Starting phenix.real_space_refine on Fri Aug 7 12:08:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ukl_64248/08_2026/9ukl_64248.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ukl_64248/08_2026/9ukl_64248.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ukl_64248/08_2026/9ukl_64248.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ukl_64248/08_2026/9ukl_64248.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ukl_64248/08_2026/9ukl_64248.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ukl_64248/08_2026/9ukl_64248.map" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 3 5.21 5 S 87 5.16 5 C 13193 2.51 5 N 3750 2.21 5 O 3953 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20995 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2413 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 12, 'TRANS': 292} Chain breaks: 1 Chain: "B" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2422 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 12, 'TRANS': 293} Chain breaks: 1 Chain: "C" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2458 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "D" Number of atoms: 2458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2458 Classifications: {'peptide': 311} Link IDs: {'PTRANS': 12, 'TRANS': 298} Chain: "E" Number of atoms: 2467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2467 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain: "F" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 12, 'TRANS': 306} Chain: "a" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1652 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 11, 'TRANS': 204} Chain: "G" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2423 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 10, 'TRANS': 293} Chain: "I" Number of atoms: 2092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2092 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 8, 'TRANS': 256} Chain breaks: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.52, per 1000 atoms: 0.22 Number of scatterers: 20995 At special positions: 0 Unit cell: (141.694, 129.13, 150.768, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 87 16.00 P 9 15.00 Mg 3 11.99 O 3953 8.00 N 3750 7.00 C 13193 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 885.5 milliseconds 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4978 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 24 sheets defined 47.6% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 102 through 107 Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 204 through 210 removed outlier: 3.752A pdb=" N MET A 208 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ARG A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 232 removed outlier: 3.955A pdb=" N ASN A 227 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYS A 232 " --> pdb=" O ILE A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 238 through 262 removed outlier: 3.772A pdb=" N GLU A 243 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 250 " --> pdb=" O ASN A 246 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR A 255 " --> pdb=" O VAL A 251 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 284 removed outlier: 3.580A pdb=" N VAL A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 283 " --> pdb=" O ASN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.833A pdb=" N ALA A 289 " --> pdb=" O ASP A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 303 removed outlier: 3.871A pdb=" N ARG A 303 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 315 removed outlier: 3.507A pdb=" N GLU A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A 313 " --> pdb=" O PHE A 309 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLY A 315 " --> pdb=" O GLN A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 50 through 63 Processing helix chain 'B' and resid 76 through 89 removed outlier: 3.551A pdb=" N ILE B 81 " --> pdb=" O LYS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 108 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.696A pdb=" N GLY B 146 " --> pdb=" O TYR B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 removed outlier: 3.621A pdb=" N PHE B 152 " --> pdb=" O PRO B 148 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL B 153 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.788A pdb=" N MET B 208 " --> pdb=" O ASN B 204 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP B 209 " --> pdb=" O GLN B 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 204 through 209' Processing helix chain 'B' and resid 221 through 233 removed outlier: 3.575A pdb=" N ASN B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 237 Processing helix chain 'B' and resid 239 through 262 removed outlier: 4.350A pdb=" N GLU B 243 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE B 244 " --> pdb=" O GLU B 240 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL B 245 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS B 247 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET B 254 " --> pdb=" O ARG B 250 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N PHE B 259 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE B 260 " --> pdb=" O ARG B 256 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN B 261 " --> pdb=" O GLN B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 284 removed outlier: 3.695A pdb=" N VAL B 273 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE B 283 " --> pdb=" O ASN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.918A pdb=" N PHE B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 56 through 63 Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 126 through 133 Processing helix chain 'C' and resid 147 through 158 removed outlier: 3.899A pdb=" N VAL C 157 " --> pdb=" O VAL C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.742A pdb=" N ARG C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP C 211 " --> pdb=" O GLN C 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 206 through 211' Processing helix chain 'C' and resid 221 through 233 removed outlier: 4.137A pdb=" N VAL C 226 " --> pdb=" O HIS C 222 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASN C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 238 through 262 removed outlier: 4.405A pdb=" N GLU C 243 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE C 244 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 284 Processing helix chain 'C' and resid 285 through 294 Processing helix chain 'C' and resid 299 through 301 No H-bonds generated for 'chain 'C' and resid 299 through 301' Processing helix chain 'C' and resid 302 through 314 removed outlier: 3.711A pdb=" N VAL C 306 " --> pdb=" O GLU C 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 53 through 64 Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 102 through 107 Processing helix chain 'D' and resid 126 through 134 removed outlier: 3.540A pdb=" N TRP D 130 " --> pdb=" O GLY D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 204 through 209 Processing helix chain 'D' and resid 221 through 233 Processing helix chain 'D' and resid 234 through 237 removed outlier: 4.197A pdb=" N GLN D 237 " --> pdb=" O LYS D 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 234 through 237' Processing helix chain 'D' and resid 238 through 260 removed outlier: 3.963A pdb=" N GLU D 243 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE D 244 " --> pdb=" O GLU D 240 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE D 260 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 280 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 299 through 315 removed outlier: 4.060A pdb=" N ALA D 304 " --> pdb=" O GLU D 300 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 63 Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 102 through 107 Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.794A pdb=" N TRP E 130 " --> pdb=" O GLY E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 146 Processing helix chain 'E' and resid 149 through 153 removed outlier: 3.704A pdb=" N VAL E 153 " --> pdb=" O VAL E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 159 removed outlier: 3.676A pdb=" N GLU E 159 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 209 Processing helix chain 'E' and resid 221 through 233 Processing helix chain 'E' and resid 234 through 237 removed outlier: 4.034A pdb=" N GLN E 237 " --> pdb=" O LYS E 234 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 234 through 237' Processing helix chain 'E' and resid 240 through 262 removed outlier: 3.755A pdb=" N ILE E 244 " --> pdb=" O GLU E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 284 Processing helix chain 'E' and resid 285 through 294 Processing helix chain 'E' and resid 302 through 315 removed outlier: 3.686A pdb=" N VAL E 306 " --> pdb=" O GLU E 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 23 Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 76 through 88 Processing helix chain 'F' and resid 102 through 108 Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 143 through 146 removed outlier: 4.144A pdb=" N GLY F 146 " --> pdb=" O TYR F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 143 through 146' Processing helix chain 'F' and resid 147 through 160 removed outlier: 3.741A pdb=" N VAL F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 209 removed outlier: 3.542A pdb=" N MET F 208 " --> pdb=" O ASN F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 231 removed outlier: 3.929A pdb=" N VAL F 226 " --> pdb=" O HIS F 222 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN F 227 " --> pdb=" O ASP F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 261 removed outlier: 4.022A pdb=" N GLU F 243 " --> pdb=" O ALA F 239 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE F 244 " --> pdb=" O GLU F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 284 Processing helix chain 'F' and resid 285 through 294 removed outlier: 4.137A pdb=" N ARG F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 298 Processing helix chain 'F' and resid 302 through 312 removed outlier: 3.644A pdb=" N GLN F 311 " --> pdb=" O ALA F 307 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 38 removed outlier: 3.617A pdb=" N GLY a 38 " --> pdb=" O ARG a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 68 through 88 removed outlier: 3.722A pdb=" N ARG a 85 " --> pdb=" O SER a 81 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLN a 86 " --> pdb=" O MET a 82 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA a 87 " --> pdb=" O ALA a 83 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG a 88 " --> pdb=" O LEU a 84 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 97 Processing helix chain 'a' and resid 101 through 124 removed outlier: 3.769A pdb=" N ALA a 106 " --> pdb=" O LYS a 102 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL a 116 " --> pdb=" O GLU a 112 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU a 117 " --> pdb=" O GLN a 113 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 141 removed outlier: 5.334A pdb=" N THR a 133 " --> pdb=" O ASP a 129 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET a 134 " --> pdb=" O ASN a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 155 through 168 Processing helix chain 'a' and resid 178 through 201 removed outlier: 4.486A pdb=" N ASP a 185 " --> pdb=" O GLU a 181 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TRP a 186 " --> pdb=" O LEU a 182 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE a 187 " --> pdb=" O TRP a 183 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA a 193 " --> pdb=" O GLN a 189 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ASP a 194 " --> pdb=" O LYS a 190 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA a 196 " --> pdb=" O SER a 192 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN a 201 " --> pdb=" O ARG a 197 " (cutoff:3.500A) Processing helix chain 'a' and resid 204 through 219 Processing helix chain 'G' and resid 330 through 335 Processing helix chain 'G' and resid 337 through 352 removed outlier: 4.407A pdb=" N ARG G 342 " --> pdb=" O ALA G 338 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N LEU G 343 " --> pdb=" O GLU G 339 " (cutoff:3.500A) Processing helix chain 'G' and resid 354 through 365 removed outlier: 3.670A pdb=" N GLY G 359 " --> pdb=" O GLN G 355 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG G 360 " --> pdb=" O GLY G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 391 through 397 removed outlier: 4.249A pdb=" N VAL G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE G 396 " --> pdb=" O VAL G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 416 removed outlier: 3.895A pdb=" N ASP G 414 " --> pdb=" O ASP G 411 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL G 416 " --> pdb=" O ARG G 413 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 447 removed outlier: 3.509A pdb=" N THR G 433 " --> pdb=" O GLY G 429 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU G 447 " --> pdb=" O ALA G 443 " (cutoff:3.500A) Processing helix chain 'G' and resid 448 through 450 No H-bonds generated for 'chain 'G' and resid 448 through 450' Processing helix chain 'G' and resid 466 through 474 removed outlier: 3.783A pdb=" N GLY G 474 " --> pdb=" O GLU G 470 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 503 Processing helix chain 'G' and resid 504 through 510 Processing helix chain 'G' and resid 519 through 532 removed outlier: 3.994A pdb=" N ALA G 523 " --> pdb=" O ILE G 519 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 578 removed outlier: 3.715A pdb=" N GLU G 564 " --> pdb=" O GLY G 560 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER G 578 " --> pdb=" O ILE G 574 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 611 removed outlier: 4.070A pdb=" N GLY G 609 " --> pdb=" O GLU G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 613 through 619 removed outlier: 4.225A pdb=" N SER G 617 " --> pdb=" O GLU G 613 " (cutoff:3.500A) Processing helix chain 'I' and resid 332 through 335 Processing helix chain 'I' and resid 336 through 352 removed outlier: 3.711A pdb=" N ARG I 342 " --> pdb=" O ALA I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 354 through 368 removed outlier: 4.211A pdb=" N GLY I 359 " --> pdb=" O GLN I 355 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ARG I 360 " --> pdb=" O GLY I 356 " (cutoff:3.500A) Processing helix chain 'I' and resid 429 through 444 removed outlier: 3.742A pdb=" N ALA I 435 " --> pdb=" O PRO I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 445 through 450 Processing helix chain 'I' and resid 466 through 475 Processing helix chain 'I' and resid 503 through 510 Processing helix chain 'I' and resid 519 through 534 removed outlier: 4.024A pdb=" N ILE I 525 " --> pdb=" O GLY I 521 " (cutoff:3.500A) Processing helix chain 'I' and resid 561 through 576 removed outlier: 3.682A pdb=" N VAL I 570 " --> pdb=" O HIS I 566 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE I 571 " --> pdb=" O LEU I 567 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU I 572 " --> pdb=" O ARG I 568 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU I 573 " --> pdb=" O ALA I 569 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE I 574 " --> pdb=" O VAL I 570 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU I 575 " --> pdb=" O ILE I 571 " (cutoff:3.500A) Processing helix chain 'I' and resid 605 through 611 removed outlier: 4.257A pdb=" N GLY I 609 " --> pdb=" O GLU I 605 " (cutoff:3.500A) Processing helix chain 'I' and resid 611 through 620 removed outlier: 4.097A pdb=" N LEU I 615 " --> pdb=" O MET I 611 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 17 removed outlier: 3.926A pdb=" N THR A 14 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.101A pdb=" N LEU A 138 " --> pdb=" O PHE A 182 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N THR A 184 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N PHE A 140 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 67 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 115 removed outlier: 3.928A pdb=" N VAL A 118 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 14 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.254A pdb=" N VAL B 93 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ASP B 141 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL B 95 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N LEU B 138 " --> pdb=" O PHE B 182 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N THR B 184 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N PHE B 140 " --> pdb=" O THR B 184 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 114 Processing sheet with id=AA7, first strand: chain 'C' and resid 14 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 92 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 108 through 115 Processing sheet with id=AB1, first strand: chain 'C' and resid 164 through 165 Processing sheet with id=AB2, first strand: chain 'D' and resid 14 through 17 Processing sheet with id=AB3, first strand: chain 'D' and resid 92 through 96 removed outlier: 6.390A pdb=" N VAL D 93 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP D 141 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N VAL D 95 " --> pdb=" O ASP D 141 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL D 67 " --> pdb=" O LEU D 181 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 108 through 115 Processing sheet with id=AB5, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AB6, first strand: chain 'E' and resid 92 through 96 removed outlier: 6.133A pdb=" N LEU E 138 " --> pdb=" O PHE E 182 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N THR E 184 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N PHE E 140 " --> pdb=" O THR E 184 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL E 67 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 108 through 115 Processing sheet with id=AB8, first strand: chain 'E' and resid 164 through 166 Processing sheet with id=AB9, first strand: chain 'F' and resid 14 through 17 Processing sheet with id=AC1, first strand: chain 'F' and resid 92 through 96 removed outlier: 6.606A pdb=" N VAL F 93 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N ASP F 141 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL F 95 " --> pdb=" O ASP F 141 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N VAL F 67 " --> pdb=" O LEU F 181 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 109 through 115 Processing sheet with id=AC3, first strand: chain 'a' and resid 43 through 46 Processing sheet with id=AC4, first strand: chain 'G' and resid 327 through 329 removed outlier: 3.901A pdb=" N HIS G 489 " --> pdb=" O GLU G 327 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N TYR G 492 " --> pdb=" O ILE G 455 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE G 455 " --> pdb=" O TYR G 492 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL G 417 " --> pdb=" O GLU G 454 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU G 456 " --> pdb=" O VAL G 417 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU G 419 " --> pdb=" O LEU G 456 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N PHE G 458 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU G 421 " --> pdb=" O PHE G 458 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N THR G 418 " --> pdb=" O MET G 542 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N ILE G 544 " --> pdb=" O THR G 418 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL G 420 " --> pdb=" O ILE G 544 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N MET G 543 " --> pdb=" O ILE G 585 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ILE G 587 " --> pdb=" O MET G 543 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N SER G 545 " --> pdb=" O ILE G 587 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE G 601 " --> pdb=" O GLY G 586 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 327 through 330 removed outlier: 6.261A pdb=" N GLU I 327 " --> pdb=" O HIS I 489 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL I 491 " --> pdb=" O GLU I 327 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL I 329 " --> pdb=" O VAL I 491 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU I 456 " --> pdb=" O VAL I 417 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU I 419 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N PHE I 458 " --> pdb=" O LEU I 419 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU I 421 " --> pdb=" O PHE I 458 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N THR I 460 " --> pdb=" O LEU I 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 327 through 330 removed outlier: 6.261A pdb=" N GLU I 327 " --> pdb=" O HIS I 489 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N VAL I 491 " --> pdb=" O GLU I 327 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N VAL I 329 " --> pdb=" O VAL I 491 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N LEU I 456 " --> pdb=" O VAL I 417 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU I 419 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N PHE I 458 " --> pdb=" O LEU I 419 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU I 421 " --> pdb=" O PHE I 458 " (cutoff:3.500A) removed outlier: 9.631A pdb=" N THR I 460 " --> pdb=" O LEU I 421 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL I 416 " --> pdb=" O ILE I 540 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET I 542 " --> pdb=" O VAL I 416 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR I 418 " --> pdb=" O MET I 542 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ILE I 544 " --> pdb=" O THR I 418 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL I 420 " --> pdb=" O ILE I 544 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N VAL I 599 " --> pdb=" O LEU I 582 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA I 584 " --> pdb=" O VAL I 599 " (cutoff:3.500A) 845 hydrogen bonds defined for protein. 2424 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: 3.88 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7188 1.34 - 1.46: 4729 1.46 - 1.58: 9324 1.58 - 1.70: 6 1.70 - 1.82: 155 Bond restraints: 21402 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.35e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.30e+01 bond pdb=" O3A ANP E 401 " pdb=" PB ANP E 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 ... (remaining 21397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.84: 28941 3.84 - 7.69: 119 7.69 - 11.53: 22 11.53 - 15.38: 1 15.38 - 19.22: 3 Bond angle restraints: 29086 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 107.73 19.22 3.00e+00 1.11e-01 4.10e+01 angle pdb=" PB ANP E 401 " pdb=" N3B ANP E 401 " pdb=" PG ANP E 401 " ideal model delta sigma weight residual 126.95 108.51 18.44 3.00e+00 1.11e-01 3.78e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 108.95 18.00 3.00e+00 1.11e-01 3.60e+01 angle pdb=" C ILE B 81 " pdb=" N GLU B 82 " pdb=" CA GLU B 82 " ideal model delta sigma weight residual 120.44 114.96 5.48 1.30e+00 5.92e-01 1.78e+01 angle pdb=" CB MET a 221 " pdb=" CG MET a 221 " pdb=" SD MET a 221 " ideal model delta sigma weight residual 112.70 124.93 -12.23 3.00e+00 1.11e-01 1.66e+01 ... (remaining 29081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.25: 11047 22.25 - 44.50: 1481 44.50 - 66.75: 277 66.75 - 89.01: 83 89.01 - 111.26: 4 Dihedral angle restraints: 12892 sinusoidal: 5200 harmonic: 7692 Sorted by residual: dihedral pdb=" O1A ANP D 401 " pdb=" O3A ANP D 401 " pdb=" PA ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sinusoidal sigma weight residual 83.11 -28.15 111.26 1 3.00e+01 1.11e-03 1.45e+01 dihedral pdb=" CA PHE F 294 " pdb=" C PHE F 294 " pdb=" N LEU F 295 " pdb=" CA LEU F 295 " ideal model delta harmonic sigma weight residual -180.00 -161.41 -18.59 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA MET A 254 " pdb=" C MET A 254 " pdb=" N THR A 255 " pdb=" CA THR A 255 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.38e+01 ... (remaining 12889 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2669 0.054 - 0.109: 540 0.109 - 0.163: 72 0.163 - 0.217: 5 0.217 - 0.272: 3 Chirality restraints: 3289 Sorted by residual: chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP E 401 " pdb=" C2' ANP E 401 " pdb=" C4' ANP E 401 " pdb=" O3' ANP E 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 3286 not shown) Planarity restraints: 3802 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 276 " 0.037 2.00e-02 2.50e+03 2.87e-02 2.06e+01 pdb=" CG TRP D 276 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TRP D 276 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP D 276 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 276 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 276 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 276 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 276 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 276 " 0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP D 276 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER D 269 " 0.055 5.00e-02 4.00e+02 8.26e-02 1.09e+01 pdb=" N PRO D 270 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO D 270 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO D 270 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER E 269 " 0.039 5.00e-02 4.00e+02 5.96e-02 5.69e+00 pdb=" N PRO E 270 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 270 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 270 " 0.033 5.00e-02 4.00e+02 ... (remaining 3799 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 205 2.53 - 3.12: 16206 3.12 - 3.71: 33698 3.71 - 4.31: 44411 4.31 - 4.90: 72797 Nonbonded interactions: 167317 Sorted by model distance: nonbonded pdb=" O2G ANP E 401 " pdb="MG MG E 402 " model vdw 1.935 2.170 nonbonded pdb=" OG SER D 78 " pdb="MG MG D 402 " model vdw 1.979 2.170 nonbonded pdb=" O2G ANP F 401 " pdb="MG MG F 402 " model vdw 1.991 2.170 nonbonded pdb=" O1B ANP E 401 " pdb="MG MG E 402 " model vdw 2.024 2.170 nonbonded pdb=" OD2 ASP F 141 " pdb="MG MG F 402 " model vdw 2.167 2.170 ... (remaining 167312 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 'A' and resid 9 through 319) selection = (chain 'B' and (resid 9 through 188 or resid 203 through 319)) selection = (chain 'C' and (resid 9 through 188 or resid 203 through 319)) selection = (chain 'D' and (resid 9 through 188 or resid 203 through 319)) selection = (chain 'E' and (resid 9 through 188 or resid 203 through 319)) selection = (chain 'F' and (resid 9 through 188 or resid 203 through 319)) } ncs_group { reference = (chain 'G' and (resid 317 through 369 or resid 414 through 620)) selection = (chain 'I' and resid 317 through 620) } 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: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 19.480 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 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 : 0.004 0.146 21402 Z= 0.218 Angle : 0.723 19.219 29086 Z= 0.364 Chirality : 0.044 0.272 3289 Planarity : 0.005 0.083 3802 Dihedral : 20.205 111.257 7914 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.24 % Favored : 92.72 % Rotamer: Outliers : 0.67 % Allowed : 43.98 % Favored : 55.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.17), residues: 2625 helix: -0.06 (0.16), residues: 1064 sheet: -0.44 (0.27), residues: 357 loop : -0.99 (0.19), residues: 1204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 250 TYR 0.017 0.001 TYR F 197 PHE 0.019 0.001 PHE B 288 TRP 0.077 0.002 TRP D 276 HIS 0.015 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.22 (21402) covalent geometry : angle 0.72329 / 0.36 (29086) hydrogen bonds : bond 0.16437 / 11.64 ( 841) hydrogen bonds : angle 6.74334 / 4.69 ( 2424) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 711 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 210 ARG cc_start: 0.8198 (ttm-80) cc_final: 0.7996 (ttm-80) REVERT: E 44 ASP cc_start: 0.7951 (t0) cc_final: 0.7748 (t0) REVERT: F 14 THR cc_start: 0.7530 (m) cc_final: 0.7272 (m) REVERT: F 79 THR cc_start: 0.7795 (m) cc_final: 0.7333 (p) REVERT: F 230 LEU cc_start: 0.8684 (mt) cc_final: 0.8298 (mp) REVERT: a 161 LEU cc_start: 0.8934 (mm) cc_final: 0.8495 (mm) outliers start: 15 outliers final: 11 residues processed: 716 average time/residue: 0.1813 time to fit residues: 187.8421 Evaluate side-chains 718 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 707 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain D residue 73 HIS Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain I residue 333 ASP Chi-restraints excluded: chain I residue 430 ARG Chi-restraints excluded: chain I residue 491 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0040 chunk 132 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 258 optimal weight: 9.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 207 GLN A 218 ASN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 155 GLN B 311 GLN D 96 ASN D 227 ASN E 296 ASN F 119 GLN F 311 GLN ** a 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.143457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.119514 restraints weight = 36609.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.123956 restraints weight = 18572.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.126894 restraints weight = 11250.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128896 restraints weight = 7720.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.130269 restraints weight = 5793.586| |-----------------------------------------------------------------------------| r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21402 Z= 0.123 Angle : 0.568 7.965 29086 Z= 0.294 Chirality : 0.042 0.180 3289 Planarity : 0.005 0.076 3802 Dihedral : 8.312 106.288 3043 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.66 % Allowed : 36.88 % Favored : 57.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.17), residues: 2625 helix: 0.05 (0.16), residues: 1094 sheet: -0.34 (0.26), residues: 378 loop : -1.00 (0.19), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 488 TYR 0.014 0.001 TYR F 219 PHE 0.017 0.001 PHE G 346 TRP 0.043 0.001 TRP D 276 HIS 0.007 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (21402) covalent geometry : angle 0.56775 / 0.29 (29086) hydrogen bonds : bond 0.04090 / 2.86 ( 841) hydrogen bonds : angle 5.26331 / 3.69 ( 2424) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 719 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8352 (ttm170) cc_final: 0.7924 (ttm170) REVERT: A 155 GLN cc_start: 0.8212 (mm110) cc_final: 0.7873 (mm-40) REVERT: A 180 ARG cc_start: 0.8378 (mmt180) cc_final: 0.8171 (mmp80) REVERT: A 278 GLU cc_start: 0.7761 (tp30) cc_final: 0.7143 (tp30) REVERT: A 303 ARG cc_start: 0.8411 (mpp80) cc_final: 0.8145 (mtm-85) REVERT: A 314 PHE cc_start: 0.7606 (m-10) cc_final: 0.7294 (m-10) REVERT: B 141 ASP cc_start: 0.7621 (m-30) cc_final: 0.7396 (m-30) REVERT: B 176 HIS cc_start: 0.8568 (OUTLIER) cc_final: 0.8285 (t-170) REVERT: B 211 TRP cc_start: 0.8569 (m100) cc_final: 0.8258 (m100) REVERT: B 236 TYR cc_start: 0.7275 (m-10) cc_final: 0.6856 (m-10) REVERT: B 250 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7331 (ttm110) REVERT: B 297 LYS cc_start: 0.8193 (mttp) cc_final: 0.7959 (mttp) REVERT: B 303 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8084 (mtm180) REVERT: C 61 PHE cc_start: 0.8001 (OUTLIER) cc_final: 0.7797 (m-80) REVERT: C 180 ARG cc_start: 0.8353 (mmt90) cc_final: 0.7956 (mmt90) REVERT: C 248 MET cc_start: 0.7986 (mmt) cc_final: 0.7772 (mmt) REVERT: D 100 HIS cc_start: 0.8399 (OUTLIER) cc_final: 0.8081 (m-70) REVERT: D 174 ARG cc_start: 0.7478 (mtt180) cc_final: 0.7134 (mtt-85) REVERT: D 216 THR cc_start: 0.8218 (p) cc_final: 0.7894 (t) REVERT: D 276 TRP cc_start: 0.8437 (t-100) cc_final: 0.8111 (t-100) REVERT: D 302 GLU cc_start: 0.7384 (mt-10) cc_final: 0.7038 (mt-10) REVERT: E 44 ASP cc_start: 0.7841 (t0) cc_final: 0.7611 (t0) REVERT: E 55 LEU cc_start: 0.8835 (tp) cc_final: 0.8500 (tt) REVERT: E 101 VAL cc_start: 0.8736 (t) cc_final: 0.8499 (p) REVERT: E 103 ARG cc_start: 0.7560 (ttt90) cc_final: 0.7317 (ttt90) REVERT: E 172 VAL cc_start: 0.8083 (m) cc_final: 0.7761 (t) REVERT: E 238 ASN cc_start: 0.8595 (p0) cc_final: 0.8333 (p0) REVERT: E 243 GLU cc_start: 0.7469 (mp0) cc_final: 0.6996 (mp0) REVERT: E 257 GLN cc_start: 0.7936 (tm-30) cc_final: 0.7660 (tm-30) REVERT: E 303 ARG cc_start: 0.7679 (mtt180) cc_final: 0.7327 (mtt180) REVERT: F 14 THR cc_start: 0.7519 (m) cc_final: 0.7298 (m) REVERT: F 79 THR cc_start: 0.7825 (m) cc_final: 0.7324 (p) REVERT: F 210 ARG cc_start: 0.7038 (mmt-90) cc_final: 0.6797 (mmt-90) REVERT: F 230 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8326 (mp) REVERT: F 248 MET cc_start: 0.7404 (mmt) cc_final: 0.7000 (mmt) REVERT: a 34 ARG cc_start: 0.8474 (ttt180) cc_final: 0.8156 (ttp80) REVERT: a 80 ASP cc_start: 0.7689 (t0) cc_final: 0.7457 (t0) REVERT: a 90 ASN cc_start: 0.8457 (t0) cc_final: 0.8250 (t0) REVERT: a 115 ARG cc_start: 0.8652 (ttt90) cc_final: 0.8377 (ttt-90) REVERT: a 117 GLU cc_start: 0.8141 (tt0) cc_final: 0.7677 (tt0) REVERT: a 188 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7699 (mm-30) REVERT: a 221 MET cc_start: 0.4905 (tpp) cc_final: 0.4418 (tpp) REVERT: G 342 ARG cc_start: 0.6218 (mtm-85) cc_final: 0.5866 (mtm-85) REVERT: G 368 ARG cc_start: 0.5897 (OUTLIER) cc_final: 0.5284 (mmt180) REVERT: G 468 SER cc_start: 0.4811 (OUTLIER) cc_final: 0.4609 (t) REVERT: G 520 ASP cc_start: 0.6873 (t0) cc_final: 0.6530 (t0) REVERT: I 458 PHE cc_start: 0.7269 (p90) cc_final: 0.7038 (p90) REVERT: I 501 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5671 (mtp85) REVERT: I 510 MET cc_start: 0.7902 (ttm) cc_final: 0.7585 (ttm) outliers start: 126 outliers final: 59 residues processed: 785 average time/residue: 0.1821 time to fit residues: 208.3086 Evaluate side-chains 772 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 705 time to evaluate : 0.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 176 HIS Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 303 ARG Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 61 PHE Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 48 LEU Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 42 GLU Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 421 LEU Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 528 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 221 optimal weight: 10.0000 chunk 237 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 229 optimal weight: 3.9990 chunk 125 optimal weight: 0.0020 chunk 140 optimal weight: 3.9990 chunk 249 optimal weight: 0.3980 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 155 GLN D 10 ASN ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 296 ASN F 64 ASN F 119 GLN F 222 HIS F 296 ASN a 189 GLN G 561 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.142505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118592 restraints weight = 36428.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.122904 restraints weight = 18630.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.125832 restraints weight = 11443.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127648 restraints weight = 7869.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.129120 restraints weight = 6005.911| |-----------------------------------------------------------------------------| r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21402 Z= 0.134 Angle : 0.564 7.434 29086 Z= 0.290 Chirality : 0.042 0.186 3289 Planarity : 0.005 0.075 3802 Dihedral : 6.997 105.246 3029 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 5.53 % Allowed : 36.48 % Favored : 58.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.17), residues: 2625 helix: 0.08 (0.16), residues: 1102 sheet: -0.26 (0.27), residues: 366 loop : -1.01 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 488 TYR 0.014 0.001 TYR F 219 PHE 0.017 0.001 PHE I 325 TRP 0.027 0.001 TRP D 276 HIS 0.012 0.001 HIS I 566 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (21402) covalent geometry : angle 0.56365 / 0.29 (29086) hydrogen bonds : bond 0.03843 / 2.67 ( 841) hydrogen bonds : angle 5.05387 / 3.55 ( 2424) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 725 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ARG cc_start: 0.8354 (ttm170) cc_final: 0.7986 (ttm170) REVERT: A 124 LYS cc_start: 0.7202 (OUTLIER) cc_final: 0.6883 (ptpp) REVERT: A 155 GLN cc_start: 0.8296 (mm110) cc_final: 0.8078 (tp40) REVERT: A 257 GLN cc_start: 0.7733 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 278 GLU cc_start: 0.7725 (tp30) cc_final: 0.7228 (tp30) REVERT: A 303 ARG cc_start: 0.8419 (mpp80) cc_final: 0.8103 (mtm-85) REVERT: B 30 VAL cc_start: 0.8520 (t) cc_final: 0.8248 (p) REVERT: B 141 ASP cc_start: 0.7664 (OUTLIER) cc_final: 0.7300 (m-30) REVERT: B 211 TRP cc_start: 0.8587 (m100) cc_final: 0.8278 (m100) REVERT: B 236 TYR cc_start: 0.7374 (m-10) cc_final: 0.6969 (m-10) REVERT: B 246 ASN cc_start: 0.7510 (p0) cc_final: 0.7258 (p0) REVERT: B 250 ARG cc_start: 0.7744 (mtp85) cc_final: 0.7144 (ttm110) REVERT: B 254 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5977 (mpp) REVERT: B 297 LYS cc_start: 0.8184 (mttp) cc_final: 0.7960 (mttp) REVERT: C 33 TYR cc_start: 0.7978 (m-10) cc_final: 0.7354 (m-10) REVERT: C 125 ASP cc_start: 0.7603 (m-30) cc_final: 0.7397 (t0) REVERT: C 163 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6772 (ttp80) REVERT: C 180 ARG cc_start: 0.8438 (mmt90) cc_final: 0.7958 (mmt90) REVERT: C 238 ASN cc_start: 0.7746 (t0) cc_final: 0.7509 (t0) REVERT: C 286 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8089 (t) REVERT: D 63 TYR cc_start: 0.7716 (m-80) cc_final: 0.7481 (m-10) REVERT: D 100 HIS cc_start: 0.8391 (OUTLIER) cc_final: 0.8120 (m-70) REVERT: D 156 ARG cc_start: 0.8254 (ttt180) cc_final: 0.7976 (ttt90) REVERT: D 174 ARG cc_start: 0.7595 (mtt180) cc_final: 0.7228 (mtt-85) REVERT: D 210 ARG cc_start: 0.8184 (ttm-80) cc_final: 0.7805 (ttm170) REVERT: D 216 THR cc_start: 0.8238 (p) cc_final: 0.7910 (t) REVERT: D 276 TRP cc_start: 0.8515 (t60) cc_final: 0.8070 (t-100) REVERT: D 279 ASN cc_start: 0.7796 (m-40) cc_final: 0.7550 (m-40) REVERT: D 292 LEU cc_start: 0.8207 (tt) cc_final: 0.7872 (tp) REVERT: E 55 LEU cc_start: 0.8856 (tp) cc_final: 0.8561 (tt) REVERT: E 61 PHE cc_start: 0.8239 (OUTLIER) cc_final: 0.7797 (t80) REVERT: E 103 ARG cc_start: 0.7666 (ttt90) cc_final: 0.7420 (ttt90) REVERT: E 172 VAL cc_start: 0.8143 (m) cc_final: 0.7713 (t) REVERT: E 238 ASN cc_start: 0.8652 (p0) cc_final: 0.8354 (p0) REVERT: E 257 GLN cc_start: 0.7997 (tm-30) cc_final: 0.7625 (tm-30) REVERT: E 303 ARG cc_start: 0.7729 (mtt180) cc_final: 0.7393 (mtt180) REVERT: F 29 MET cc_start: 0.6898 (mmm) cc_final: 0.6301 (mmm) REVERT: F 66 ARG cc_start: 0.7429 (mmt90) cc_final: 0.6975 (mpt-90) REVERT: F 94 ARG cc_start: 0.7291 (OUTLIER) cc_final: 0.6948 (mtp85) REVERT: F 144 ASP cc_start: 0.7561 (p0) cc_final: 0.7119 (p0) REVERT: F 197 TYR cc_start: 0.6929 (m-80) cc_final: 0.6686 (m-80) REVERT: F 210 ARG cc_start: 0.7042 (mmt-90) cc_final: 0.6796 (mmt-90) REVERT: F 219 TYR cc_start: 0.8202 (m-10) cc_final: 0.7986 (m-10) REVERT: F 230 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8304 (mp) REVERT: F 248 MET cc_start: 0.7465 (mmt) cc_final: 0.7047 (mmt) REVERT: F 291 ARG cc_start: 0.8202 (mtp85) cc_final: 0.7925 (mtp180) REVERT: F 318 LEU cc_start: 0.6331 (tp) cc_final: 0.5987 (tp) REVERT: a 80 ASP cc_start: 0.7694 (t0) cc_final: 0.7437 (t0) REVERT: a 108 PHE cc_start: 0.7865 (t80) cc_final: 0.7486 (t80) REVERT: a 115 ARG cc_start: 0.8672 (ttt90) cc_final: 0.8440 (ttt-90) REVERT: a 213 ARG cc_start: 0.7858 (mmt90) cc_final: 0.7598 (mmt-90) REVERT: a 215 MET cc_start: 0.7746 (mmm) cc_final: 0.7532 (mmm) REVERT: G 342 ARG cc_start: 0.6230 (mtm-85) cc_final: 0.6018 (mtm-85) REVERT: G 368 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5320 (mmt180) REVERT: G 520 ASP cc_start: 0.6805 (t0) cc_final: 0.6471 (t0) REVERT: I 499 TRP cc_start: 0.8507 (t-100) cc_final: 0.8250 (t-100) REVERT: I 501 ARG cc_start: 0.6085 (OUTLIER) cc_final: 0.5669 (mtp85) REVERT: I 510 MET cc_start: 0.7822 (ttm) cc_final: 0.7310 (ttm) REVERT: I 566 HIS cc_start: 0.7531 (t-90) cc_final: 0.7316 (t-90) outliers start: 123 outliers final: 73 residues processed: 791 average time/residue: 0.1738 time to fit residues: 201.1429 Evaluate side-chains 800 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 716 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 70 SER Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 94 ARG Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain G residue 319 LYS Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 543 MET Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 585 ILE Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 452 LYS Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain I residue 528 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 247 optimal weight: 10.0000 chunk 228 optimal weight: 8.9990 chunk 191 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 106 optimal weight: 0.0170 chunk 86 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 overall best weight: 2.6024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 80 HIS B 155 GLN D 10 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 186 ASN E 296 ASN F 64 ASN F 222 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN G 561 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.138429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.114538 restraints weight = 36732.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.118861 restraints weight = 18902.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.121771 restraints weight = 11604.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.123749 restraints weight = 8008.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.125091 restraints weight = 6054.287| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 21402 Z= 0.282 Angle : 0.639 8.292 29086 Z= 0.337 Chirality : 0.045 0.194 3289 Planarity : 0.005 0.084 3802 Dihedral : 6.855 104.352 3028 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.81 % Favored : 92.19 % Rotamer: Outliers : 7.23 % Allowed : 35.58 % Favored : 57.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.16), residues: 2625 helix: -0.22 (0.15), residues: 1115 sheet: -0.49 (0.27), residues: 362 loop : -1.09 (0.19), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 65 TYR 0.018 0.002 TYR E 47 PHE 0.026 0.002 PHE E 179 TRP 0.024 0.002 TRP D 276 HIS 0.007 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.28 (21402) covalent geometry : angle 0.63942 / 0.34 (29086) hydrogen bonds : bond 0.04733 / 3.28 ( 841) hydrogen bonds : angle 5.23925 / 3.68 ( 2424) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 753 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8274 (t0) cc_final: 0.7910 (t0) REVERT: A 124 LYS cc_start: 0.7371 (OUTLIER) cc_final: 0.7110 (ptpp) REVERT: A 155 GLN cc_start: 0.8277 (mm110) cc_final: 0.8076 (tp40) REVERT: A 257 GLN cc_start: 0.7843 (tm-30) cc_final: 0.7148 (tm-30) REVERT: A 261 ASN cc_start: 0.8171 (m-40) cc_final: 0.7434 (m-40) REVERT: A 278 GLU cc_start: 0.7736 (tp30) cc_final: 0.7210 (tp30) REVERT: A 303 ARG cc_start: 0.8422 (mpp80) cc_final: 0.8095 (mtm-85) REVERT: B 30 VAL cc_start: 0.8539 (t) cc_final: 0.8300 (p) REVERT: B 47 TYR cc_start: 0.8517 (t80) cc_final: 0.8229 (t80) REVERT: B 141 ASP cc_start: 0.7737 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: B 211 TRP cc_start: 0.8577 (m100) cc_final: 0.8224 (m100) REVERT: B 236 TYR cc_start: 0.7624 (m-10) cc_final: 0.7223 (m-10) REVERT: B 250 ARG cc_start: 0.7849 (mtp85) cc_final: 0.7320 (ttm110) REVERT: B 297 LYS cc_start: 0.8280 (mttp) cc_final: 0.8077 (mttp) REVERT: C 19 ARG cc_start: 0.7907 (mmm-85) cc_final: 0.7662 (mmm-85) REVERT: C 33 TYR cc_start: 0.8084 (m-10) cc_final: 0.7587 (m-10) REVERT: C 163 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.7018 (ttp80) REVERT: C 180 ARG cc_start: 0.8605 (mmt90) cc_final: 0.7979 (mmt90) REVERT: D 42 GLU cc_start: 0.6665 (tm-30) cc_final: 0.6311 (tm-30) REVERT: D 100 HIS cc_start: 0.8489 (OUTLIER) cc_final: 0.8212 (m-70) REVERT: D 147 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7274 (mtm-85) REVERT: D 156 ARG cc_start: 0.8366 (ttt180) cc_final: 0.8052 (ttt90) REVERT: D 216 THR cc_start: 0.8248 (p) cc_final: 0.7912 (t) REVERT: D 217 LEU cc_start: 0.8069 (tp) cc_final: 0.7806 (tt) REVERT: D 256 ARG cc_start: 0.7373 (ttm-80) cc_final: 0.6769 (ttm-80) REVERT: D 276 TRP cc_start: 0.8615 (t60) cc_final: 0.8294 (t-100) REVERT: E 55 LEU cc_start: 0.8873 (tp) cc_final: 0.8611 (tp) REVERT: E 61 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7916 (t80) REVERT: E 172 VAL cc_start: 0.8208 (m) cc_final: 0.7759 (t) REVERT: E 184 THR cc_start: 0.8421 (m) cc_final: 0.7703 (p) REVERT: E 238 ASN cc_start: 0.8684 (p0) cc_final: 0.8410 (p0) REVERT: E 257 GLN cc_start: 0.8170 (tm-30) cc_final: 0.7756 (tm-30) REVERT: E 303 ARG cc_start: 0.7747 (mtt180) cc_final: 0.7378 (mtt180) REVERT: F 29 MET cc_start: 0.6966 (mmm) cc_final: 0.6478 (mmm) REVERT: F 142 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6887 (mt-10) REVERT: F 144 ASP cc_start: 0.7563 (p0) cc_final: 0.7129 (p0) REVERT: F 209 ASP cc_start: 0.7317 (t0) cc_final: 0.7117 (t0) REVERT: F 230 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8413 (mp) REVERT: F 248 MET cc_start: 0.7553 (mmt) cc_final: 0.7231 (mmt) REVERT: F 291 ARG cc_start: 0.8529 (mtp85) cc_final: 0.8293 (mtp180) REVERT: a 80 ASP cc_start: 0.7761 (t0) cc_final: 0.7442 (t0) REVERT: a 108 PHE cc_start: 0.7891 (t80) cc_final: 0.7396 (t80) REVERT: a 197 ARG cc_start: 0.8221 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: a 215 MET cc_start: 0.7776 (mmm) cc_final: 0.7556 (mmm) REVERT: G 342 ARG cc_start: 0.6436 (OUTLIER) cc_final: 0.6232 (mtm-85) REVERT: G 368 ARG cc_start: 0.6083 (OUTLIER) cc_final: 0.5495 (mmt180) REVERT: G 391 LEU cc_start: 0.8730 (tp) cc_final: 0.8081 (mt) REVERT: G 468 SER cc_start: 0.4992 (OUTLIER) cc_final: 0.4781 (t) REVERT: G 503 ARG cc_start: 0.7741 (tmm-80) cc_final: 0.7388 (ptm160) REVERT: G 596 GLN cc_start: 0.6251 (OUTLIER) cc_final: 0.5998 (pm20) REVERT: I 483 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.7089 (ttm170) REVERT: I 499 TRP cc_start: 0.8550 (t-100) cc_final: 0.8261 (t-100) REVERT: I 501 ARG cc_start: 0.6137 (OUTLIER) cc_final: 0.5716 (mtp85) REVERT: I 510 MET cc_start: 0.7947 (ttm) cc_final: 0.7374 (ttm) REVERT: I 566 HIS cc_start: 0.7627 (t-170) cc_final: 0.7406 (t-90) outliers start: 161 outliers final: 96 residues processed: 835 average time/residue: 0.1633 time to fit residues: 199.1151 Evaluate side-chains 856 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 747 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 124 LYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 224 ASN Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 266 THR Chi-restraints excluded: chain E residue 268 MET Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 49 PHE Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 62 ASP Chi-restraints excluded: chain a residue 86 GLN Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 156 GLU Chi-restraints excluded: chain a residue 167 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 543 MET Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 596 GLN Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 323 ARG Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 452 LYS Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 528 HIS Chi-restraints excluded: chain I residue 531 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 155 optimal weight: 0.2980 chunk 82 optimal weight: 0.0470 chunk 78 optimal weight: 10.0000 chunk 115 optimal weight: 0.9980 chunk 189 optimal weight: 7.9990 chunk 244 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 1 optimal weight: 0.0670 chunk 179 optimal weight: 0.8980 chunk 227 optimal weight: 1.9990 chunk 193 optimal weight: 9.9990 overall best weight: 0.4616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN B 80 HIS ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 GLN D 227 ASN E 186 ASN E 296 ASN F 64 ASN F 133 GLN a 189 GLN G 537 GLN G 561 ASN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.142999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.119065 restraints weight = 36565.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.123515 restraints weight = 18614.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126473 restraints weight = 11327.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.128481 restraints weight = 7776.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.129827 restraints weight = 5828.356| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 21402 Z= 0.110 Angle : 0.561 9.233 29086 Z= 0.291 Chirality : 0.042 0.203 3289 Planarity : 0.005 0.076 3802 Dihedral : 6.351 101.235 3028 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.97 % Allowed : 37.78 % Favored : 56.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.16), residues: 2625 helix: 0.02 (0.15), residues: 1108 sheet: -0.38 (0.26), residues: 382 loop : -0.99 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 163 TYR 0.019 0.001 TYR E 219 PHE 0.023 0.002 PHE F 61 TRP 0.018 0.001 TRP D 276 HIS 0.013 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (21402) covalent geometry : angle 0.56150 / 0.29 (29086) hydrogen bonds : bond 0.03515 / 2.44 ( 841) hydrogen bonds : angle 4.91278 / 3.45 ( 2424) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 881 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 748 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8289 (t0) cc_final: 0.8028 (t0) REVERT: A 155 GLN cc_start: 0.8249 (mm110) cc_final: 0.7992 (tp40) REVERT: A 180 ARG cc_start: 0.8337 (mmt180) cc_final: 0.8101 (mmp80) REVERT: A 257 GLN cc_start: 0.7794 (tm-30) cc_final: 0.7028 (tm-30) REVERT: A 278 GLU cc_start: 0.7700 (tp30) cc_final: 0.7181 (tp30) REVERT: A 294 PHE cc_start: 0.7479 (t80) cc_final: 0.7200 (t80) REVERT: B 30 VAL cc_start: 0.8506 (t) cc_final: 0.8275 (p) REVERT: B 141 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7317 (m-30) REVERT: B 208 MET cc_start: 0.8022 (tpp) cc_final: 0.7503 (mpp) REVERT: B 211 TRP cc_start: 0.8524 (m100) cc_final: 0.8179 (m100) REVERT: B 236 TYR cc_start: 0.7598 (m-10) cc_final: 0.7150 (m-10) REVERT: B 250 ARG cc_start: 0.7706 (mtp85) cc_final: 0.6746 (ttm110) REVERT: B 254 MET cc_start: 0.6671 (mpp) cc_final: 0.6405 (mpp) REVERT: B 297 LYS cc_start: 0.8242 (mttp) cc_final: 0.7994 (mttp) REVERT: C 33 TYR cc_start: 0.7955 (m-10) cc_final: 0.7361 (m-10) REVERT: C 144 ASP cc_start: 0.7785 (p0) cc_final: 0.7569 (p0) REVERT: C 152 PHE cc_start: 0.7778 (m-80) cc_final: 0.7034 (m-80) REVERT: C 163 ARG cc_start: 0.7372 (OUTLIER) cc_final: 0.6732 (ttp80) REVERT: C 180 ARG cc_start: 0.8454 (mmt90) cc_final: 0.8143 (mmt90) REVERT: C 248 MET cc_start: 0.8005 (mmt) cc_final: 0.7693 (mmt) REVERT: C 276 TRP cc_start: 0.8553 (t60) cc_final: 0.8329 (t60) REVERT: D 42 GLU cc_start: 0.6582 (tm-30) cc_final: 0.6225 (tm-30) REVERT: D 47 TYR cc_start: 0.8066 (t80) cc_final: 0.7856 (t80) REVERT: D 100 HIS cc_start: 0.8390 (OUTLIER) cc_final: 0.8087 (m-70) REVERT: D 147 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7096 (mtm-85) REVERT: D 156 ARG cc_start: 0.8318 (ttt180) cc_final: 0.7941 (ttt90) REVERT: D 210 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7829 (ttm170) REVERT: D 216 THR cc_start: 0.8220 (p) cc_final: 0.7947 (t) REVERT: D 256 ARG cc_start: 0.7041 (ttm-80) cc_final: 0.6603 (ttm-80) REVERT: D 276 TRP cc_start: 0.8553 (t60) cc_final: 0.8210 (t-100) REVERT: D 301 LEU cc_start: 0.7554 (pt) cc_final: 0.7337 (pt) REVERT: E 55 LEU cc_start: 0.8831 (tp) cc_final: 0.8431 (tp) REVERT: E 61 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7817 (t80) REVERT: E 238 ASN cc_start: 0.8684 (p0) cc_final: 0.8363 (p0) REVERT: E 257 GLN cc_start: 0.8025 (tm-30) cc_final: 0.7578 (tm-30) REVERT: E 303 ARG cc_start: 0.7701 (mtt180) cc_final: 0.7495 (mtt180) REVERT: F 29 MET cc_start: 0.6817 (mmm) cc_final: 0.6321 (mmm) REVERT: F 79 THR cc_start: 0.7956 (m) cc_final: 0.7521 (p) REVERT: F 138 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8114 (tt) REVERT: F 142 GLU cc_start: 0.7462 (mt-10) cc_final: 0.6932 (mt-10) REVERT: F 210 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6728 (mmt-90) REVERT: F 230 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8326 (mp) REVERT: F 243 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6508 (mm-30) REVERT: F 248 MET cc_start: 0.7461 (mmt) cc_final: 0.7212 (mmt) REVERT: F 291 ARG cc_start: 0.8343 (mtp85) cc_final: 0.8131 (mtp180) REVERT: a 80 ASP cc_start: 0.7700 (t0) cc_final: 0.7323 (t0) REVERT: a 108 PHE cc_start: 0.7871 (t80) cc_final: 0.7400 (t80) REVERT: a 117 GLU cc_start: 0.8176 (tt0) cc_final: 0.7699 (tt0) REVERT: a 161 LEU cc_start: 0.8969 (mm) cc_final: 0.8499 (mm) REVERT: a 188 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7655 (mm-30) REVERT: a 197 ARG cc_start: 0.8249 (mmm-85) cc_final: 0.7825 (mmm-85) REVERT: a 213 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7642 (mmt-90) REVERT: a 215 MET cc_start: 0.7712 (mmm) cc_final: 0.7462 (mmm) REVERT: a 221 MET cc_start: 0.4764 (tpp) cc_final: 0.4314 (tpp) REVERT: G 339 GLU cc_start: 0.5571 (OUTLIER) cc_final: 0.4980 (tm-30) REVERT: G 368 ARG cc_start: 0.5905 (OUTLIER) cc_final: 0.5343 (mmt180) REVERT: G 468 SER cc_start: 0.4839 (OUTLIER) cc_final: 0.4606 (t) REVERT: G 503 ARG cc_start: 0.7517 (tmm-80) cc_final: 0.7311 (ptm160) REVERT: G 596 GLN cc_start: 0.6099 (OUTLIER) cc_final: 0.5620 (pm20) REVERT: G 597 ARG cc_start: 0.6781 (mtp85) cc_final: 0.6464 (mtp85) REVERT: G 618 LEU cc_start: 0.8510 (tp) cc_final: 0.7799 (tp) REVERT: I 483 ARG cc_start: 0.7229 (OUTLIER) cc_final: 0.6949 (ttm170) REVERT: I 499 TRP cc_start: 0.8490 (t-100) cc_final: 0.8248 (t-100) REVERT: I 501 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.5702 (mtp85) REVERT: I 510 MET cc_start: 0.7742 (ttm) cc_final: 0.7166 (ttm) REVERT: I 566 HIS cc_start: 0.7548 (t-170) cc_final: 0.7336 (t-90) outliers start: 133 outliers final: 83 residues processed: 810 average time/residue: 0.1639 time to fit residues: 193.3761 Evaluate side-chains 829 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 732 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 222 HIS Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 53 LEU Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 124 MET Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 187 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 339 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 596 GLN Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 452 LYS Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 528 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 122 optimal weight: 8.9990 chunk 167 optimal weight: 0.7980 chunk 243 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 210 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 ASN ** B 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 96 ASN E 186 ASN E 296 ASN F 64 ASN F 133 GLN F 222 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN G 561 ASN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.144556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.120253 restraints weight = 36349.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124598 restraints weight = 18798.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127524 restraints weight = 11625.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129539 restraints weight = 8096.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.130761 restraints weight = 6130.240| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 21402 Z= 0.255 Angle : 0.635 8.981 29086 Z= 0.332 Chirality : 0.045 0.214 3289 Planarity : 0.005 0.081 3802 Dihedral : 6.525 103.859 3021 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 6.24 % Allowed : 37.87 % Favored : 55.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.97 (0.16), residues: 2625 helix: -0.15 (0.15), residues: 1117 sheet: -0.45 (0.27), residues: 358 loop : -1.10 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG a 115 TYR 0.028 0.002 TYR E 219 PHE 0.019 0.002 PHE E 179 TRP 0.020 0.002 TRP D 276 HIS 0.011 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.25 (21402) covalent geometry : angle 0.63484 / 0.33 (29086) hydrogen bonds : bond 0.04429 / 3.06 ( 841) hydrogen bonds : angle 5.13928 / 3.62 ( 2424) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 896 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 757 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8253 (t0) cc_final: 0.7944 (t0) REVERT: A 155 GLN cc_start: 0.8241 (mm110) cc_final: 0.7972 (tp40) REVERT: A 261 ASN cc_start: 0.8212 (m-40) cc_final: 0.7947 (m110) REVERT: A 278 GLU cc_start: 0.7726 (tp30) cc_final: 0.7239 (tp30) REVERT: B 30 VAL cc_start: 0.8540 (t) cc_final: 0.8284 (p) REVERT: B 73 HIS cc_start: 0.7914 (t-170) cc_final: 0.7624 (t-170) REVERT: B 141 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: B 236 TYR cc_start: 0.7706 (m-10) cc_final: 0.7226 (m-10) REVERT: B 250 ARG cc_start: 0.7815 (mtp85) cc_final: 0.6836 (ttm110) REVERT: B 254 MET cc_start: 0.6922 (mpp) cc_final: 0.6642 (mpp) REVERT: B 297 LYS cc_start: 0.8247 (mttp) cc_final: 0.8006 (mttp) REVERT: C 19 ARG cc_start: 0.7953 (mmm-85) cc_final: 0.7655 (mmm-85) REVERT: C 144 ASP cc_start: 0.7787 (p0) cc_final: 0.7519 (p0) REVERT: C 163 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6927 (ttp80) REVERT: C 180 ARG cc_start: 0.8617 (mmt90) cc_final: 0.7931 (mmt90) REVERT: C 225 GLU cc_start: 0.8154 (tp30) cc_final: 0.7748 (tp30) REVERT: C 248 MET cc_start: 0.8080 (mmt) cc_final: 0.7722 (mmt) REVERT: C 276 TRP cc_start: 0.8576 (t60) cc_final: 0.8280 (t60) REVERT: D 42 GLU cc_start: 0.6670 (tm-30) cc_final: 0.6294 (tm-30) REVERT: D 75 THR cc_start: 0.8471 (m) cc_final: 0.8094 (t) REVERT: D 100 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.8170 (m-70) REVERT: D 147 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.7246 (mtm-85) REVERT: D 156 ARG cc_start: 0.8332 (ttt180) cc_final: 0.8020 (ttt180) REVERT: D 216 THR cc_start: 0.8203 (p) cc_final: 0.7907 (t) REVERT: D 250 ARG cc_start: 0.7799 (mtt90) cc_final: 0.7453 (mtt90) REVERT: D 276 TRP cc_start: 0.8632 (t60) cc_final: 0.8288 (t-100) REVERT: E 55 LEU cc_start: 0.8870 (tp) cc_final: 0.8452 (tp) REVERT: E 61 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7936 (t80) REVERT: E 89 ASN cc_start: 0.7764 (m-40) cc_final: 0.7301 (t0) REVERT: E 169 GLN cc_start: 0.7181 (pt0) cc_final: 0.6849 (pt0) REVERT: E 184 THR cc_start: 0.8395 (m) cc_final: 0.7689 (p) REVERT: E 238 ASN cc_start: 0.8690 (p0) cc_final: 0.8387 (p0) REVERT: E 257 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7723 (tm-30) REVERT: E 303 ARG cc_start: 0.7762 (mtt180) cc_final: 0.7403 (mtt180) REVERT: F 29 MET cc_start: 0.6897 (mmm) cc_final: 0.6452 (mmm) REVERT: F 79 THR cc_start: 0.7885 (m) cc_final: 0.7409 (p) REVERT: F 138 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8184 (tt) REVERT: F 142 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6845 (mt-10) REVERT: F 230 LEU cc_start: 0.8741 (mt) cc_final: 0.8383 (mp) REVERT: F 248 MET cc_start: 0.7435 (mmt) cc_final: 0.7155 (mmt) REVERT: F 291 ARG cc_start: 0.8549 (mtp85) cc_final: 0.8147 (mtp180) REVERT: a 80 ASP cc_start: 0.7795 (t0) cc_final: 0.7427 (t0) REVERT: a 100 GLU cc_start: 0.5501 (OUTLIER) cc_final: 0.4999 (pm20) REVERT: a 108 PHE cc_start: 0.7939 (t80) cc_final: 0.7411 (t80) REVERT: a 197 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7820 (mmm-85) REVERT: a 206 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7231 (tm-30) REVERT: a 215 MET cc_start: 0.7761 (mmm) cc_final: 0.7513 (mmm) REVERT: G 339 GLU cc_start: 0.5757 (OUTLIER) cc_final: 0.5061 (tm-30) REVERT: G 468 SER cc_start: 0.4925 (OUTLIER) cc_final: 0.4706 (t) REVERT: G 503 ARG cc_start: 0.7693 (tmm-80) cc_final: 0.7403 (ptm160) REVERT: G 596 GLN cc_start: 0.6202 (OUTLIER) cc_final: 0.5959 (pm20) REVERT: I 483 ARG cc_start: 0.7359 (OUTLIER) cc_final: 0.7038 (ttm170) REVERT: I 499 TRP cc_start: 0.8531 (t-100) cc_final: 0.8264 (t-100) REVERT: I 501 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5785 (mtp85) REVERT: I 510 MET cc_start: 0.7850 (ttm) cc_final: 0.7421 (ttm) REVERT: I 517 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6309 (mt-10) REVERT: I 566 HIS cc_start: 0.7601 (t-170) cc_final: 0.7360 (t-90) outliers start: 139 outliers final: 99 residues processed: 829 average time/residue: 0.1581 time to fit residues: 191.9540 Evaluate side-chains 864 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 752 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 260 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 153 VAL Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 222 HIS Chi-restraints excluded: chain F residue 255 THR Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 GLU Chi-restraints excluded: chain a residue 124 MET Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain a residue 156 GLU Chi-restraints excluded: chain a residue 167 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 187 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 339 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 543 MET Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 596 GLN Chi-restraints excluded: chain G residue 599 VAL Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 323 ARG Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 452 LYS Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain I residue 517 GLU Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 528 HIS Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 82 optimal weight: 0.1980 chunk 229 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 201 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 165 optimal weight: 0.9990 chunk 211 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN B 80 HIS C 135 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 96 ASN E 186 ASN E 296 ASN F 64 ASN F 133 GLN F 222 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN G 561 ASN G 589 HIS ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.147651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.123345 restraints weight = 36226.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.127724 restraints weight = 18686.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.130690 restraints weight = 11501.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.132650 restraints weight = 7978.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133994 restraints weight = 6062.754| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21402 Z= 0.131 Angle : 0.596 9.683 29086 Z= 0.307 Chirality : 0.043 0.261 3289 Planarity : 0.005 0.077 3802 Dihedral : 6.317 101.060 3021 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.97 % Allowed : 38.63 % Favored : 55.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.16), residues: 2625 helix: -0.02 (0.15), residues: 1113 sheet: -0.36 (0.27), residues: 372 loop : -1.05 (0.19), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG a 115 TYR 0.021 0.001 TYR E 219 PHE 0.017 0.001 PHE E 179 TRP 0.017 0.001 TRP D 276 HIS 0.021 0.001 HIS F 222 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (21402) covalent geometry : angle 0.59574 / 0.31 (29086) hydrogen bonds : bond 0.03653 / 2.53 ( 841) hydrogen bonds : angle 4.94292 / 3.48 ( 2424) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 747 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8272 (t0) cc_final: 0.8000 (t0) REVERT: A 155 GLN cc_start: 0.8223 (mm110) cc_final: 0.7983 (tp40) REVERT: A 180 ARG cc_start: 0.8336 (mmt180) cc_final: 0.8136 (mmp80) REVERT: A 250 ARG cc_start: 0.7940 (ttm110) cc_final: 0.7252 (ttm-80) REVERT: A 261 ASN cc_start: 0.8265 (m-40) cc_final: 0.7993 (m110) REVERT: A 278 GLU cc_start: 0.7707 (tp30) cc_final: 0.7198 (tp30) REVERT: B 30 VAL cc_start: 0.8517 (t) cc_final: 0.8300 (p) REVERT: B 87 ARG cc_start: 0.8673 (OUTLIER) cc_final: 0.7182 (mpt-90) REVERT: B 94 ARG cc_start: 0.7927 (mmm160) cc_final: 0.7615 (mmm160) REVERT: B 141 ASP cc_start: 0.7727 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: B 210 ARG cc_start: 0.7272 (tpp80) cc_final: 0.6941 (tpp80) REVERT: B 211 TRP cc_start: 0.8509 (m100) cc_final: 0.8183 (m100) REVERT: B 236 TYR cc_start: 0.7617 (m-10) cc_final: 0.7158 (m-10) REVERT: B 250 ARG cc_start: 0.7716 (mtp85) cc_final: 0.6750 (ttm110) REVERT: B 254 MET cc_start: 0.6806 (mpp) cc_final: 0.6479 (mpp) REVERT: B 297 LYS cc_start: 0.8222 (mttp) cc_final: 0.7942 (mttp) REVERT: C 19 ARG cc_start: 0.7921 (mmm-85) cc_final: 0.7622 (mmm-85) REVERT: C 33 TYR cc_start: 0.7974 (m-10) cc_final: 0.7389 (m-10) REVERT: C 144 ASP cc_start: 0.7807 (p0) cc_final: 0.7601 (p0) REVERT: C 163 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6835 (ttp80) REVERT: C 180 ARG cc_start: 0.8499 (mmt90) cc_final: 0.8161 (mmt90) REVERT: C 248 MET cc_start: 0.7972 (mmt) cc_final: 0.7688 (mmt) REVERT: C 276 TRP cc_start: 0.8542 (t60) cc_final: 0.8272 (t60) REVERT: D 42 GLU cc_start: 0.6574 (tm-30) cc_final: 0.6207 (tm-30) REVERT: D 44 ASP cc_start: 0.7587 (t0) cc_final: 0.7345 (t0) REVERT: D 100 HIS cc_start: 0.8410 (OUTLIER) cc_final: 0.8060 (m-70) REVERT: D 147 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7129 (mtm-85) REVERT: D 156 ARG cc_start: 0.8317 (ttt180) cc_final: 0.8025 (ttt180) REVERT: D 210 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7780 (ttm170) REVERT: D 216 THR cc_start: 0.8172 (p) cc_final: 0.7929 (t) REVERT: D 256 ARG cc_start: 0.7127 (ttm-80) cc_final: 0.6518 (ttm-80) REVERT: D 276 TRP cc_start: 0.8600 (t60) cc_final: 0.8279 (t-100) REVERT: D 292 LEU cc_start: 0.8566 (tp) cc_final: 0.8337 (tp) REVERT: E 55 LEU cc_start: 0.8827 (tp) cc_final: 0.8384 (tp) REVERT: E 61 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7896 (t80) REVERT: E 89 ASN cc_start: 0.7694 (m-40) cc_final: 0.7262 (t0) REVERT: E 238 ASN cc_start: 0.8679 (p0) cc_final: 0.8345 (p0) REVERT: E 257 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7656 (tm-30) REVERT: E 303 ARG cc_start: 0.7739 (mtt180) cc_final: 0.7538 (mtt180) REVERT: F 29 MET cc_start: 0.6864 (mmm) cc_final: 0.6423 (mmm) REVERT: F 51 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7605 (ttp-110) REVERT: F 79 THR cc_start: 0.7905 (m) cc_final: 0.7490 (p) REVERT: F 138 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8150 (tt) REVERT: F 142 GLU cc_start: 0.7374 (mt-10) cc_final: 0.6852 (mt-10) REVERT: F 155 GLN cc_start: 0.8270 (tm-30) cc_final: 0.7910 (tm-30) REVERT: F 230 LEU cc_start: 0.8718 (mt) cc_final: 0.8369 (mp) REVERT: F 291 ARG cc_start: 0.8356 (mtp85) cc_final: 0.8072 (mtp180) REVERT: a 76 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6744 (ptm160) REVERT: a 80 ASP cc_start: 0.7766 (t0) cc_final: 0.7390 (t0) REVERT: a 100 GLU cc_start: 0.5443 (OUTLIER) cc_final: 0.5046 (pm20) REVERT: a 108 PHE cc_start: 0.7877 (t80) cc_final: 0.7347 (t80) REVERT: a 188 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7672 (mm-30) REVERT: a 197 ARG cc_start: 0.8250 (mmm-85) cc_final: 0.7742 (mmm-85) REVERT: a 213 ARG cc_start: 0.7928 (mmt90) cc_final: 0.7676 (mmt-90) REVERT: a 215 MET cc_start: 0.7722 (mmm) cc_final: 0.7480 (mmm) REVERT: G 339 GLU cc_start: 0.5803 (OUTLIER) cc_final: 0.5299 (tm-30) REVERT: G 364 ARG cc_start: 0.7117 (tpt170) cc_final: 0.6862 (tpt170) REVERT: G 368 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5424 (mmt180) REVERT: G 468 SER cc_start: 0.4847 (OUTLIER) cc_final: 0.4608 (t) REVERT: G 503 ARG cc_start: 0.7594 (tmm-80) cc_final: 0.7288 (ptm160) REVERT: G 596 GLN cc_start: 0.6188 (OUTLIER) cc_final: 0.5692 (pm20) REVERT: I 483 ARG cc_start: 0.7286 (OUTLIER) cc_final: 0.6971 (ttm170) REVERT: I 499 TRP cc_start: 0.8506 (t-100) cc_final: 0.8275 (t-100) REVERT: I 501 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.5748 (mtp85) REVERT: I 510 MET cc_start: 0.7744 (ttm) cc_final: 0.7318 (ttm) REVERT: I 517 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6276 (mt-10) REVERT: I 566 HIS cc_start: 0.7523 (t-170) cc_final: 0.7295 (t-90) outliers start: 133 outliers final: 91 residues processed: 815 average time/residue: 0.1671 time to fit residues: 199.5773 Evaluate side-chains 844 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 736 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 142 GLU Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 29 ILE Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 76 ARG Chi-restraints excluded: chain a residue 86 GLN Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 GLU Chi-restraints excluded: chain a residue 124 MET Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 187 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 339 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 596 GLN Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 452 LYS Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain I residue 517 GLU Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 528 HIS Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 152 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 153 optimal weight: 5.9990 chunk 133 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 chunk 121 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 120 optimal weight: 0.9990 chunk 256 optimal weight: 9.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN B 80 HIS C 135 ASN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 96 ASN E 186 ASN E 296 ASN F 64 ASN F 133 GLN F 222 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN G 561 ASN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.141643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.117695 restraints weight = 36322.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.122069 restraints weight = 18646.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124989 restraints weight = 11430.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.127033 restraints weight = 7904.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.128286 restraints weight = 5942.624| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21402 Z= 0.155 Angle : 0.614 11.758 29086 Z= 0.314 Chirality : 0.043 0.203 3289 Planarity : 0.005 0.077 3802 Dihedral : 6.295 101.702 3021 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 6.06 % Allowed : 39.04 % Favored : 54.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.16), residues: 2625 helix: 0.01 (0.15), residues: 1115 sheet: -0.34 (0.28), residues: 359 loop : -1.07 (0.19), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 210 TYR 0.020 0.001 TYR D 72 PHE 0.020 0.001 PHE C 290 TRP 0.019 0.002 TRP F 276 HIS 0.008 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (21402) covalent geometry : angle 0.61380 / 0.31 (29086) hydrogen bonds : bond 0.03757 / 2.61 ( 841) hydrogen bonds : angle 4.96042 / 3.49 ( 2424) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 742 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8263 (t0) cc_final: 0.8018 (t0) REVERT: A 155 GLN cc_start: 0.8247 (mm110) cc_final: 0.7980 (tp40) REVERT: A 180 ARG cc_start: 0.8356 (mmt180) cc_final: 0.8132 (mmp80) REVERT: A 250 ARG cc_start: 0.7935 (ttm110) cc_final: 0.7221 (ttm-80) REVERT: A 261 ASN cc_start: 0.8224 (m-40) cc_final: 0.7942 (m110) REVERT: A 278 GLU cc_start: 0.7729 (tp30) cc_final: 0.7223 (tp30) REVERT: B 30 VAL cc_start: 0.8526 (t) cc_final: 0.8300 (p) REVERT: B 73 HIS cc_start: 0.7785 (t-170) cc_final: 0.7519 (t-170) REVERT: B 87 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7149 (mpt-90) REVERT: B 94 ARG cc_start: 0.7915 (mmm160) cc_final: 0.7585 (mmm160) REVERT: B 141 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7156 (m-30) REVERT: B 210 ARG cc_start: 0.7317 (tpp80) cc_final: 0.6932 (tpp80) REVERT: B 211 TRP cc_start: 0.8527 (m100) cc_final: 0.8158 (m100) REVERT: B 236 TYR cc_start: 0.7620 (m-10) cc_final: 0.7154 (m-10) REVERT: B 250 ARG cc_start: 0.7735 (mtp85) cc_final: 0.6752 (ttm110) REVERT: B 254 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6525 (mpp) REVERT: B 297 LYS cc_start: 0.8235 (mttp) cc_final: 0.7958 (mttp) REVERT: C 19 ARG cc_start: 0.7939 (mmm-85) cc_final: 0.7638 (mmm-85) REVERT: C 33 TYR cc_start: 0.7993 (m-10) cc_final: 0.7426 (m-10) REVERT: C 144 ASP cc_start: 0.7814 (p0) cc_final: 0.7598 (p0) REVERT: C 157 VAL cc_start: 0.8200 (m) cc_final: 0.7979 (m) REVERT: C 163 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6872 (ttp80) REVERT: C 180 ARG cc_start: 0.8526 (mmt90) cc_final: 0.8162 (mmt90) REVERT: C 225 GLU cc_start: 0.8101 (tp30) cc_final: 0.7710 (tp30) REVERT: C 248 MET cc_start: 0.7981 (mmt) cc_final: 0.7747 (mmt) REVERT: C 276 TRP cc_start: 0.8519 (t60) cc_final: 0.8296 (t60) REVERT: D 42 GLU cc_start: 0.6637 (tm-30) cc_final: 0.6249 (tm-30) REVERT: D 75 THR cc_start: 0.8406 (m) cc_final: 0.8166 (p) REVERT: D 100 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.8077 (m-70) REVERT: D 147 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.7145 (mtm-85) REVERT: D 156 ARG cc_start: 0.8290 (ttt180) cc_final: 0.7956 (ttt90) REVERT: D 216 THR cc_start: 0.8129 (p) cc_final: 0.7874 (t) REVERT: D 250 ARG cc_start: 0.7761 (mtt90) cc_final: 0.7391 (mtt90) REVERT: D 256 ARG cc_start: 0.7090 (ttm-80) cc_final: 0.6504 (ttm-80) REVERT: D 276 TRP cc_start: 0.8592 (t60) cc_final: 0.8231 (t-100) REVERT: D 292 LEU cc_start: 0.8603 (tp) cc_final: 0.8350 (tp) REVERT: E 55 LEU cc_start: 0.8833 (tp) cc_final: 0.8387 (tp) REVERT: E 61 PHE cc_start: 0.8270 (OUTLIER) cc_final: 0.7895 (t80) REVERT: E 89 ASN cc_start: 0.7698 (m-40) cc_final: 0.7274 (t0) REVERT: E 140 PHE cc_start: 0.8537 (m-80) cc_final: 0.8121 (m-80) REVERT: E 158 LEU cc_start: 0.8084 (mp) cc_final: 0.7875 (mp) REVERT: E 169 GLN cc_start: 0.7068 (pt0) cc_final: 0.6770 (pt0) REVERT: E 238 ASN cc_start: 0.8697 (p0) cc_final: 0.8368 (p0) REVERT: E 257 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7633 (tm-30) REVERT: E 303 ARG cc_start: 0.7749 (mtt180) cc_final: 0.7420 (mtt180) REVERT: F 29 MET cc_start: 0.6830 (mmm) cc_final: 0.6433 (mmm) REVERT: F 51 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7661 (ttp-110) REVERT: F 79 THR cc_start: 0.7869 (m) cc_final: 0.7453 (p) REVERT: F 138 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8121 (tt) REVERT: F 142 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6847 (mt-10) REVERT: F 155 GLN cc_start: 0.8262 (tm-30) cc_final: 0.8005 (tm-30) REVERT: F 230 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8374 (mp) REVERT: F 291 ARG cc_start: 0.8330 (mtp85) cc_final: 0.8108 (mtp180) REVERT: a 76 ARG cc_start: 0.6989 (OUTLIER) cc_final: 0.6762 (ptm160) REVERT: a 80 ASP cc_start: 0.7760 (t0) cc_final: 0.7374 (t0) REVERT: a 100 GLU cc_start: 0.5443 (OUTLIER) cc_final: 0.5058 (pm20) REVERT: a 161 LEU cc_start: 0.8948 (mm) cc_final: 0.8558 (mm) REVERT: a 188 GLU cc_start: 0.8217 (mm-30) cc_final: 0.7688 (mm-30) REVERT: a 197 ARG cc_start: 0.8276 (mmm-85) cc_final: 0.7794 (mmm-85) REVERT: a 213 ARG cc_start: 0.7948 (mmt90) cc_final: 0.7684 (mmt-90) REVERT: a 215 MET cc_start: 0.7752 (mmm) cc_final: 0.7486 (mmm) REVERT: G 339 GLU cc_start: 0.5818 (OUTLIER) cc_final: 0.5326 (tm-30) REVERT: G 364 ARG cc_start: 0.7126 (tpt170) cc_final: 0.6858 (tpt170) REVERT: G 368 ARG cc_start: 0.6075 (OUTLIER) cc_final: 0.5470 (mmt180) REVERT: G 468 SER cc_start: 0.4831 (OUTLIER) cc_final: 0.4597 (t) REVERT: G 503 ARG cc_start: 0.7575 (tmm-80) cc_final: 0.7336 (ptm160) REVERT: G 596 GLN cc_start: 0.6195 (OUTLIER) cc_final: 0.5700 (pm20) REVERT: I 483 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6996 (ttm170) REVERT: I 499 TRP cc_start: 0.8516 (t-100) cc_final: 0.8301 (t-100) REVERT: I 501 ARG cc_start: 0.6160 (OUTLIER) cc_final: 0.5744 (mtp85) REVERT: I 510 MET cc_start: 0.7800 (ttm) cc_final: 0.7144 (ttm) REVERT: I 517 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.6308 (mt-10) outliers start: 135 outliers final: 98 residues processed: 816 average time/residue: 0.1763 time to fit residues: 211.1739 Evaluate side-chains 857 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 740 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 200 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 46 ASP Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 302 GLU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 76 ARG Chi-restraints excluded: chain a residue 86 GLN Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 GLU Chi-restraints excluded: chain a residue 124 MET Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 167 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 187 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 339 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 596 GLN Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain I residue 517 GLU Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 528 HIS Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 97 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 126 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 235 optimal weight: 4.9990 chunk 257 optimal weight: 9.9990 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 221 optimal weight: 10.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN B 80 HIS ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 96 ASN E 296 ASN F 222 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 GLN G 561 ASN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.147601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.123194 restraints weight = 36259.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.127613 restraints weight = 18778.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.130553 restraints weight = 11609.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132551 restraints weight = 8059.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.133914 restraints weight = 6129.345| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 21402 Z= 0.142 Angle : 0.617 12.403 29086 Z= 0.315 Chirality : 0.043 0.200 3289 Planarity : 0.005 0.076 3802 Dihedral : 6.264 100.253 3021 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.88 % Allowed : 39.04 % Favored : 55.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.17), residues: 2625 helix: 0.04 (0.16), residues: 1111 sheet: -0.37 (0.27), residues: 373 loop : -1.08 (0.19), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG a 115 TYR 0.027 0.001 TYR F 197 PHE 0.019 0.001 PHE C 290 TRP 0.015 0.001 TRP D 276 HIS 0.008 0.001 HIS B 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (21402) covalent geometry : angle 0.61673 / 0.32 (29086) hydrogen bonds : bond 0.03710 / 2.58 ( 841) hydrogen bonds : angle 4.93288 / 3.47 ( 2424) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 734 time to evaluate : 0.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8253 (t0) cc_final: 0.8036 (t0) REVERT: A 155 GLN cc_start: 0.8246 (mm110) cc_final: 0.7996 (tp40) REVERT: A 180 ARG cc_start: 0.8359 (mmt180) cc_final: 0.8127 (mmp80) REVERT: A 250 ARG cc_start: 0.7896 (ttm110) cc_final: 0.7164 (ttm-80) REVERT: A 261 ASN cc_start: 0.8224 (m-40) cc_final: 0.7956 (m110) REVERT: A 278 GLU cc_start: 0.7723 (tp30) cc_final: 0.7218 (tp30) REVERT: B 30 VAL cc_start: 0.8544 (t) cc_final: 0.8329 (p) REVERT: B 87 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7108 (mpt-90) REVERT: B 94 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7596 (mmm160) REVERT: B 141 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7137 (m-30) REVERT: B 210 ARG cc_start: 0.7302 (tpp80) cc_final: 0.6964 (tpp80) REVERT: B 211 TRP cc_start: 0.8540 (m100) cc_final: 0.8143 (m100) REVERT: B 236 TYR cc_start: 0.7621 (m-10) cc_final: 0.7181 (m-10) REVERT: B 250 ARG cc_start: 0.7722 (mtp85) cc_final: 0.6725 (ttm110) REVERT: B 254 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.6483 (mpp) REVERT: B 297 LYS cc_start: 0.8227 (mttp) cc_final: 0.7948 (mttp) REVERT: C 19 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7630 (mmm-85) REVERT: C 33 TYR cc_start: 0.7965 (m-10) cc_final: 0.7413 (m-10) REVERT: C 144 ASP cc_start: 0.7838 (p0) cc_final: 0.7595 (p0) REVERT: C 152 PHE cc_start: 0.7821 (m-80) cc_final: 0.7062 (m-80) REVERT: C 157 VAL cc_start: 0.8155 (m) cc_final: 0.7929 (m) REVERT: C 163 ARG cc_start: 0.7361 (OUTLIER) cc_final: 0.6845 (ttp80) REVERT: C 180 ARG cc_start: 0.8496 (mmt90) cc_final: 0.8126 (mmt90) REVERT: C 224 ASN cc_start: 0.7716 (m110) cc_final: 0.7515 (p0) REVERT: C 225 GLU cc_start: 0.8091 (tp30) cc_final: 0.7589 (tp30) REVERT: C 248 MET cc_start: 0.7957 (mmt) cc_final: 0.7741 (mmt) REVERT: C 276 TRP cc_start: 0.8503 (t60) cc_final: 0.8249 (t60) REVERT: D 42 GLU cc_start: 0.6601 (tm-30) cc_final: 0.6215 (tm-30) REVERT: D 75 THR cc_start: 0.8425 (m) cc_final: 0.8053 (t) REVERT: D 100 HIS cc_start: 0.8420 (OUTLIER) cc_final: 0.8100 (m-70) REVERT: D 147 ARG cc_start: 0.7352 (OUTLIER) cc_final: 0.7140 (mtm-85) REVERT: D 156 ARG cc_start: 0.8235 (ttt180) cc_final: 0.8000 (ttt180) REVERT: D 210 ARG cc_start: 0.8229 (ttm170) cc_final: 0.7676 (ttm170) REVERT: D 216 THR cc_start: 0.8127 (p) cc_final: 0.7903 (t) REVERT: D 250 ARG cc_start: 0.7744 (mtt90) cc_final: 0.7375 (mtt90) REVERT: D 256 ARG cc_start: 0.7096 (ttm-80) cc_final: 0.6484 (ttm-80) REVERT: D 276 TRP cc_start: 0.8580 (t60) cc_final: 0.8130 (t-100) REVERT: D 292 LEU cc_start: 0.8585 (tp) cc_final: 0.8307 (tp) REVERT: E 55 LEU cc_start: 0.8828 (tp) cc_final: 0.8401 (tp) REVERT: E 61 PHE cc_start: 0.8285 (OUTLIER) cc_final: 0.7883 (t80) REVERT: E 140 PHE cc_start: 0.8512 (m-80) cc_final: 0.8138 (m-80) REVERT: E 238 ASN cc_start: 0.8698 (p0) cc_final: 0.8372 (p0) REVERT: E 257 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7607 (tm-30) REVERT: F 29 MET cc_start: 0.6829 (mmm) cc_final: 0.6427 (mmm) REVERT: F 51 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7628 (ttp-110) REVERT: F 79 THR cc_start: 0.7886 (m) cc_final: 0.7485 (p) REVERT: F 138 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8183 (tt) REVERT: F 142 GLU cc_start: 0.7356 (mt-10) cc_final: 0.6848 (mt-10) REVERT: F 155 GLN cc_start: 0.8269 (tm-30) cc_final: 0.7960 (tm-30) REVERT: F 157 VAL cc_start: 0.8548 (t) cc_final: 0.8347 (p) REVERT: F 230 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8323 (mp) REVERT: F 291 ARG cc_start: 0.8310 (mtp85) cc_final: 0.8097 (mtp180) REVERT: a 76 ARG cc_start: 0.6968 (OUTLIER) cc_final: 0.6762 (ptm160) REVERT: a 80 ASP cc_start: 0.7761 (t0) cc_final: 0.7385 (t0) REVERT: a 100 GLU cc_start: 0.5441 (OUTLIER) cc_final: 0.5046 (pm20) REVERT: a 108 PHE cc_start: 0.7839 (t80) cc_final: 0.7297 (t80) REVERT: a 115 ARG cc_start: 0.8570 (ttt-90) cc_final: 0.8344 (ttp80) REVERT: a 161 LEU cc_start: 0.8969 (mm) cc_final: 0.8553 (mm) REVERT: a 188 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7673 (mm-30) REVERT: a 197 ARG cc_start: 0.8281 (mmm-85) cc_final: 0.7803 (mmm-85) REVERT: a 215 MET cc_start: 0.7734 (mmm) cc_final: 0.7498 (mmm) REVERT: G 339 GLU cc_start: 0.5838 (OUTLIER) cc_final: 0.5347 (tm-30) REVERT: G 368 ARG cc_start: 0.6059 (OUTLIER) cc_final: 0.5479 (mmt180) REVERT: G 413 ARG cc_start: 0.5944 (OUTLIER) cc_final: 0.5491 (tpp-160) REVERT: G 468 SER cc_start: 0.4821 (OUTLIER) cc_final: 0.4583 (t) REVERT: G 503 ARG cc_start: 0.7556 (tmm-80) cc_final: 0.7297 (ptm160) REVERT: G 546 ASP cc_start: 0.7495 (t0) cc_final: 0.7243 (t0) REVERT: G 596 GLN cc_start: 0.6205 (OUTLIER) cc_final: 0.5708 (pm20) REVERT: I 483 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.7004 (ttm170) REVERT: I 499 TRP cc_start: 0.8517 (t-100) cc_final: 0.8308 (t-100) REVERT: I 501 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5771 (mtp85) REVERT: I 510 MET cc_start: 0.7872 (ttm) cc_final: 0.7185 (ttm) REVERT: I 517 GLU cc_start: 0.6589 (OUTLIER) cc_final: 0.6316 (mt-10) REVERT: I 566 HIS cc_start: 0.7525 (t-170) cc_final: 0.7293 (t-90) outliers start: 131 outliers final: 96 residues processed: 805 average time/residue: 0.1728 time to fit residues: 203.9994 Evaluate side-chains 847 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 731 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 274 ILE Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 136 VAL Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 301 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 76 ARG Chi-restraints excluded: chain a residue 86 GLN Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 GLU Chi-restraints excluded: chain a residue 124 MET Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 167 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 187 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 339 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 413 ARG Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 596 GLN Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 452 LYS Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 517 GLU Chi-restraints excluded: chain I residue 518 ASN Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 528 HIS Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 41 optimal weight: 7.9990 chunk 141 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 205 optimal weight: 10.0000 chunk 254 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 90 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN B 80 HIS ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 96 ASN E 186 ASN E 296 ASN F 64 ASN F 133 GLN F 222 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 561 ASN ** G 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.121702 restraints weight = 36397.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126058 restraints weight = 18820.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.129003 restraints weight = 11621.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.131004 restraints weight = 8058.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.132402 restraints weight = 6112.414| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 21402 Z= 0.198 Angle : 0.654 12.843 29086 Z= 0.336 Chirality : 0.044 0.208 3289 Planarity : 0.005 0.077 3802 Dihedral : 6.385 101.015 3021 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 5.80 % Allowed : 39.08 % Favored : 55.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.92 (0.16), residues: 2625 helix: -0.10 (0.15), residues: 1130 sheet: -0.37 (0.27), residues: 369 loop : -1.12 (0.19), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG a 115 TYR 0.026 0.002 TYR F 197 PHE 0.020 0.002 PHE G 346 TRP 0.023 0.002 TRP D 276 HIS 0.013 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.20 (21402) covalent geometry : angle 0.65423 / 0.34 (29086) hydrogen bonds : bond 0.04046 / 2.81 ( 841) hydrogen bonds : angle 5.04903 / 3.56 ( 2424) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5250 Ramachandran restraints generated. 2625 Oldfield, 0 Emsley, 2625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 753 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 96 ASN cc_start: 0.8231 (t0) cc_final: 0.7989 (t0) REVERT: A 155 GLN cc_start: 0.8252 (mm110) cc_final: 0.7985 (tp40) REVERT: A 250 ARG cc_start: 0.7960 (ttm110) cc_final: 0.7214 (ttm-80) REVERT: A 261 ASN cc_start: 0.8193 (m-40) cc_final: 0.7904 (m110) REVERT: A 278 GLU cc_start: 0.7758 (tp30) cc_final: 0.7268 (tp30) REVERT: B 30 VAL cc_start: 0.8532 (t) cc_final: 0.8277 (p) REVERT: B 73 HIS cc_start: 0.7813 (t-170) cc_final: 0.7569 (t-170) REVERT: B 87 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7188 (mpt-90) REVERT: B 94 ARG cc_start: 0.7929 (mmm160) cc_final: 0.7596 (mmm160) REVERT: B 141 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7192 (m-30) REVERT: B 210 ARG cc_start: 0.7321 (tpp80) cc_final: 0.7076 (tpp80) REVERT: B 211 TRP cc_start: 0.8531 (m100) cc_final: 0.8146 (m100) REVERT: B 250 ARG cc_start: 0.7765 (mtp85) cc_final: 0.6778 (ttm110) REVERT: B 254 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6566 (mpp) REVERT: B 297 LYS cc_start: 0.8229 (mttp) cc_final: 0.7948 (mttp) REVERT: C 19 ARG cc_start: 0.7950 (mmm-85) cc_final: 0.7645 (mmm-85) REVERT: C 144 ASP cc_start: 0.7831 (p0) cc_final: 0.7609 (p0) REVERT: C 163 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.6928 (ttp80) REVERT: C 180 ARG cc_start: 0.8556 (mmt90) cc_final: 0.8190 (mmt90) REVERT: C 248 MET cc_start: 0.7973 (mmt) cc_final: 0.7742 (mmt) REVERT: C 276 TRP cc_start: 0.8496 (t60) cc_final: 0.8264 (t60) REVERT: C 279 ASN cc_start: 0.8358 (m-40) cc_final: 0.7993 (m-40) REVERT: D 42 GLU cc_start: 0.6653 (tm-30) cc_final: 0.6266 (tm-30) REVERT: D 100 HIS cc_start: 0.8449 (OUTLIER) cc_final: 0.8111 (m-70) REVERT: D 147 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7184 (mtm-85) REVERT: D 156 ARG cc_start: 0.8253 (ttt180) cc_final: 0.7935 (ttt90) REVERT: D 210 ARG cc_start: 0.8299 (ttm170) cc_final: 0.8086 (ttm170) REVERT: D 216 THR cc_start: 0.8152 (p) cc_final: 0.7888 (t) REVERT: D 256 ARG cc_start: 0.7191 (ttm-80) cc_final: 0.6624 (ttm-80) REVERT: D 276 TRP cc_start: 0.8592 (t60) cc_final: 0.8059 (t-100) REVERT: D 292 LEU cc_start: 0.8680 (tp) cc_final: 0.8386 (tp) REVERT: E 55 LEU cc_start: 0.8818 (tp) cc_final: 0.8407 (tp) REVERT: E 61 PHE cc_start: 0.8296 (OUTLIER) cc_final: 0.7926 (t80) REVERT: E 89 ASN cc_start: 0.7743 (m-40) cc_final: 0.7309 (t0) REVERT: E 140 PHE cc_start: 0.8519 (m-80) cc_final: 0.8136 (m-80) REVERT: E 158 LEU cc_start: 0.8088 (mp) cc_final: 0.7887 (mp) REVERT: E 169 GLN cc_start: 0.7110 (pt0) cc_final: 0.6806 (pt0) REVERT: E 238 ASN cc_start: 0.8703 (p0) cc_final: 0.8374 (p0) REVERT: E 257 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 303 ARG cc_start: 0.7702 (mtt180) cc_final: 0.7434 (mtt180) REVERT: E 308 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6747 (mm-30) REVERT: F 29 MET cc_start: 0.6846 (mmm) cc_final: 0.6467 (mmm) REVERT: F 51 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7642 (ttp-110) REVERT: F 79 THR cc_start: 0.7850 (m) cc_final: 0.7442 (p) REVERT: F 138 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8101 (tt) REVERT: F 142 GLU cc_start: 0.7348 (mt-10) cc_final: 0.6835 (mt-10) REVERT: F 155 GLN cc_start: 0.8192 (tm-30) cc_final: 0.7816 (tm-30) REVERT: F 230 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8349 (mp) REVERT: F 291 ARG cc_start: 0.8371 (mtp85) cc_final: 0.8131 (mtp180) REVERT: F 293 THR cc_start: 0.8147 (m) cc_final: 0.7927 (m) REVERT: a 76 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.6767 (ptm160) REVERT: a 80 ASP cc_start: 0.7764 (t0) cc_final: 0.7390 (t0) REVERT: a 100 GLU cc_start: 0.5537 (OUTLIER) cc_final: 0.5139 (pm20) REVERT: a 108 PHE cc_start: 0.7836 (t80) cc_final: 0.7311 (t80) REVERT: a 115 ARG cc_start: 0.8588 (ttt-90) cc_final: 0.8381 (ttp80) REVERT: a 161 LEU cc_start: 0.8965 (mm) cc_final: 0.8563 (mm) REVERT: a 188 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7655 (mm-30) REVERT: a 197 ARG cc_start: 0.8293 (mmm-85) cc_final: 0.7819 (mmm-85) REVERT: a 213 ARG cc_start: 0.7966 (mmt90) cc_final: 0.7736 (mmt-90) REVERT: a 215 MET cc_start: 0.7732 (mmm) cc_final: 0.7491 (mmm) REVERT: G 339 GLU cc_start: 0.5859 (OUTLIER) cc_final: 0.5386 (tm-30) REVERT: G 364 ARG cc_start: 0.7175 (tpt170) cc_final: 0.6857 (tpt170) REVERT: G 368 ARG cc_start: 0.6145 (OUTLIER) cc_final: 0.5525 (mmt180) REVERT: G 386 LEU cc_start: 0.9321 (tp) cc_final: 0.9061 (tp) REVERT: G 391 LEU cc_start: 0.8680 (tp) cc_final: 0.8255 (mt) REVERT: G 413 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5458 (tpp-160) REVERT: G 468 SER cc_start: 0.4883 (OUTLIER) cc_final: 0.4647 (t) REVERT: G 503 ARG cc_start: 0.7592 (tmm-80) cc_final: 0.7351 (ptm160) REVERT: G 509 MET cc_start: 0.6528 (mmp) cc_final: 0.6233 (mmp) REVERT: G 546 ASP cc_start: 0.7539 (t0) cc_final: 0.7279 (t0) REVERT: G 596 GLN cc_start: 0.6170 (OUTLIER) cc_final: 0.5901 (pm20) REVERT: I 483 ARG cc_start: 0.7348 (OUTLIER) cc_final: 0.7056 (ttm170) REVERT: I 499 TRP cc_start: 0.8533 (t-100) cc_final: 0.8311 (t-100) REVERT: I 501 ARG cc_start: 0.6189 (OUTLIER) cc_final: 0.5766 (mtp85) REVERT: I 510 MET cc_start: 0.7763 (ttm) cc_final: 0.7190 (ttm) REVERT: I 517 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6288 (mt-10) outliers start: 129 outliers final: 98 residues processed: 823 average time/residue: 0.1536 time to fit residues: 185.4287 Evaluate side-chains 869 residues out of total 2226 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 751 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 57 ILE Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 173 ILE Chi-restraints excluded: chain A residue 207 GLN Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 317 GLU Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain B residue 90 TRP Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 123 PHE Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 254 MET Chi-restraints excluded: chain B residue 293 THR Chi-restraints excluded: chain B residue 324 ASN Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 87 ARG Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 134 HIS Chi-restraints excluded: chain C residue 149 ASP Chi-restraints excluded: chain C residue 155 GLN Chi-restraints excluded: chain C residue 163 ARG Chi-restraints excluded: chain C residue 184 THR Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 254 MET Chi-restraints excluded: chain C residue 285 ASP Chi-restraints excluded: chain C residue 292 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 100 HIS Chi-restraints excluded: chain D residue 102 SER Chi-restraints excluded: chain D residue 147 ARG Chi-restraints excluded: chain D residue 165 THR Chi-restraints excluded: chain D residue 215 THR Chi-restraints excluded: chain D residue 229 VAL Chi-restraints excluded: chain D residue 295 LEU Chi-restraints excluded: chain D residue 299 ASP Chi-restraints excluded: chain E residue 61 PHE Chi-restraints excluded: chain E residue 80 HIS Chi-restraints excluded: chain E residue 92 CYS Chi-restraints excluded: chain E residue 96 ASN Chi-restraints excluded: chain E residue 151 MET Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 166 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 295 LEU Chi-restraints excluded: chain E residue 306 VAL Chi-restraints excluded: chain F residue 30 VAL Chi-restraints excluded: chain F residue 51 ARG Chi-restraints excluded: chain F residue 52 GLN Chi-restraints excluded: chain F residue 80 HIS Chi-restraints excluded: chain F residue 138 LEU Chi-restraints excluded: chain F residue 188 VAL Chi-restraints excluded: chain F residue 198 HIS Chi-restraints excluded: chain F residue 230 LEU Chi-restraints excluded: chain F residue 237 GLN Chi-restraints excluded: chain F residue 316 VAL Chi-restraints excluded: chain a residue 32 CYS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 47 SER Chi-restraints excluded: chain a residue 76 ARG Chi-restraints excluded: chain a residue 86 GLN Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 100 GLU Chi-restraints excluded: chain a residue 124 MET Chi-restraints excluded: chain a residue 135 LEU Chi-restraints excluded: chain a residue 149 THR Chi-restraints excluded: chain a residue 157 GLU Chi-restraints excluded: chain a residue 167 LEU Chi-restraints excluded: chain a residue 182 LEU Chi-restraints excluded: chain a residue 187 ILE Chi-restraints excluded: chain G residue 320 VAL Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain G residue 339 GLU Chi-restraints excluded: chain G residue 340 LEU Chi-restraints excluded: chain G residue 342 ARG Chi-restraints excluded: chain G residue 368 ARG Chi-restraints excluded: chain G residue 410 THR Chi-restraints excluded: chain G residue 413 ARG Chi-restraints excluded: chain G residue 449 CYS Chi-restraints excluded: chain G residue 468 SER Chi-restraints excluded: chain G residue 508 LEU Chi-restraints excluded: chain G residue 531 LEU Chi-restraints excluded: chain G residue 532 LEU Chi-restraints excluded: chain G residue 544 ILE Chi-restraints excluded: chain G residue 567 LEU Chi-restraints excluded: chain G residue 595 TYR Chi-restraints excluded: chain G residue 596 GLN Chi-restraints excluded: chain G residue 600 THR Chi-restraints excluded: chain G residue 607 LEU Chi-restraints excluded: chain I residue 342 ARG Chi-restraints excluded: chain I residue 357 VAL Chi-restraints excluded: chain I residue 452 LYS Chi-restraints excluded: chain I residue 483 ARG Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 491 VAL Chi-restraints excluded: chain I residue 501 ARG Chi-restraints excluded: chain I residue 504 ARG Chi-restraints excluded: chain I residue 517 GLU Chi-restraints excluded: chain I residue 525 ILE Chi-restraints excluded: chain I residue 528 HIS Chi-restraints excluded: chain I residue 595 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 261 random chunks: chunk 35 optimal weight: 0.8980 chunk 206 optimal weight: 4.9990 chunk 126 optimal weight: 0.2980 chunk 141 optimal weight: 4.9990 chunk 221 optimal weight: 4.9990 chunk 258 optimal weight: 0.0870 chunk 151 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 179 optimal weight: 0.6980 chunk 241 optimal weight: 6.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN B 80 HIS B 311 GLN ** D 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 ASN E 96 ASN E 296 ASN F 133 GLN F 222 HIS ** a 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 528 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 561 ASN G 614 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.148923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.124643 restraints weight = 36234.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.129036 restraints weight = 18716.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.131981 restraints weight = 11511.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.133992 restraints weight = 7984.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135273 restraints weight = 6043.555| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 21402 Z= 0.120 Angle : 0.625 13.045 29086 Z= 0.318 Chirality : 0.043 0.195 3289 Planarity : 0.005 0.075 3802 Dihedral : 6.180 98.428 3021 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 5.12 % Allowed : 39.67 % Favored : 55.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.17), residues: 2625 helix: 0.07 (0.16), residues: 1100 sheet: -0.38 (0.27), residues: 365 loop : -1.03 (0.19), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG a 115 TYR 0.020 0.001 TYR F 197 PHE 0.021 0.001 PHE G 346 TRP 0.036 0.002 TRP I 472 HIS 0.012 0.001 HIS G 528 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (21402) covalent geometry : angle 0.62513 / 0.32 (29086) hydrogen bonds : bond 0.03497 / 2.43 ( 841) hydrogen bonds : angle 4.95217 / 3.49 ( 2424) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4458.48 seconds wall clock time: 77 minutes 14.69 seconds (4634.69 seconds total)