.064 1995 Dihedral : 6.208 55.389 1646 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.07 % Favored : 94.86 % Rotamer: Outliers : 3.52 % Allowed : 21.62 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.22), residues: 1439 helix: 0.99 (0.21), residues: 619 sheet: -1.17 (0.31), residues: 291 loop : -2.42 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE R 78 TYR 0.025 0.001 TYR S 235 ARG 0.010 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 550) hydrogen bonds : angle 4.40462 ( 1602) SS BOND : bond 0.00761 ( 3) SS BOND : angle 1.72815 ( 6) covalent geometry : bond 0.00258 (11795) covalent geometry : angle 0.62655 (16012) *********************** 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 383 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 339 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7799 (ptt-90) cc_final: 0.7584 (ptt-90) REVERT: A 197 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7662 (mtpp) REVERT: A 209 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8166 (mtpt) REVERT: A 231 ASP cc_start: 0.7342 (t70) cc_final: 0.7012 (t0) REVERT: A 242 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7353 (mtt90) REVERT: A 247 MET cc_start: 0.7690 (mtm) cc_final: 0.7416 (mtm) REVERT: A 289 GLU cc_start: 0.7032 (pm20) cc_final: 0.6731 (pm20) REVERT: A 308 GLU cc_start: 0.7560 (tt0) cc_final: 0.7255 (tt0) REVERT: A 345 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7853 (mtpp) REVERT: B 61 MET cc_start: 0.7253 (tmm) cc_final: 0.6804 (tmm) REVERT: B 98 SER cc_start: 0.8293 (m) cc_final: 0.7673 (t) REVERT: B 111 TYR cc_start: 0.8591 (m-80) cc_final: 0.8101 (m-80) REVERT: B 188 MET cc_start: 0.7835 (mmm) cc_final: 0.7390 (mmm) REVERT: B 195 ASP cc_start: 0.7639 (t70) cc_final: 0.7322 (t0) REVERT: B 237 ASN cc_start: 0.7648 (t0) cc_final: 0.7226 (t0) REVERT: B 239 ASN cc_start: 0.8381 (m-40) cc_final: 0.7779 (m-40) REVERT: B 291 ASP cc_start: 0.7778 (t70) cc_final: 0.7381 (t70) REVERT: B 300 LEU cc_start: 0.8214 (mt) cc_final: 0.7784 (mt) REVERT: C 55 ASN cc_start: 0.7661 (m-40) cc_final: 0.7326 (m-40) REVERT: Q 71 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8578 (tp) REVERT: Q 107 TYR cc_start: 0.7946 (t80) cc_final: 0.7468 (t80) REVERT: Q 162 MET cc_start: 0.7641 (mmm) cc_final: 0.7428 (mmm) REVERT: Q 179 VAL cc_start: 0.7046 (OUTLIER) cc_final: 0.6624 (t) REVERT: Q 201 LEU cc_start: 0.7944 (tp) cc_final: 0.7717 (tp) REVERT: Q 262 MET cc_start: 0.6259 (tmm) cc_final: 0.5855 (tmm) REVERT: Q 268 LYS cc_start: 0.8747 (tttm) cc_final: 0.8460 (ttmt) REVERT: Q 283 PHE cc_start: 0.7276 (t80) cc_final: 0.6724 (t80) REVERT: R 35 TYR cc_start: 0.8245 (m-80) cc_final: 0.7957 (m-80) REVERT: R 79 VAL cc_start: 0.8625 (t) cc_final: 0.8278 (p) REVERT: R 160 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8267 (mp) REVERT: R 166 VAL cc_start: 0.8491 (m) cc_final: 0.8205 (p) REVERT: R 201 LEU cc_start: 0.8469 (mt) cc_final: 0.8234 (mt) REVERT: R 220 CYS cc_start: 0.8079 (m) cc_final: 0.7655 (m) REVERT: R 228 ILE cc_start: 0.8518 (tp) cc_final: 0.8215 (tt) REVERT: R 317 ARG cc_start: 0.7213 (mtm-85) cc_final: 0.6924 (mtm-85) REVERT: S 3 GLN cc_start: 0.7555 (tm-30) cc_final: 0.6858 (tm-30) REVERT: S 42 GLU cc_start: 0.7053 (mp0) cc_final: 0.6850 (mp0) REVERT: S 65 LYS cc_start: 0.8667 (tmtt) cc_final: 0.8297 (tmtt) REVERT: S 77 ASN cc_start: 0.8891 (m-40) cc_final: 0.8648 (m110) outliers start: 44 outliers final: 25 residues processed: 364 average time/residue: 0.2927 time to fit residues: 149.2566 Evaluate side-chains 359 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 331 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 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 67 SER 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 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 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 160 LEU Chi-restraints excluded: chain R residue 284 ASP Chi-restraints excluded: chain R residue 315 ARG Chi-restraints excluded: chain S residue 5 VAL Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 1.9990 chunk 39 optimal weight: 0.0370 chunk 40 optimal weight: 0.7980 chunk 15 optimal weight: 0.3980 chunk 31 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 108 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.126833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.103126 restraints weight = 19311.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106618 restraints weight = 9223.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.108905 restraints weight = 5781.447| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2507 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= 0.125 Angle : 0.615 6.955 16018 Z= 0.315 Chirality : 0.041 0.165 1814 Planarity : 0.004 0.060 1995 Dihedral : 5.723 50.292 1646 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.37 % Rotamer: Outliers : 3.28 % Allowed : 22.90 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.22), residues: 1439 helix: 1.12 (0.21), residues: 619 sheet: -0.98 (0.32), residues: 296 loop : -2.35 (0.24), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 47 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE R 78 TYR 0.022 0.001 TYR S 235 ARG 0.012 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 550) hydrogen bonds : angle 4.32620 ( 1602) SS BOND : bond 0.00744 ( 3) SS BOND : angle 1.71072 ( 6) covalent geometry : bond 0.00267 (11795) covalent geometry : angle 0.61445 (16012) *********************** 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 382 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 341 time to evaluate : 2.673 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7758 (ptt-90) cc_final: 0.7540 (ptt-90) REVERT: A 46 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8001 (mtmm) REVERT: A 209 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8161 (mtpt) REVERT: A 218 VAL cc_start: 0.7344 (m) cc_final: 0.7116 (t) REVERT: A 231 ASP cc_start: 0.7302 (t70) cc_final: 0.6976 (t0) REVERT: A 242 ARG cc_start: 0.7924 (mtt90) cc_final: 0.7314 (mtt90) REVERT: A 247 MET cc_start: 0.7614 (mtm) cc_final: 0.7340 (mtm) REVERT: A 308 GLU cc_start: 0.7544 (tt0) cc_final: 0.7262 (tt0) REVERT: A 345 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7838 (mtpp) REVERT: B 17 GLN cc_start: 0.8014 (tm-30) cc_final: 0.7573 (tm-30) REVERT: B 61 MET cc_start: 0.7245 (tmm) cc_final: 0.6696 (tmm) REVERT: B 98 SER cc_start: 0.8263 (m) cc_final: 0.7676 (t) REVERT: B 111 TYR cc_start: 0.8580 (m-80) cc_final: 0.8108 (m-80) REVERT: B 188 MET cc_start: 0.7915 (mmm) cc_final: 0.7454 (mmm) REVERT: B 195 ASP cc_start: 0.7634 (t70) cc_final: 0.7303 (t0) REVERT: B 237 ASN cc_start: 0.7666 (t0) cc_final: 0.7109 (t0) REVERT: B 239 ASN cc_start: 0.8384 (m-40) cc_final: 0.7759 (m110) REVERT: B 291 ASP cc_start: 0.7802 (t70) cc_final: 0.7378 (t70) REVERT: B 300 LEU cc_start: 0.8106 (mt) cc_final: 0.7735 (mt) REVERT: C 55 ASN cc_start: 0.7617 (m-40) cc_final: 0.7237 (m-40) REVERT: Q 107 TYR cc_start: 0.7975 (t80) cc_final: 0.7589 (t80) REVERT: Q 179 VAL cc_start: 0.7008 (OUTLIER) cc_final: 0.6596 (t) REVERT: Q 253 LEU cc_start: 0.8514 (mm) cc_final: 0.8199 (mm) REVERT: Q 262 MET cc_start: 0.6268 (tmm) cc_final: 0.5870 (tmm) REVERT: Q 268 LYS cc_start: 0.8728 (tttm) cc_final: 0.8462 (ttmt) REVERT: Q 283 PHE cc_start: 0.7219 (t80) cc_final: 0.6637 (t80) REVERT: Q 288 MET cc_start: 0.7998 (mmt) cc_final: 0.7683 (mmt) REVERT: R 79 VAL cc_start: 0.8603 (t) cc_final: 0.8354 (p) REVERT: R 160 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8304 (mp) REVERT: R 165 MET cc_start: 0.7995 (tpt) cc_final: 0.7625 (tpp) REVERT: R 166 VAL cc_start: 0.8515 (m) cc_final: 0.8251 (p) REVERT: R 220 CYS cc_start: 0.8072 (m) cc_final: 0.7612 (m) REVERT: S 3 GLN cc_start: 0.7541 (tm-30) cc_final: 0.6858 (tm-30) REVERT: S 42 GLU cc_start: 0.7121 (mp0) cc_final: 0.6888 (mp0) REVERT: S 65 LYS cc_start: 0.8611 (tmtt) cc_final: 0.8256 (tmtt) REVERT: S 77 ASN cc_start: 0.8879 (m-40) cc_final: 0.8666 (m-40) REVERT: S 230 MET cc_start: 0.7763 (ttt) cc_final: 0.7504 (tpp) REVERT: S 245 LEU cc_start: 0.8386 (mt) cc_final: 0.8175 (mt) outliers start: 41 outliers final: 27 residues processed: 365 average time/residue: 0.3123 time to fit residues: 161.9948 Evaluate side-chains 359 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 329 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LYS Chi-restraints excluded: chain A residue 295 THR 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 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 40 LEU Chi-restraints excluded: chain Q residue 67 PHE 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 284 ASP Chi-restraints excluded: chain S residue 5 VAL 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 Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 105 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 86 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 54 optimal weight: 0.0470 chunk 129 optimal weight: 0.0010 chunk 14 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 overall best weight: 0.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.128044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.103829 restraints weight = 19410.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.107409 restraints weight = 9151.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.109756 restraints weight = 5710.998| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11798 Z= 0.131 Angle : 0.628 10.431 16018 Z= 0.319 Chirality : 0.041 0.200 1814 Planarity : 0.004 0.064 1995 Dihedral : 5.657 46.521 1646 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.44 % Rotamer: Outliers : 2.96 % Allowed : 24.50 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1439 helix: 1.15 (0.21), residues: 619 sheet: -0.81 (0.32), residues: 289 loop : -2.32 (0.24), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 261 HIS 0.004 0.001 HIS S 35 PHE 0.031 0.001 PHE R 222 TYR 0.024 0.001 TYR S 235 ARG 0.012 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04272 ( 550) hydrogen bonds : angle 4.31673 ( 1602) SS BOND : bond 0.00732 ( 3) SS BOND : angle 1.75773 ( 6) covalent geometry : bond 0.00287 (11795) covalent geometry : angle 0.62670 (16012) *********************** 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 380 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 1.363 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7750 (ptt-90) cc_final: 0.7545 (ptt-90) REVERT: A 209 LYS cc_start: 0.8442 (mtpt) cc_final: 0.8207 (mtpt) REVERT: A 218 VAL cc_start: 0.7343 (m) cc_final: 0.7105 (t) REVERT: A 231 ASP cc_start: 0.7307 (t70) cc_final: 0.6982 (t0) REVERT: A 247 MET cc_start: 0.7619 (mtm) cc_final: 0.7350 (mtm) REVERT: A 256 ASN cc_start: 0.8246 (t0) cc_final: 0.8035 (t0) REVERT: A 308 GLU cc_start: 0.7567 (tt0) cc_final: 0.7261 (tt0) REVERT: A 345 LYS cc_start: 0.8211 (mtpt) cc_final: 0.7852 (mtpp) REVERT: B 17 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7632 (tm-30) REVERT: B 61 MET cc_start: 0.7254 (tmm) cc_final: 0.6743 (tmm) REVERT: B 98 SER cc_start: 0.8267 (m) cc_final: 0.7677 (t) REVERT: B 188 MET cc_start: 0.7930 (mmm) cc_final: 0.7491 (mmm) REVERT: B 195 ASP cc_start: 0.7642 (t70) cc_final: 0.7294 (t0) REVERT: B 237 ASN cc_start: 0.7693 (t0) cc_final: 0.7193 (t0) REVERT: B 239 ASN cc_start: 0.8388 (m-40) cc_final: 0.7730 (m110) REVERT: B 291 ASP cc_start: 0.7834 (t70) cc_final: 0.7379 (t70) REVERT: B 300 LEU cc_start: 0.8166 (mt) cc_final: 0.7790 (mt) REVERT: C 55 ASN cc_start: 0.7613 (m-40) cc_final: 0.7208 (m-40) REVERT: Q 107 TYR cc_start: 0.8024 (t80) cc_final: 0.7524 (t80) REVERT: Q 162 MET cc_start: 0.7677 (mmm) cc_final: 0.7423 (mmm) REVERT: Q 179 VAL cc_start: 0.6962 (OUTLIER) cc_final: 0.6562 (t) REVERT: Q 253 LEU cc_start: 0.8521 (mm) cc_final: 0.8222 (mm) REVERT: Q 262 MET cc_start: 0.6359 (tmm) cc_final: 0.5936 (tmm) REVERT: Q 268 LYS cc_start: 0.8720 (tttm) cc_final: 0.8487 (ttmt) REVERT: Q 283 PHE cc_start: 0.7202 (t80) cc_final: 0.6632 (t80) REVERT: Q 288 MET cc_start: 0.8017 (mmt) cc_final: 0.7776 (mmt) REVERT: R 79 VAL cc_start: 0.8603 (t) cc_final: 0.8337 (p) REVERT: R 160 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8288 (mp) REVERT: R 165 MET cc_start: 0.7985 (tpt) cc_final: 0.7604 (tpp) REVERT: R 166 VAL cc_start: 0.8493 (m) cc_final: 0.8245 (p) REVERT: R 220 CYS cc_start: 0.8117 (m) cc_final: 0.7687 (m) REVERT: R 317 ARG cc_start: 0.7207 (mtm-85) cc_final: 0.6906 (mtm-85) REVERT: S 3 GLN cc_start: 0.7499 (tm-30) cc_final: 0.6814 (tm-30) REVERT: S 42 GLU cc_start: 0.7080 (mp0) cc_final: 0.6860 (mp0) REVERT: S 65 LYS cc_start: 0.8583 (tmtt) cc_final: 0.8219 (tmtt) REVERT: S 77 ASN cc_start: 0.8885 (m-40) cc_final: 0.8678 (m-40) outliers start: 37 outliers final: 30 residues processed: 362 average time/residue: 0.2993 time to fit residues: 153.7748 Evaluate side-chains 367 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 335 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU 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 278 PHE Chi-restraints excluded: chain Q residue 40 LEU 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 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 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 LEU Chi-restraints excluded: chain S residue 213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 125 optimal weight: 0.0970 chunk 54 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 60 optimal weight: 0.0570 chunk 22 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3592 r_free = 0.3592 target = 0.127015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.103096 restraints weight = 19657.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106543 restraints weight = 9354.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108907 restraints weight = 5879.090| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11798 Z= 0.130 Angle : 0.632 9.880 16018 Z= 0.320 Chirality : 0.042 0.185 1814 Planarity : 0.004 0.066 1995 Dihedral : 5.700 43.517 1646 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.70 % Favored : 94.23 % Rotamer: Outliers : 3.04 % Allowed : 25.14 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1439 helix: 1.13 (0.21), residues: 621 sheet: -0.71 (0.33), residues: 281 loop : -2.33 (0.24), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 261 HIS 0.004 0.001 HIS S 35 PHE 0.014 0.001 PHE R 78 TYR 0.023 0.001 TYR S 235 ARG 0.012 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04169 ( 550) hydrogen bonds : angle 4.30118 ( 1602) SS BOND : bond 0.00677 ( 3) SS BOND : angle 1.78523 ( 6) covalent geometry : bond 0.00285 (11795) covalent geometry : angle 0.63163 (16012) *********************** 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 379 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 341 time to evaluate : 2.172 Fit side-chains revert: symmetry clash REVERT: A 209 LYS cc_start: 0.8438 (mtpt) cc_final: 0.8201 (mtpt) REVERT: A 218 VAL cc_start: 0.7343 (m) cc_final: 0.7107 (t) REVERT: A 231 ASP cc_start: 0.7304 (t70) cc_final: 0.6987 (t0) REVERT: A 247 MET cc_start: 0.7631 (mtm) cc_final: 0.7361 (mtm) REVERT: A 256 ASN cc_start: 0.8243 (t0) cc_final: 0.8037 (t0) REVERT: A 308 GLU cc_start: 0.7577 (tt0) cc_final: 0.7262 (tt0) REVERT: A 345 LYS cc_start: 0.8203 (mtpt) cc_final: 0.7817 (mtpp) REVERT: B 17 GLN cc_start: 0.8057 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 61 MET cc_start: 0.7256 (tmm) cc_final: 0.6679 (tmm) REVERT: B 98 SER cc_start: 0.8267 (m) cc_final: 0.7693 (t) REVERT: B 188 MET cc_start: 0.7887 (mmm) cc_final: 0.7434 (mmm) REVERT: B 195 ASP cc_start: 0.7656 (t70) cc_final: 0.7311 (t0) REVERT: B 291 ASP cc_start: 0.7849 (t70) cc_final: 0.7388 (t70) REVERT: B 300 LEU cc_start: 0.8158 (mt) cc_final: 0.7789 (mt) REVERT: C 55 ASN cc_start: 0.7628 (m-40) cc_final: 0.7232 (m-40) REVERT: Q 107 TYR cc_start: 0.8001 (t80) cc_final: 0.7502 (t80) REVERT: Q 162 MET cc_start: 0.7647 (mmm) cc_final: 0.7406 (mmm) REVERT: Q 179 VAL cc_start: 0.6879 (OUTLIER) cc_final: 0.6485 (t) REVERT: Q 253 LEU cc_start: 0.8522 (mm) cc_final: 0.8189 (mm) REVERT: Q 262 MET cc_start: 0.6390 (tmm) cc_final: 0.5934 (tmm) REVERT: Q 268 LYS cc_start: 0.8696 (tttm) cc_final: 0.8422 (ttmt) REVERT: Q 283 PHE cc_start: 0.7209 (t80) cc_final: 0.6663 (t80) REVERT: Q 288 MET cc_start: 0.8070 (mmt) cc_final: 0.7815 (mmt) REVERT: R 79 VAL cc_start: 0.8609 (t) cc_final: 0.8284 (p) REVERT: R 82 LEU cc_start: 0.8617 (mt) cc_final: 0.8265 (mm) REVERT: R 160 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8297 (mp) REVERT: R 165 MET cc_start: 0.7966 (tpt) cc_final: 0.7587 (tpp) REVERT: R 166 VAL cc_start: 0.8481 (m) cc_final: 0.8231 (p) REVERT: R 201 LEU cc_start: 0.8451 (mt) cc_final: 0.8017 (mt) REVERT: R 220 CYS cc_start: 0.8120 (m) cc_final: 0.7683 (m) REVERT: R 317 ARG cc_start: 0.7197 (mtm-85) cc_final: 0.6905 (mtm-85) REVERT: S 3 GLN cc_start: 0.7472 (tm-30) cc_final: 0.6744 (tm-30) REVERT: S 42 GLU cc_start: 0.7097 (mp0) cc_final: 0.6877 (mp0) REVERT: S 65 LYS cc_start: 0.8580 (tmtt) cc_final: 0.8218 (tmtt) REVERT: S 77 ASN cc_start: 0.8901 (m-40) cc_final: 0.8689 (m-40) outliers start: 38 outliers final: 30 residues processed: 358 average time/residue: 0.3187 time to fit residues: 163.0013 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 : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 LEU 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 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 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 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 169 ASN Chi-restraints excluded: chain S residue 174 LEU Chi-restraints excluded: chain S residue 195 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: chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 137 optimal weight: 0.0670 chunk 53 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.126529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.102612 restraints weight = 19377.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.106098 restraints weight = 9287.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108396 restraints weight = 5836.260| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2777 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 : 0.648 9.793 16018 Z= 0.328 Chirality : 0.042 0.170 1814 Planarity : 0.004 0.065 1995 Dihedral : 5.814 41.392 1646 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 2.96 % Allowed : 25.46 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.22), residues: 1439 helix: 1.16 (0.21), residues: 620 sheet: -0.79 (0.33), residues: 285 loop : -2.33 (0.24), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 261 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.001 PHE R 78 TYR 0.025 0.001 TYR S 235 ARG 0.012 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04328 ( 550) hydrogen bonds : angle 4.34826 ( 1602) SS BOND : bond 0.00810 ( 3) SS BOND : angle 2.00589 ( 6) covalent geometry : bond 0.00322 (11795) covalent geometry : angle 0.64732 (16012) *********************** 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 373 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 336 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8124 (mttp) cc_final: 0.7919 (mttp) REVERT: A 209 LYS cc_start: 0.8461 (mtpt) cc_final: 0.8216 (mtpt) REVERT: A 231 ASP cc_start: 0.7333 (t70) cc_final: 0.7017 (t0) REVERT: A 247 MET cc_start: 0.7717 (mtm) cc_final: 0.7413 (mtm) REVERT: A 308 GLU cc_start: 0.7571 (tt0) cc_final: 0.7259 (tt0) REVERT: A 345 LYS cc_start: 0.8215 (mtpt) cc_final: 0.7824 (mtpp) REVERT: B 17 GLN cc_start: 0.8024 (tm-30) cc_final: 0.7638 (tm-30) REVERT: B 61 MET cc_start: 0.7260 (tmm) cc_final: 0.6671 (tmm) REVERT: B 98 SER cc_start: 0.8280 (m) cc_final: 0.7701 (t) REVERT: B 188 MET cc_start: 0.7931 (mmm) cc_final: 0.7479 (mmm) REVERT: B 195 ASP cc_start: 0.7683 (t70) cc_final: 0.7343 (t0) REVERT: B 291 ASP cc_start: 0.7863 (t70) cc_final: 0.7399 (t70) REVERT: B 300 LEU cc_start: 0.8198 (mt) cc_final: 0.7800 (mt) REVERT: C 55 ASN cc_start: 0.7623 (m-40) cc_final: 0.7242 (m-40) REVERT: Q 107 TYR cc_start: 0.8021 (t80) cc_final: 0.7639 (t80) REVERT: Q 179 VAL cc_start: 0.6860 (OUTLIER) cc_final: 0.6466 (t) REVERT: Q 262 MET cc_start: 0.6376 (tmm) cc_final: 0.5938 (tmm) REVERT: Q 268 LYS cc_start: 0.8702 (tttm) cc_final: 0.8419 (ttmt) REVERT: Q 283 PHE cc_start: 0.7184 (t80) cc_final: 0.6675 (t80) REVERT: Q 288 MET cc_start: 0.8084 (mmt) cc_final: 0.7811 (mmt) REVERT: R 79 VAL cc_start: 0.8622 (t) cc_final: 0.8285 (p) REVERT: R 82 LEU cc_start: 0.8627 (mt) cc_final: 0.8290 (mm) REVERT: R 160 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8317 (mp) REVERT: R 165 MET cc_start: 0.7964 (tpt) cc_final: 0.7596 (tpp) REVERT: R 166 VAL cc_start: 0.8483 (m) cc_final: 0.8232 (p) REVERT: R 220 CYS cc_start: 0.8105 (m) cc_final: 0.7673 (m) REVERT: R 317 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6944 (mtm-85) REVERT: S 3 GLN cc_start: 0.7469 (tm-30) cc_final: 0.6714 (tm-30) REVERT: S 5 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7945 (p) REVERT: S 42 GLU cc_start: 0.7100 (mp0) cc_final: 0.6875 (mp0) REVERT: S 65 LYS cc_start: 0.8617 (tmtt) cc_final: 0.8250 (tmtt) REVERT: S 77 ASN cc_start: 0.8899 (m-40) cc_final: 0.8676 (m-40) outliers start: 37 outliers final: 29 residues processed: 354 average time/residue: 0.2481 time to fit residues: 123.8233 Evaluate side-chains 366 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 334 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 312 LYS Chi-restraints excluded: chain A residue 353 LEU 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 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 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL 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: chunk 124 optimal weight: 1.9990 chunk 68 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 131 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 111 optimal weight: 0.0050 chunk 37 optimal weight: 0.7980 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.104271 restraints weight = 19266.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107849 restraints weight = 9139.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.110182 restraints weight = 5697.063| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11798 Z= 0.133 Angle : 0.642 9.851 16018 Z= 0.324 Chirality : 0.042 0.161 1814 Planarity : 0.004 0.066 1995 Dihedral : 5.755 38.978 1646 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.77 % Favored : 94.16 % Rotamer: Outliers : 3.20 % Allowed : 25.62 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.22), residues: 1439 helix: 1.19 (0.21), residues: 621 sheet: -0.88 (0.32), residues: 296 loop : -2.35 (0.25), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 261 HIS 0.004 0.001 HIS S 35 PHE 0.015 0.001 PHE R 78 TYR 0.024 0.001 TYR S 235 ARG 0.010 0.000 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 550) hydrogen bonds : angle 4.30502 ( 1602) SS BOND : bond 0.00727 ( 3) SS BOND : angle 1.72307 ( 6) covalent geometry : bond 0.00293 (11795) covalent geometry : angle 0.64147 (16012) *********************** 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 377 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 337 time to evaluate : 1.286 Fit side-chains revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8124 (mttp) cc_final: 0.7886 (mttp) REVERT: A 209 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8217 (mtpt) REVERT: A 231 ASP cc_start: 0.7336 (t70) cc_final: 0.7022 (t0) REVERT: A 247 MET cc_start: 0.7703 (mtm) cc_final: 0.7409 (mtm) REVERT: A 308 GLU cc_start: 0.7562 (tt0) cc_final: 0.7245 (tt0) REVERT: A 345 LYS cc_start: 0.8212 (mtpt) cc_final: 0.7812 (mtpp) REVERT: B 17 GLN cc_start: 0.8050 (tm-30) cc_final: 0.7691 (tm-30) REVERT: B 61 MET cc_start: 0.7256 (tmm) cc_final: 0.6674 (tmm) REVERT: B 98 SER cc_start: 0.8286 (m) cc_final: 0.7710 (t) REVERT: B 188 MET cc_start: 0.7897 (mmm) cc_final: 0.7418 (mmm) REVERT: B 195 ASP cc_start: 0.7682 (t70) cc_final: 0.7347 (t0) REVERT: B 291 ASP cc_start: 0.7869 (t70) cc_final: 0.7405 (t70) REVERT: B 300 LEU cc_start: 0.8188 (mt) cc_final: 0.7811 (mt) REVERT: C 55 ASN cc_start: 0.7609 (m-40) cc_final: 0.7241 (m-40) REVERT: Q 107 TYR cc_start: 0.8014 (t80) cc_final: 0.7550 (t80) REVERT: Q 140 LEU cc_start: -0.1224 (OUTLIER) cc_final: -0.1464 (pp) REVERT: Q 179 VAL cc_start: 0.6906 (OUTLIER) cc_final: 0.6502 (t) REVERT: Q 262 MET cc_start: 0.6359 (tmm) cc_final: 0.5914 (tmm) REVERT: Q 268 LYS cc_start: 0.8697 (tttm) cc_final: 0.8412 (ttmt) REVERT: Q 283 PHE cc_start: 0.7205 (t80) cc_final: 0.6681 (t80) REVERT: Q 288 MET cc_start: 0.8068 (mmt) cc_final: 0.7795 (mmt) REVERT: R 79 VAL cc_start: 0.8602 (t) cc_final: 0.8266 (p) REVERT: R 82 LEU cc_start: 0.8609 (mt) cc_final: 0.8265 (mm) REVERT: R 160 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8315 (mp) REVERT: R 165 MET cc_start: 0.7958 (tpt) cc_final: 0.7576 (tpp) REVERT: R 166 VAL cc_start: 0.8466 (m) cc_final: 0.8226 (p) REVERT: R 220 CYS cc_start: 0.8099 (m) cc_final: 0.7662 (m) REVERT: R 317 ARG cc_start: 0.7206 (mtm-85) cc_final: 0.6944 (mtm-85) REVERT: S 3 GLN cc_start: 0.7441 (tm-30) cc_final: 0.6702 (tm-30) REVERT: S 42 GLU cc_start: 0.7102 (mp0) cc_final: 0.6875 (mp0) REVERT: S 65 LYS cc_start: 0.8615 (tmtt) cc_final: 0.8244 (tmtt) REVERT: S 77 ASN cc_start: 0.8878 (m-40) cc_final: 0.8678 (m-40) outliers start: 40 outliers final: 32 residues processed: 356 average time/residue: 0.2821 time to fit residues: 141.3870 Evaluate side-chains 371 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 336 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 353 LEU 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 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 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 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 64 optimal weight: 9.9990 chunk 102 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 109 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 132 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 57 optimal weight: 0.9990 chunk 48 optimal weight: 0.0270 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.127185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.102553 restraints weight = 19199.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.106220 restraints weight = 8872.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108629 restraints weight = 5469.575| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.003 0.031 11798 Z= 0.137 Angle : 0.662 10.672 16018 Z= 0.335 Chirality : 0.042 0.181 1814 Planarity : 0.004 0.065 1995 Dihedral : 5.789 37.276 1646 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 3.20 % Allowed : 26.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.22), residues: 1439 helix: 1.20 (0.21), residues: 621 sheet: -0.80 (0.32), residues: 289 loop : -2.32 (0.24), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 261 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.001 PHE R 78 TYR 0.024 0.001 TYR S 235 ARG 0.010 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 550) hydrogen bonds : angle 4.32757 ( 1602) SS BOND : bond 0.00766 ( 3) SS BOND : angle 1.78791 ( 6) covalent geometry : bond 0.00301 (11795) covalent geometry : angle 0.66123 (16012) ********************** 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 376 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 336 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 LYS cc_start: 0.8159 (mttp) cc_final: 0.7889 (mttp) REVERT: A 209 LYS cc_start: 0.8489 (mtpt) cc_final: 0.8249 (mtpt) REVERT: A 231 ASP cc_start: 0.7414 (t70) cc_final: 0.7094 (t0) REVERT: A 247 MET cc_start: 0.7803 (mtm) cc_final: 0.7474 (mtm) REVERT: A 280 LYS cc_start: 0.8062 (tppt) cc_final: 0.7600 (tppt) REVERT: A 308 GLU cc_start: 0.7638 (tt0) cc_final: 0.7286 (tt0) REVERT: A 345 LYS cc_start: 0.8177 (mtpt) cc_final: 0.7791 (mtpp) REVERT: B 17 GLN cc_start: 0.8066 (tm-30) cc_final: 0.7762 (tm-30) REVERT: B 61 MET cc_start: 0.7309 (tmm) cc_final: 0.6696 (tmm) REVERT: B 98 SER cc_start: 0.8287 (m) cc_final: 0.7676 (t) REVERT: B 188 MET cc_start: 0.7987 (mmm) cc_final: 0.7484 (mmm) REVERT: B 195 ASP cc_start: 0.7730 (t70) cc_final: 0.7356 (t0) REVERT: B 291 ASP cc_start: 0.7892 (t70) cc_final: 0.7440 (t70) REVERT: B 300 LEU cc_start: 0.8150 (mt) cc_final: 0.7746 (mt) REVERT: C 55 ASN cc_start: 0.7559 (m-40) cc_final: 0.7197 (m-40) REVERT: Q 107 TYR cc_start: 0.8023 (t80) cc_final: 0.7549 (t80) REVERT: Q 140 LEU cc_start: -0.1195 (OUTLIER) cc_final: -0.1436 (pp) REVERT: Q 162 MET cc_start: 0.7636 (tpp) cc_final: 0.7191 (mpp) REVERT: Q 179 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6532 (t) REVERT: Q 262 MET cc_start: 0.6508 (tmm) cc_final: 0.6033 (tmm) REVERT: Q 268 LYS cc_start: 0.8722 (tttm) cc_final: 0.8432 (ttmt) REVERT: Q 283 PHE cc_start: 0.7276 (t80) cc_final: 0.6720 (t80) REVERT: Q 288 MET cc_start: 0.8111 (mmt) cc_final: 0.7824 (mmt) REVERT: R 79 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8231 (p) REVERT: R 82 LEU cc_start: 0.8593 (mt) cc_final: 0.8266 (mm) REVERT: R 160 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8289 (mp) REVERT: R 165 MET cc_start: 0.7960 (tpt) cc_final: 0.7566 (tpp) REVERT: R 166 VAL cc_start: 0.8434 (m) cc_final: 0.8205 (p) REVERT: R 220 CYS cc_start: 0.8104 (m) cc_final: 0.7667 (m) REVERT: R 317 ARG cc_start: 0.7217 (mtm-85) cc_final: 0.6988 (mtm-85) REVERT: S 3 GLN cc_start: 0.7499 (tm-30) cc_final: 0.6703 (tm-30) REVERT: S 42 GLU cc_start: 0.7107 (mp0) cc_final: 0.6860 (mp0) REVERT: S 77 ASN cc_start: 0.8884 (m-40) cc_final: 0.8647 (m-40) outliers start: 40 outliers final: 31 residues processed: 354 average time/residue: 0.2348 time to fit residues: 116.2610 Evaluate side-chains 368 residues out of total 1251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 333 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 295 THR Chi-restraints excluded: chain A residue 353 LEU 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 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 R residue 79 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 83 MET Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 155 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 65 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 140 optimal weight: 0.6980 chunk 4 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 117 optimal weight: 0.0270 chunk 41 optimal weight: 0.3980 chunk 129 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 259 GLN S 142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.103397 restraints weight = 19309.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.107062 restraints weight = 8869.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.109495 restraints weight = 5457.831| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3116 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= 0.122 Angle : 0.641 10.922 16018 Z= 0.323 Chirality : 0.041 0.163 1814 Planarity : 0.004 0.062 1995 Dihedral : 5.562 34.363 1646 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 3.12 % Allowed : 26.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.22), residues: 1439 helix: 1.28 (0.21), residues: 624 sheet: -0.67 (0.33), residues: 270 loop : -2.31 (0.24), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP R 261 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE R 78 TYR 0.023 0.001 TYR S 235 ARG 0.010 0.001 ARG B 219 Details of bonding type rmsd hydrogen bonds : bond 0.04010 ( 550) hydrogen bonds : angle 4.26067 ( 1602) SS BOND : bond 0.00682 ( 3) SS BOND : angle 1.41135 ( 6) covalent geometry : bond 0.00260 (11795) covalent geometry : angle 0.64032 (16012) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5050.97 seconds wall clock time: 91 minutes 7.37 seconds (5467.37 seconds total)