Starting phenix.real_space_refine on Sat Sep 12 01:08:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.cif Found real_map, /net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2026/6he4_0209.map" } resolution = 4.85 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= 0.000 sd= 0.002 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 14 5.49 5 Mg 5 5.21 5 S 42 5.16 5 C 8042 2.51 5 N 2161 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 168 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12684 Number of models: 1 Model: "" Number of chains: 11 Chain: "H" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 247} Chain: "I" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 3, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 248} Chain: "K" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} Chain: "L" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 249} Chain: "M" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 13, 'TRANS': 249} Chain: "J" Number of atoms: 2088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2088 Classifications: {'peptide': 267} Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 245} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.91, per 1000 atoms: 0.23 Number of scatterers: 12684 At special positions: 0 Unit cell: (134, 128.64, 80.4, 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 42 16.00 P 14 15.00 Mg 5 11.99 O 2420 8.00 N 2161 7.00 C 8042 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: 0.94 Conformation dependent library (CDL) restraints added in 433.0 milliseconds 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2964 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 7 sheets defined 53.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'H' and resid 124 through 129 Processing helix chain 'H' and resid 147 through 157 removed outlier: 3.984A pdb=" N GLU H 151 " --> pdb=" O ASP H 147 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU H 152 " --> pdb=" O VAL H 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 157 through 162 Processing helix chain 'H' and resid 163 through 171 removed outlier: 3.644A pdb=" N PHE H 167 " --> pdb=" O LYS H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 200 removed outlier: 3.539A pdb=" N LEU H 191 " --> pdb=" O GLY H 187 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARG H 200 " --> pdb=" O ALA H 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 233 removed outlier: 3.642A pdb=" N VAL H 223 " --> pdb=" O GLY H 219 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE H 227 " --> pdb=" O VAL H 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 256 through 275 removed outlier: 4.190A pdb=" N GLU H 260 " --> pdb=" O SER H 256 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU H 269 " --> pdb=" O MET H 265 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU H 271 " --> pdb=" O GLN H 267 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE H 275 " --> pdb=" O GLU H 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 328 removed outlier: 3.809A pdb=" N ILE H 318 " --> pdb=" O PHE H 314 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 343 removed outlier: 3.804A pdb=" N LEU H 339 " --> pdb=" O ASP H 335 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG H 341 " --> pdb=" O LYS H 337 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE H 342 " --> pdb=" O GLU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 347 through 365 Processing helix chain 'H' and resid 371 through 385 removed outlier: 3.654A pdb=" N PHE H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 124 through 129 Processing helix chain 'I' and resid 147 through 163 removed outlier: 3.719A pdb=" N GLU I 151 " --> pdb=" O ASP I 147 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 164 through 171 removed outlier: 3.541A pdb=" N VAL I 170 " --> pdb=" O LEU I 166 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 200 removed outlier: 3.721A pdb=" N ASN I 197 " --> pdb=" O LYS I 193 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN I 198 " --> pdb=" O ALA I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 217 through 234 removed outlier: 3.690A pdb=" N LEU I 222 " --> pdb=" O GLU I 218 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU I 232 " --> pdb=" O GLN I 228 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS I 233 " --> pdb=" O LEU I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 242 through 246 removed outlier: 3.687A pdb=" N ILE I 246 " --> pdb=" O LEU I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 257 through 273 removed outlier: 3.574A pdb=" N VAL I 261 " --> pdb=" O GLY I 257 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN I 262 " --> pdb=" O ASP I 258 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N GLN I 267 " --> pdb=" O ARG I 263 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA I 270 " --> pdb=" O MET I 266 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP I 273 " --> pdb=" O LEU I 269 " (cutoff:3.500A) Processing helix chain 'I' and resid 294 through 299 Processing helix chain 'I' and resid 313 through 328 removed outlier: 3.769A pdb=" N ILE I 318 " --> pdb=" O PHE I 314 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LYS I 327 " --> pdb=" O ILE I 323 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 343 Processing helix chain 'I' and resid 347 through 365 Processing helix chain 'I' and resid 371 through 387 removed outlier: 3.652A pdb=" N LYS I 381 " --> pdb=" O LYS I 377 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL I 382 " --> pdb=" O ALA I 378 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS I 385 " --> pdb=" O LYS I 381 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR I 386 " --> pdb=" O VAL I 382 " (cutoff:3.500A) Processing helix chain 'K' and resid 146 through 163 removed outlier: 3.660A pdb=" N GLU K 152 " --> pdb=" O VAL K 148 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL K 157 " --> pdb=" O ILE K 153 " (cutoff:3.500A) Proline residue: K 160 - end of helix Processing helix chain 'K' and resid 163 through 171 removed outlier: 4.254A pdb=" N PHE K 167 " --> pdb=" O LYS K 163 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA K 168 " --> pdb=" O PRO K 164 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU K 169 " --> pdb=" O GLU K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 187 through 199 Processing helix chain 'K' and resid 209 through 211 No H-bonds generated for 'chain 'K' and resid 209 through 211' Processing helix chain 'K' and resid 217 through 233 Processing helix chain 'K' and resid 261 through 269 removed outlier: 3.962A pdb=" N GLN K 267 " --> pdb=" O ARG K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 294 through 299 removed outlier: 3.541A pdb=" N LEU K 298 " --> pdb=" O ASP K 294 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 328 removed outlier: 3.532A pdb=" N HIS K 324 " --> pdb=" O ILE K 320 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS K 327 " --> pdb=" O ILE K 323 " (cutoff:3.500A) Processing helix chain 'K' and resid 335 through 343 removed outlier: 3.675A pdb=" N LEU K 339 " --> pdb=" O ASP K 335 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE K 342 " --> pdb=" O GLU K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 347 through 365 Processing helix chain 'K' and resid 371 through 385 removed outlier: 3.534A pdb=" N PHE K 375 " --> pdb=" O THR K 371 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 129 Processing helix chain 'L' and resid 146 through 157 removed outlier: 3.523A pdb=" N GLU L 152 " --> pdb=" O VAL L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 158 through 163 Processing helix chain 'L' and resid 164 through 169 removed outlier: 3.684A pdb=" N ALA L 168 " --> pdb=" O PRO L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 200 removed outlier: 3.956A pdb=" N ARG L 200 " --> pdb=" O ALA L 196 " (cutoff:3.500A) Processing helix chain 'L' and resid 217 through 233 removed outlier: 3.521A pdb=" N VAL L 223 " --> pdb=" O GLY L 219 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 274 removed outlier: 4.097A pdb=" N ARG L 259 " --> pdb=" O THR L 255 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU L 260 " --> pdb=" O SER L 256 " (cutoff:3.500A) Processing helix chain 'L' and resid 294 through 299 removed outlier: 3.734A pdb=" N ARG L 299 " --> pdb=" O PRO L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 327 removed outlier: 3.841A pdb=" N ILE L 318 " --> pdb=" O PHE L 314 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS L 327 " --> pdb=" O ILE L 323 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 344 removed outlier: 4.379A pdb=" N LEU L 339 " --> pdb=" O ASP L 335 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE L 342 " --> pdb=" O GLU L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 347 through 365 removed outlier: 3.512A pdb=" N CYS L 355 " --> pdb=" O ILE L 351 " (cutoff:3.500A) Processing helix chain 'L' and resid 371 through 387 removed outlier: 4.417A pdb=" N LYS L 385 " --> pdb=" O LYS L 381 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N THR L 386 " --> pdb=" O VAL L 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 146 through 157 removed outlier: 3.847A pdb=" N GLU M 151 " --> pdb=" O ASP M 147 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 163 Processing helix chain 'M' and resid 165 through 170 Processing helix chain 'M' and resid 187 through 200 Processing helix chain 'M' and resid 220 through 233 Processing helix chain 'M' and resid 255 through 275 removed outlier: 3.692A pdb=" N GLU M 260 " --> pdb=" O SER M 256 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL M 261 " --> pdb=" O GLY M 257 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLN M 267 " --> pdb=" O ARG M 263 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU M 268 " --> pdb=" O THR M 264 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU M 271 " --> pdb=" O GLN M 267 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASP M 273 " --> pdb=" O LEU M 269 " (cutoff:3.500A) Processing helix chain 'M' and resid 313 through 326 removed outlier: 3.833A pdb=" N ILE M 323 " --> pdb=" O GLN M 319 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N HIS M 324 " --> pdb=" O ILE M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 343 removed outlier: 3.926A pdb=" N LEU M 339 " --> pdb=" O ASP M 335 " (cutoff:3.500A) Processing helix chain 'M' and resid 347 through 365 removed outlier: 3.644A pdb=" N GLY M 359 " --> pdb=" O CYS M 355 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET M 360 " --> pdb=" O THR M 356 " (cutoff:3.500A) Processing helix chain 'M' and resid 371 through 382 Processing helix chain 'J' and resid 126 through 131 removed outlier: 3.801A pdb=" N PHE J 130 " --> pdb=" O MET J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 157 Processing helix chain 'J' and resid 157 through 163 Processing helix chain 'J' and resid 164 through 171 removed outlier: 3.670A pdb=" N ALA J 168 " --> pdb=" O PRO J 164 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL J 170 " --> pdb=" O LEU J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 200 removed outlier: 3.883A pdb=" N GLN J 198 " --> pdb=" O ALA J 194 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG J 200 " --> pdb=" O ALA J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 217 through 233 Processing helix chain 'J' and resid 242 through 247 Processing helix chain 'J' and resid 261 through 273 removed outlier: 3.895A pdb=" N MET J 265 " --> pdb=" O VAL J 261 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET J 266 " --> pdb=" O GLN J 262 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN J 267 " --> pdb=" O ARG J 263 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU J 268 " --> pdb=" O THR J 264 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP J 273 " --> pdb=" O LEU J 269 " (cutoff:3.500A) Processing helix chain 'J' and resid 294 through 299 removed outlier: 3.553A pdb=" N ARG J 299 " --> pdb=" O PRO J 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 328 removed outlier: 3.678A pdb=" N ILE J 318 " --> pdb=" O PHE J 314 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE J 323 " --> pdb=" O GLN J 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS J 324 " --> pdb=" O ILE J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 335 through 343 Processing helix chain 'J' and resid 347 through 365 Processing helix chain 'J' and resid 371 through 385 removed outlier: 3.525A pdb=" N LYS J 385 " --> pdb=" O LYS J 381 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 204 through 205 removed outlier: 3.514A pdb=" N ILE H 204 " --> pdb=" O ILE H 237 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N ILE H 238 " --> pdb=" O ILE H 284 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU H 180 " --> pdb=" O GLY H 285 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLY H 177 " --> pdb=" O ARG H 305 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ILE H 307 " --> pdb=" O GLY H 177 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU H 179 " --> pdb=" O ILE H 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 203 through 206 removed outlier: 6.333A pdb=" N ILE I 238 " --> pdb=" O ILE I 284 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA I 286 " --> pdb=" O ILE I 238 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ILE I 240 " --> pdb=" O ALA I 286 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL I 178 " --> pdb=" O GLY I 285 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ILE I 307 " --> pdb=" O GLY I 177 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU I 179 " --> pdb=" O ILE I 307 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 203 through 207 removed outlier: 6.470A pdb=" N ILE K 204 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N ASP K 241 " --> pdb=" O ILE K 204 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL K 206 " --> pdb=" O ASP K 241 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N VAL K 178 " --> pdb=" O GLY K 285 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N GLY K 177 " --> pdb=" O ARG K 305 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE K 307 " --> pdb=" O GLY K 177 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU K 179 " --> pdb=" O ILE K 307 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 285 through 287 removed outlier: 3.632A pdb=" N GLY L 285 " --> pdb=" O VAL L 178 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU L 179 " --> pdb=" O ILE L 307 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 202 through 207 removed outlier: 3.506A pdb=" N ASP L 241 " --> pdb=" O VAL L 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'M' and resid 132 through 134 removed outlier: 6.166A pdb=" N THR M 202 " --> pdb=" O ILE M 237 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N PHE M 239 " --> pdb=" O THR M 202 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE M 204 " --> pdb=" O PHE M 239 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N SER M 236 " --> pdb=" O LYS M 282 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ILE M 284 " --> pdb=" O SER M 236 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE M 238 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ALA M 286 " --> pdb=" O ILE M 238 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE M 240 " --> pdb=" O ALA M 286 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL M 178 " --> pdb=" O GLY M 285 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU M 179 " --> pdb=" O ARG M 305 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 202 through 206 removed outlier: 8.185A pdb=" N ILE J 284 " --> pdb=" O SER J 236 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE J 238 " --> pdb=" O ILE J 284 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ALA J 286 " --> pdb=" O ILE J 238 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE J 240 " --> pdb=" O ALA J 286 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR J 287 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY J 177 " --> pdb=" O ARG J 305 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N ILE J 307 " --> pdb=" O GLY J 177 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU J 179 " --> pdb=" O ILE J 307 " (cutoff:3.500A) 507 hydrogen bonds defined for protein. 1518 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.44 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.30: 2235 1.30 - 1.45: 3773 1.45 - 1.60: 6582 1.60 - 1.75: 210 1.75 - 1.90: 81 Bond restraints: 12881 Sorted by residual: bond pdb=" O3A ATP J 401 " pdb=" PB ATP J 401 " ideal model delta sigma weight residual 1.592 1.786 -0.194 1.10e-02 8.26e+03 3.11e+02 bond pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 1.592 1.764 -0.172 1.10e-02 8.26e+03 2.45e+02 bond pdb=" CA VAL H 206 " pdb=" C VAL H 206 " ideal model delta sigma weight residual 1.523 1.381 0.141 1.17e-02 7.31e+03 1.46e+02 bond pdb=" N ALA L 353 " pdb=" CA ALA L 353 " ideal model delta sigma weight residual 1.459 1.314 0.145 1.23e-02 6.61e+03 1.40e+02 bond pdb=" O3A ATP I 401 " pdb=" PB ATP I 401 " ideal model delta sigma weight residual 1.592 1.716 -0.124 1.10e-02 8.26e+03 1.26e+02 ... (remaining 12876 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.46: 15202 5.46 - 10.93: 2104 10.93 - 16.39: 91 16.39 - 21.85: 8 21.85 - 27.31: 2 Bond angle restraints: 17407 Sorted by residual: angle pdb=" PA ATP K 401 " pdb=" O3A ATP K 401 " pdb=" PB ATP K 401 " ideal model delta sigma weight residual 136.83 158.87 -22.04 1.00e+00 1.00e+00 4.86e+02 angle pdb=" PA ATP H 401 " pdb=" O3A ATP H 401 " pdb=" PB ATP H 401 " ideal model delta sigma weight residual 136.83 158.43 -21.60 1.00e+00 1.00e+00 4.66e+02 angle pdb=" PB ATP I 401 " pdb=" O3B ATP I 401 " pdb=" PG ATP I 401 " ideal model delta sigma weight residual 139.87 158.05 -18.18 1.00e+00 1.00e+00 3.30e+02 angle pdb=" PB ATP J 401 " pdb=" O3B ATP J 401 " pdb=" PG ATP J 401 " ideal model delta sigma weight residual 139.87 157.49 -17.62 1.00e+00 1.00e+00 3.10e+02 angle pdb=" PB ATP H 401 " pdb=" O3B ATP H 401 " pdb=" PG ATP H 401 " ideal model delta sigma weight residual 139.87 156.19 -16.32 1.00e+00 1.00e+00 2.66e+02 ... (remaining 17402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.64: 7510 28.64 - 57.28: 302 57.28 - 85.92: 114 85.92 - 114.56: 14 114.56 - 143.20: 3 Dihedral angle restraints: 7943 sinusoidal: 3359 harmonic: 4584 Sorted by residual: dihedral pdb=" CA GLU H 218 " pdb=" C GLU H 218 " pdb=" N GLY H 219 " pdb=" CA GLY H 219 " ideal model delta harmonic sigma weight residual -180.00 -45.34 -134.66 0 5.00e+00 4.00e-02 7.25e+02 dihedral pdb=" CA ASP I 254 " pdb=" C ASP I 254 " pdb=" N THR I 255 " pdb=" CA THR I 255 " ideal model delta harmonic sigma weight residual 180.00 45.62 134.38 0 5.00e+00 4.00e-02 7.22e+02 dihedral pdb=" CA ILE H 240 " pdb=" C ILE H 240 " pdb=" N ASP H 241 " pdb=" CA ASP H 241 " ideal model delta harmonic sigma weight residual -180.00 -86.63 -93.37 0 5.00e+00 4.00e-02 3.49e+02 ... (remaining 7940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.161: 1148 0.161 - 0.323: 632 0.323 - 0.484: 164 0.484 - 0.645: 50 0.645 - 0.806: 6 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CA LYS K 282 " pdb=" N LYS K 282 " pdb=" C LYS K 282 " pdb=" CB LYS K 282 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.62e+01 chirality pdb=" CB VAL I 195 " pdb=" CA VAL I 195 " pdb=" CG1 VAL I 195 " pdb=" CG2 VAL I 195 " both_signs ideal model delta sigma weight residual False -2.63 -1.91 -0.72 2.00e-01 2.50e+01 1.28e+01 chirality pdb=" CA PHE I 361 " pdb=" N PHE I 361 " pdb=" C PHE I 361 " pdb=" CB PHE I 361 " both_signs ideal model delta sigma weight residual False 2.51 1.82 0.69 2.00e-01 2.50e+01 1.18e+01 ... (remaining 1997 not shown) Planarity restraints: 2243 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP K 401 " 0.191 2.00e-02 2.50e+03 1.12e-01 3.43e+02 pdb=" C2 ATP K 401 " -0.047 2.00e-02 2.50e+03 pdb=" C4 ATP K 401 " -0.039 2.00e-02 2.50e+03 pdb=" C5 ATP K 401 " -0.130 2.00e-02 2.50e+03 pdb=" C6 ATP K 401 " -0.057 2.00e-02 2.50e+03 pdb=" C8 ATP K 401 " -0.026 2.00e-02 2.50e+03 pdb=" N1 ATP K 401 " 0.029 2.00e-02 2.50e+03 pdb=" N3 ATP K 401 " -0.039 2.00e-02 2.50e+03 pdb=" N6 ATP K 401 " 0.238 2.00e-02 2.50e+03 pdb=" N7 ATP K 401 " -0.131 2.00e-02 2.50e+03 pdb=" N9 ATP K 401 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 128 " 0.250 2.00e-02 2.50e+03 1.30e-01 3.39e+02 pdb=" CG TYR I 128 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TYR I 128 " -0.121 2.00e-02 2.50e+03 pdb=" CD2 TYR I 128 " -0.122 2.00e-02 2.50e+03 pdb=" CE1 TYR I 128 " -0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR I 128 " -0.064 2.00e-02 2.50e+03 pdb=" CZ TYR I 128 " 0.014 2.00e-02 2.50e+03 pdb=" OH TYR I 128 " 0.173 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 215 " 0.220 2.00e-02 2.50e+03 1.16e-01 2.70e+02 pdb=" CG TYR H 215 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 TYR H 215 " -0.080 2.00e-02 2.50e+03 pdb=" CD2 TYR H 215 " -0.058 2.00e-02 2.50e+03 pdb=" CE1 TYR H 215 " -0.033 2.00e-02 2.50e+03 pdb=" CE2 TYR H 215 " -0.063 2.00e-02 2.50e+03 pdb=" CZ TYR H 215 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR H 215 " 0.165 2.00e-02 2.50e+03 ... (remaining 2240 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 117 2.54 - 3.13: 8663 3.13 - 3.72: 19148 3.72 - 4.31: 28913 4.31 - 4.90: 45979 Nonbonded interactions: 102820 Sorted by model distance: nonbonded pdb=" O2G ATP I 401 " pdb="MG MG I 402 " model vdw 1.953 2.170 nonbonded pdb=" O2G ATP K 401 " pdb="MG MG K 402 " model vdw 1.998 2.170 nonbonded pdb=" O2G ATP H 401 " pdb="MG MG H 402 " model vdw 1.999 2.170 nonbonded pdb=" O2B ATP K 401 " pdb="MG MG K 402 " model vdw 2.103 2.170 nonbonded pdb=" O2B ATP I 401 " pdb="MG MG I 402 " model vdw 2.153 2.170 ... (remaining 102815 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 'H' and resid 123 through 389) selection = (chain 'I' and resid 123 through 389) selection = (chain 'J' and resid 123 through 389) selection = (chain 'K' and resid 123 through 389) selection = (chain 'L' and resid 123 through 389) selection = chain 'M' } 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: 3.980 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.890 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5555 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 : 0.036 0.205 12881 Z= 2.303 Angle : 3.648 27.314 17407 Z= 2.465 Chirality : 0.208 0.806 2000 Planarity : 0.031 0.256 2243 Dihedral : 18.704 143.201 4979 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 4.09 % Allowed : 6.42 % Favored : 89.50 % Rotamer: Outliers : 3.66 % Allowed : 9.12 % Favored : 87.22 % Cbeta Deviations : 7.49 % Peptide Plane: Cis-proline : 7.78 % Cis-general : 1.13 % Twisted Proline : 5.56 % Twisted General : 1.66 % 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: -2.84 (0.18), residues: 1590 helix: -1.19 (0.16), residues: 763 sheet: -1.00 (0.37), residues: 141 loop : -2.88 (0.21), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.079 0.011 ARG J 221 TYR 0.250 0.051 TYR I 128 PHE 0.167 0.040 PHE I 167 HIS 0.037 0.016 HIS L 324 Details of bonding type rmsd/Z covalent geometry : bond 0.03563 / 2.30 (12881) covalent geometry : angle 3.64778 / 2.47 (17407) hydrogen bonds : bond 0.31085 / 20.23 ( 507) hydrogen bonds : angle 9.10549 / 6.27 ( 1518) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 827 time to evaluate : 0.483 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 179 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8370 (mt) REVERT: H 229 LEU cc_start: 0.8759 (tp) cc_final: 0.8351 (tp) REVERT: H 268 LEU cc_start: 0.7203 (tp) cc_final: 0.6899 (tp) REVERT: H 269 LEU cc_start: 0.8934 (mt) cc_final: 0.8611 (mp) REVERT: H 336 PHE cc_start: 0.6878 (m-80) cc_final: 0.6644 (m-80) REVERT: H 337 LYS cc_start: 0.7673 (mtpp) cc_final: 0.7445 (mtmt) REVERT: H 354 ILE cc_start: 0.8837 (mt) cc_final: 0.8550 (mt) REVERT: H 361 PHE cc_start: 0.5086 (t80) cc_final: 0.4407 (t80) REVERT: H 363 ILE cc_start: 0.8559 (mt) cc_final: 0.8309 (mt) REVERT: H 373 LEU cc_start: 0.7768 (tp) cc_final: 0.7273 (tp) REVERT: H 379 ILE cc_start: 0.8435 (mt) cc_final: 0.8097 (mt) REVERT: I 127 VAL cc_start: 0.6645 (m) cc_final: 0.5638 (m) REVERT: I 150 ILE cc_start: 0.7193 (mt) cc_final: 0.6371 (mt) REVERT: I 159 LEU cc_start: 0.8150 (tp) cc_final: 0.7887 (tp) REVERT: I 184 PRO cc_start: 0.8121 (Cg_exo) cc_final: 0.7808 (Cg_endo) REVERT: I 186 THR cc_start: 0.7500 (p) cc_final: 0.7159 (p) REVERT: I 207 VAL cc_start: 0.8450 (t) cc_final: 0.7531 (t) REVERT: I 231 LYS cc_start: 0.8767 (mttm) cc_final: 0.8550 (mmmt) REVERT: I 294 ASP cc_start: 0.8611 (m-30) cc_final: 0.8322 (t0) REVERT: I 297 ILE cc_start: 0.8609 (mp) cc_final: 0.7966 (mp) REVERT: I 309 VAL cc_start: 0.9142 (t) cc_final: 0.8715 (p) REVERT: I 320 ILE cc_start: 0.8850 (mt) cc_final: 0.8581 (mm) REVERT: I 370 VAL cc_start: 0.4447 (t) cc_final: 0.3680 (p) REVERT: I 371 THR cc_start: 0.6842 (p) cc_final: 0.5426 (p) REVERT: K 149 GLN cc_start: 0.9100 (mp10) cc_final: 0.8883 (mp10) REVERT: K 150 ILE cc_start: 0.8252 (mt) cc_final: 0.7772 (mt) REVERT: K 165 GLU cc_start: 0.7284 (OUTLIER) cc_final: 0.6906 (pm20) REVERT: K 173 GLU cc_start: 0.7514 (mp0) cc_final: 0.7029 (mp0) REVERT: K 186 THR cc_start: 0.5477 (p) cc_final: 0.5224 (p) REVERT: K 188 LYS cc_start: 0.8299 (mtmm) cc_final: 0.7337 (ptpt) REVERT: K 189 THR cc_start: 0.8674 (OUTLIER) cc_final: 0.6342 (m) REVERT: K 190 LEU cc_start: 0.7340 (mt) cc_final: 0.7055 (mt) REVERT: K 204 ILE cc_start: 0.7858 (mt) cc_final: 0.7619 (mt) REVERT: K 207 VAL cc_start: 0.8388 (t) cc_final: 0.7755 (m) REVERT: K 216 ILE cc_start: 0.6022 (OUTLIER) cc_final: 0.5678 (pt) REVERT: K 243 LEU cc_start: 0.8507 (mt) cc_final: 0.7963 (mt) REVERT: K 255 THR cc_start: 0.6485 (OUTLIER) cc_final: 0.6211 (p) REVERT: K 269 LEU cc_start: 0.8561 (mt) cc_final: 0.8240 (mt) REVERT: K 287 THR cc_start: 0.8333 (t) cc_final: 0.7993 (m) REVERT: K 324 HIS cc_start: 0.7725 (m-70) cc_final: 0.7078 (m-70) REVERT: K 330 LEU cc_start: 0.7005 (pt) cc_final: 0.6419 (pt) REVERT: K 351 ILE cc_start: 0.8522 (mm) cc_final: 0.7711 (mm) REVERT: K 356 THR cc_start: 0.8995 (m) cc_final: 0.8699 (m) REVERT: K 365 GLU cc_start: 0.6488 (mt-10) cc_final: 0.6012 (mt-10) REVERT: K 376 THR cc_start: 0.8237 (p) cc_final: 0.7954 (p) REVERT: L 132 VAL cc_start: 0.6721 (p) cc_final: 0.6459 (p) REVERT: L 161 LEU cc_start: 0.9127 (mt) cc_final: 0.8863 (mm) REVERT: L 202 THR cc_start: 0.7891 (m) cc_final: 0.7158 (p) REVERT: L 260 GLU cc_start: 0.5090 (tt0) cc_final: 0.4596 (tt0) REVERT: L 268 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7355 (pp) REVERT: L 292 ILE cc_start: 0.6422 (tt) cc_final: 0.6191 (tt) REVERT: L 297 ILE cc_start: 0.6505 (tt) cc_final: 0.6080 (tt) REVERT: L 318 ILE cc_start: 0.8065 (mt) cc_final: 0.7474 (tt) REVERT: L 320 ILE cc_start: 0.8108 (mt) cc_final: 0.7851 (mt) REVERT: L 336 PHE cc_start: 0.6837 (m-80) cc_final: 0.6217 (m-80) REVERT: L 364 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6716 (mtt-85) REVERT: M 149 GLN cc_start: 0.8379 (mp10) cc_final: 0.7837 (mp10) REVERT: M 188 LYS cc_start: 0.5654 (mmtp) cc_final: 0.4881 (pttm) REVERT: M 199 THR cc_start: 0.8414 (p) cc_final: 0.7991 (t) REVERT: M 203 PHE cc_start: 0.7633 (t80) cc_final: 0.7021 (t80) REVERT: M 218 GLU cc_start: 0.4206 (OUTLIER) cc_final: 0.3953 (tm-30) REVERT: M 246 ILE cc_start: 0.5909 (tt) cc_final: 0.5179 (tt) REVERT: M 269 LEU cc_start: 0.7967 (mt) cc_final: 0.7751 (mt) REVERT: M 343 THR cc_start: 0.8801 (p) cc_final: 0.8441 (p) REVERT: M 354 ILE cc_start: 0.8506 (mt) cc_final: 0.8232 (tp) REVERT: M 363 ILE cc_start: 0.8518 (mt) cc_final: 0.8318 (mm) REVERT: J 158 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6772 (mt-10) REVERT: J 159 LEU cc_start: 0.7846 (tp) cc_final: 0.7290 (tp) REVERT: J 180 LEU cc_start: 0.7731 (mt) cc_final: 0.7273 (mt) REVERT: J 231 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8075 (mtmp) REVERT: J 272 LEU cc_start: 0.5191 (OUTLIER) cc_final: 0.4407 (tp) REVERT: J 321 PHE cc_start: 0.6739 (m-80) cc_final: 0.6164 (m-80) REVERT: J 324 HIS cc_start: 0.7007 (m170) cc_final: 0.6795 (m-70) REVERT: J 325 THR cc_start: 0.8140 (m) cc_final: 0.7304 (t) REVERT: J 327 LYS cc_start: 0.7672 (tttt) cc_final: 0.7232 (tptt) REVERT: J 339 LEU cc_start: 0.8699 (mt) cc_final: 0.8113 (mt) REVERT: J 364 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6714 (ptp-110) REVERT: J 374 ASP cc_start: 0.8188 (m-30) cc_final: 0.7366 (m-30) outliers start: 49 outliers final: 10 residues processed: 852 average time/residue: 0.1367 time to fit residues: 156.2380 Evaluate side-chains 649 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 630 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 198 GLN H 252 ASN ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 324 HIS ** I 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN K 149 GLN K 262 GLN L 213 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 262 GLN J 198 GLN J 262 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.135890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.108995 restraints weight = 31765.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.112752 restraints weight = 23296.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.115794 restraints weight = 17997.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.118267 restraints weight = 14371.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.120267 restraints weight = 11765.381| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.5255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12881 Z= 0.247 Angle : 0.977 15.335 17407 Z= 0.526 Chirality : 0.052 0.272 2000 Planarity : 0.008 0.073 2243 Dihedral : 9.460 135.914 1757 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.35 % Favored : 92.83 % Rotamer: Outliers : 0.75 % Allowed : 4.78 % Favored : 94.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 1.11 % Twisted General : 0.40 % 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: -1.45 (0.20), residues: 1590 helix: -0.10 (0.17), residues: 800 sheet: -1.16 (0.38), residues: 145 loop : -1.97 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG J 278 TYR 0.024 0.003 TYR M 215 PHE 0.040 0.003 PHE H 167 HIS 0.010 0.002 HIS J 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.25 (12881) covalent geometry : angle 0.97734 / 0.53 (17407) hydrogen bonds : bond 0.06337 / 3.99 ( 507) hydrogen bonds : angle 5.91043 / 4.17 ( 1518) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 756 time to evaluate : 0.437 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: 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: 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: 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: H 128 TYR cc_start: 0.8695 (t80) cc_final: 0.8381 (m-80) REVERT: H 130 PHE cc_start: 0.9391 (m-80) cc_final: 0.8997 (m-80) REVERT: H 141 GLU cc_start: 0.8619 (pm20) cc_final: 0.8268 (pm20) REVERT: H 154 ARG cc_start: 0.9172 (mtp85) cc_final: 0.8952 (mmm-85) REVERT: H 186 THR cc_start: 0.9520 (p) cc_final: 0.9263 (p) REVERT: H 198 GLN cc_start: 0.8910 (mm110) cc_final: 0.8685 (mm110) REVERT: H 227 PHE cc_start: 0.9437 (m-80) cc_final: 0.8889 (m-80) REVERT: H 231 LYS cc_start: 0.9737 (mtmm) cc_final: 0.9499 (mtmm) REVERT: H 241 ASP cc_start: 0.8786 (p0) cc_final: 0.7847 (p0) REVERT: H 269 LEU cc_start: 0.9135 (mt) cc_final: 0.8882 (mt) REVERT: H 315 GLU cc_start: 0.9492 (mp0) cc_final: 0.9208 (mp0) REVERT: H 321 PHE cc_start: 0.9411 (m-80) cc_final: 0.8904 (m-80) REVERT: H 324 HIS cc_start: 0.8762 (m90) cc_final: 0.7817 (m90) REVERT: H 338 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8972 (mp0) REVERT: H 356 THR cc_start: 0.9517 (p) cc_final: 0.9187 (p) REVERT: H 361 PHE cc_start: 0.9120 (t80) cc_final: 0.8781 (t80) REVERT: H 367 ARG cc_start: 0.7183 (mtm110) cc_final: 0.6331 (ttp-110) REVERT: H 372 MET cc_start: 0.8324 (mmm) cc_final: 0.7912 (mmm) REVERT: I 130 PHE cc_start: 0.8688 (m-80) cc_final: 0.8153 (m-80) REVERT: I 152 GLU cc_start: 0.9483 (mt-10) cc_final: 0.9139 (mt-10) REVERT: I 186 THR cc_start: 0.9223 (p) cc_final: 0.8907 (p) REVERT: I 207 VAL cc_start: 0.8396 (t) cc_final: 0.8171 (t) REVERT: I 227 PHE cc_start: 0.8841 (t80) cc_final: 0.8455 (t80) REVERT: I 231 LYS cc_start: 0.9484 (mttm) cc_final: 0.9201 (mmmt) REVERT: I 258 ASP cc_start: 0.7901 (m-30) cc_final: 0.7321 (t0) REVERT: I 289 ARG cc_start: 0.6557 (mtt180) cc_final: 0.6252 (ttm110) REVERT: I 307 ILE cc_start: 0.9391 (tp) cc_final: 0.9171 (tt) REVERT: I 309 VAL cc_start: 0.9629 (t) cc_final: 0.9286 (p) REVERT: I 311 LEU cc_start: 0.8651 (mm) cc_final: 0.8309 (mt) REVERT: I 318 ILE cc_start: 0.9095 (mt) cc_final: 0.8699 (mt) REVERT: I 319 GLN cc_start: 0.9566 (mm110) cc_final: 0.9295 (mm-40) REVERT: I 321 PHE cc_start: 0.8142 (m-10) cc_final: 0.7711 (m-10) REVERT: I 322 LYS cc_start: 0.9551 (mmtm) cc_final: 0.9210 (mmtm) REVERT: I 326 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7534 (mtm110) REVERT: I 327 LYS cc_start: 0.9293 (mmpt) cc_final: 0.8896 (mmpt) REVERT: I 333 ASP cc_start: 0.8655 (t0) cc_final: 0.8453 (t70) REVERT: I 351 ILE cc_start: 0.9328 (mt) cc_final: 0.9089 (mt) REVERT: I 357 GLU cc_start: 0.8670 (tp30) cc_final: 0.8161 (tp30) REVERT: I 372 MET cc_start: 0.9226 (mmm) cc_final: 0.8226 (mmm) REVERT: K 131 GLU cc_start: 0.8015 (tm-30) cc_final: 0.7732 (tm-30) REVERT: K 149 GLN cc_start: 0.9733 (mp-120) cc_final: 0.9373 (mp10) REVERT: K 151 GLU cc_start: 0.9463 (mt-10) cc_final: 0.8886 (mm-30) REVERT: K 154 ARG cc_start: 0.8391 (ttt-90) cc_final: 0.7270 (tmm160) REVERT: K 179 LEU cc_start: 0.9304 (tp) cc_final: 0.8847 (tp) REVERT: K 189 THR cc_start: 0.8559 (m) cc_final: 0.8273 (p) REVERT: K 190 LEU cc_start: 0.9180 (mt) cc_final: 0.8962 (mt) REVERT: K 193 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8562 (mtmm) REVERT: K 206 VAL cc_start: 0.9512 (p) cc_final: 0.9307 (p) REVERT: K 243 LEU cc_start: 0.9336 (mt) cc_final: 0.9020 (mt) REVERT: K 259 ARG cc_start: 0.8237 (mmm160) cc_final: 0.7771 (mmm160) REVERT: K 287 THR cc_start: 0.8586 (t) cc_final: 0.8112 (m) REVERT: K 303 PHE cc_start: 0.9489 (m-80) cc_final: 0.9240 (m-80) REVERT: K 311 LEU cc_start: 0.9072 (mt) cc_final: 0.8660 (tt) REVERT: K 318 ILE cc_start: 0.8754 (mt) cc_final: 0.8166 (mt) REVERT: K 319 GLN cc_start: 0.9531 (mt0) cc_final: 0.9162 (mt0) REVERT: K 320 ILE cc_start: 0.9545 (mt) cc_final: 0.9324 (mt) REVERT: K 321 PHE cc_start: 0.8670 (m-80) cc_final: 0.8014 (m-80) REVERT: K 322 LYS cc_start: 0.9304 (mtmt) cc_final: 0.8836 (tptm) REVERT: K 351 ILE cc_start: 0.9358 (mm) cc_final: 0.9026 (mm) REVERT: K 372 MET cc_start: 0.5843 (mmm) cc_final: 0.5002 (mmm) REVERT: K 375 PHE cc_start: 0.9072 (m-80) cc_final: 0.8781 (m-10) REVERT: L 132 VAL cc_start: 0.8323 (p) cc_final: 0.6864 (p) REVERT: L 143 ILE cc_start: 0.9004 (tt) cc_final: 0.8728 (tt) REVERT: L 193 LYS cc_start: 0.9150 (tptt) cc_final: 0.8872 (tptt) REVERT: L 224 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.7455 (mtm-85) REVERT: L 225 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8432 (mt-10) REVERT: L 228 GLN cc_start: 0.9117 (tp40) cc_final: 0.8788 (tp40) REVERT: L 231 LYS cc_start: 0.9252 (mmmt) cc_final: 0.9036 (mmtt) REVERT: L 232 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8691 (mm-30) REVERT: L 258 ASP cc_start: 0.8066 (p0) cc_final: 0.7816 (p0) REVERT: L 263 ARG cc_start: 0.9427 (ttm110) cc_final: 0.9205 (mtt180) REVERT: L 265 MET cc_start: 0.9066 (tmm) cc_final: 0.8815 (tmm) REVERT: L 273 ASP cc_start: 0.9009 (t70) cc_final: 0.8632 (t70) REVERT: L 284 ILE cc_start: 0.9125 (mm) cc_final: 0.8646 (mm) REVERT: L 317 ARG cc_start: 0.8894 (mmt-90) cc_final: 0.8679 (mpt90) REVERT: L 320 ILE cc_start: 0.9313 (mt) cc_final: 0.9056 (mm) REVERT: L 337 LYS cc_start: 0.9492 (mmtm) cc_final: 0.9243 (mmtm) REVERT: L 338 GLU cc_start: 0.9289 (pt0) cc_final: 0.8862 (pm20) REVERT: L 356 THR cc_start: 0.8872 (p) cc_final: 0.8209 (p) REVERT: L 360 MET cc_start: 0.8968 (ttt) cc_final: 0.8734 (ttt) REVERT: L 364 ARG cc_start: 0.9145 (mtt90) cc_final: 0.8814 (mtm-85) REVERT: L 372 MET cc_start: 0.5274 (mmm) cc_final: 0.4968 (mmm) REVERT: M 151 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8641 (pt0) REVERT: M 152 GLU cc_start: 0.9466 (mp0) cc_final: 0.9221 (mp0) REVERT: M 155 GLU cc_start: 0.9555 (mp0) cc_final: 0.9282 (mp0) REVERT: M 202 THR cc_start: 0.8615 (p) cc_final: 0.8158 (p) REVERT: M 228 GLN cc_start: 0.9410 (tp40) cc_final: 0.8817 (tp40) REVERT: M 264 THR cc_start: 0.9184 (m) cc_final: 0.8901 (m) REVERT: M 294 ASP cc_start: 0.8928 (p0) cc_final: 0.8667 (p0) REVERT: M 306 ILE cc_start: 0.9519 (pt) cc_final: 0.9288 (pt) REVERT: M 310 PRO cc_start: 0.8938 (Cg_endo) cc_final: 0.8587 (Cg_exo) REVERT: M 321 PHE cc_start: 0.8476 (m-10) cc_final: 0.8049 (m-80) REVERT: M 357 GLU cc_start: 0.8743 (tm-30) cc_final: 0.7297 (tp30) REVERT: M 361 PHE cc_start: 0.8553 (m-80) cc_final: 0.8067 (m-10) REVERT: M 367 ARG cc_start: 0.7021 (ptt90) cc_final: 0.5742 (ptt-90) REVERT: M 374 ASP cc_start: 0.8550 (m-30) cc_final: 0.7304 (m-30) REVERT: M 376 THR cc_start: 0.9673 (p) cc_final: 0.9348 (p) REVERT: J 149 GLN cc_start: 0.9505 (mp10) cc_final: 0.8989 (mp10) REVERT: J 159 LEU cc_start: 0.9216 (tp) cc_final: 0.8975 (tp) REVERT: J 190 LEU cc_start: 0.9225 (tp) cc_final: 0.8993 (tp) REVERT: J 214 LYS cc_start: 0.8863 (ptmm) cc_final: 0.8635 (ptmm) REVERT: J 216 ILE cc_start: 0.7464 (mp) cc_final: 0.6495 (mp) REVERT: J 228 GLN cc_start: 0.9259 (mt0) cc_final: 0.8906 (mm-40) REVERT: J 262 GLN cc_start: 0.8754 (tt0) cc_final: 0.8291 (tt0) REVERT: J 308 GLU cc_start: 0.8378 (pp20) cc_final: 0.8163 (pp20) REVERT: J 319 GLN cc_start: 0.9394 (mm110) cc_final: 0.9025 (mt0) REVERT: J 326 ARG cc_start: 0.8524 (ppt170) cc_final: 0.8071 (ppt170) REVERT: J 327 LYS cc_start: 0.9324 (tttt) cc_final: 0.8943 (tptt) REVERT: J 350 ASP cc_start: 0.9635 (m-30) cc_final: 0.9419 (m-30) REVERT: J 366 GLU cc_start: 0.8961 (tp30) cc_final: 0.8065 (tp30) REVERT: J 375 PHE cc_start: 0.9470 (m-10) cc_final: 0.9192 (m-80) outliers start: 10 outliers final: 2 residues processed: 760 average time/residue: 0.1355 time to fit residues: 137.7133 Evaluate side-chains 616 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 614 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 150 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 130 optimal weight: 0.0470 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 134 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 146 optimal weight: 0.9980 chunk 148 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 252 ASN ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN I 228 GLN M 197 ASN M 262 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.137845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.110220 restraints weight = 32729.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.113776 restraints weight = 24226.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116823 restraints weight = 18958.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.119245 restraints weight = 15243.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.121254 restraints weight = 12565.684| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.6442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12881 Z= 0.208 Angle : 0.885 16.566 17407 Z= 0.474 Chirality : 0.051 0.293 2000 Planarity : 0.007 0.114 2243 Dihedral : 8.797 138.242 1757 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.16 % Favored : 92.96 % Rotamer: Outliers : 0.37 % Allowed : 4.11 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.27 % 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: -1.20 (0.21), residues: 1590 helix: -0.00 (0.18), residues: 799 sheet: -1.04 (0.40), residues: 151 loop : -1.67 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 317 TYR 0.017 0.002 TYR K 140 PHE 0.034 0.003 PHE L 375 HIS 0.028 0.006 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (12881) covalent geometry : angle 0.88454 / 0.47 (17407) hydrogen bonds : bond 0.05231 / 3.31 ( 507) hydrogen bonds : angle 5.59175 / 3.92 ( 1518) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 722 time to evaluate : 0.418 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 130 PHE cc_start: 0.9293 (m-80) cc_final: 0.8949 (m-80) REVERT: H 141 GLU cc_start: 0.8684 (pm20) cc_final: 0.8339 (pm20) REVERT: H 143 ILE cc_start: 0.7336 (mt) cc_final: 0.7124 (mt) REVERT: H 227 PHE cc_start: 0.9451 (m-80) cc_final: 0.8873 (m-80) REVERT: H 237 ILE cc_start: 0.6911 (OUTLIER) cc_final: 0.6612 (mp) REVERT: H 241 ASP cc_start: 0.8621 (p0) cc_final: 0.7894 (p0) REVERT: H 267 GLN cc_start: 0.9349 (mt0) cc_final: 0.9041 (mt0) REVERT: H 321 PHE cc_start: 0.9554 (m-80) cc_final: 0.9298 (m-80) REVERT: H 324 HIS cc_start: 0.8506 (m90) cc_final: 0.7977 (m90) REVERT: H 328 MET cc_start: 0.7992 (ptp) cc_final: 0.7747 (ptp) REVERT: H 352 LYS cc_start: 0.9531 (mmmt) cc_final: 0.9223 (mmmt) REVERT: H 356 THR cc_start: 0.9528 (p) cc_final: 0.9223 (p) REVERT: H 364 ARG cc_start: 0.8889 (mtm180) cc_final: 0.8399 (mtm-85) REVERT: H 372 MET cc_start: 0.8307 (mmm) cc_final: 0.7682 (mmm) REVERT: H 383 LEU cc_start: 0.8922 (tp) cc_final: 0.8659 (tp) REVERT: I 127 VAL cc_start: 0.8726 (m) cc_final: 0.8399 (m) REVERT: I 130 PHE cc_start: 0.8933 (m-10) cc_final: 0.8445 (m-80) REVERT: I 186 THR cc_start: 0.9301 (p) cc_final: 0.9089 (p) REVERT: I 205 ARG cc_start: 0.8075 (pmt170) cc_final: 0.7822 (ptt-90) REVERT: I 227 PHE cc_start: 0.8789 (t80) cc_final: 0.8559 (t80) REVERT: I 231 LYS cc_start: 0.9645 (mttm) cc_final: 0.9366 (mmmt) REVERT: I 266 MET cc_start: 0.8499 (mtp) cc_final: 0.8298 (mtp) REVERT: I 294 ASP cc_start: 0.8720 (t0) cc_final: 0.8231 (t0) REVERT: I 303 PHE cc_start: 0.8956 (m-80) cc_final: 0.8679 (m-80) REVERT: I 308 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8697 (tm-30) REVERT: I 311 LEU cc_start: 0.8763 (mm) cc_final: 0.8314 (mt) REVERT: I 318 ILE cc_start: 0.9066 (mt) cc_final: 0.8564 (mt) REVERT: I 321 PHE cc_start: 0.8296 (m-10) cc_final: 0.7593 (m-10) REVERT: I 326 ARG cc_start: 0.7858 (mtm110) cc_final: 0.7492 (mtm110) REVERT: I 327 LYS cc_start: 0.9098 (mmpt) cc_final: 0.8749 (mmpt) REVERT: I 341 ARG cc_start: 0.9116 (ttp80) cc_final: 0.8794 (ttp80) REVERT: I 342 ILE cc_start: 0.9163 (mt) cc_final: 0.8677 (mt) REVERT: I 351 ILE cc_start: 0.9336 (mt) cc_final: 0.9101 (mt) REVERT: I 357 GLU cc_start: 0.8713 (tp30) cc_final: 0.8219 (tp30) REVERT: I 372 MET cc_start: 0.9276 (mmm) cc_final: 0.8399 (mmm) REVERT: K 149 GLN cc_start: 0.9690 (mp-120) cc_final: 0.9302 (mp10) REVERT: K 151 GLU cc_start: 0.9525 (mt-10) cc_final: 0.9234 (mt-10) REVERT: K 152 GLU cc_start: 0.9405 (mp0) cc_final: 0.9136 (mp0) REVERT: K 189 THR cc_start: 0.8618 (m) cc_final: 0.8244 (p) REVERT: K 190 LEU cc_start: 0.9168 (mt) cc_final: 0.8914 (mt) REVERT: K 193 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8647 (mtmm) REVERT: K 267 GLN cc_start: 0.8525 (tp40) cc_final: 0.7887 (tp40) REVERT: K 287 THR cc_start: 0.8983 (t) cc_final: 0.8555 (m) REVERT: K 288 ASN cc_start: 0.8757 (p0) cc_final: 0.8451 (t0) REVERT: K 290 ILE cc_start: 0.9112 (pt) cc_final: 0.8885 (tp) REVERT: K 311 LEU cc_start: 0.9152 (mt) cc_final: 0.8782 (tt) REVERT: K 315 GLU cc_start: 0.8826 (pm20) cc_final: 0.8531 (mp0) REVERT: K 319 GLN cc_start: 0.9524 (mt0) cc_final: 0.9117 (mt0) REVERT: K 321 PHE cc_start: 0.8723 (m-80) cc_final: 0.7980 (m-80) REVERT: K 338 GLU cc_start: 0.9110 (tp30) cc_final: 0.8523 (tp30) REVERT: K 372 MET cc_start: 0.6149 (mmm) cc_final: 0.5149 (mmm) REVERT: K 375 PHE cc_start: 0.8974 (m-80) cc_final: 0.8706 (m-80) REVERT: L 137 GLU cc_start: 0.9139 (pm20) cc_final: 0.8694 (pm20) REVERT: L 143 ILE cc_start: 0.9013 (tt) cc_final: 0.8779 (tt) REVERT: L 149 GLN cc_start: 0.9264 (mp10) cc_final: 0.8882 (mp10) REVERT: L 204 ILE cc_start: 0.9356 (mm) cc_final: 0.8861 (tp) REVERT: L 206 VAL cc_start: 0.8944 (m) cc_final: 0.8706 (m) REVERT: L 222 LEU cc_start: 0.9470 (mt) cc_final: 0.9208 (mt) REVERT: L 225 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8157 (mt-10) REVERT: L 228 GLN cc_start: 0.9180 (tp40) cc_final: 0.8772 (tp40) REVERT: L 231 LYS cc_start: 0.9392 (mmmt) cc_final: 0.9162 (mmtp) REVERT: L 232 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8698 (mm-30) REVERT: L 273 ASP cc_start: 0.9118 (t70) cc_final: 0.8668 (t70) REVERT: L 281 VAL cc_start: 0.9350 (m) cc_final: 0.9144 (m) REVERT: L 284 ILE cc_start: 0.9100 (mm) cc_final: 0.8557 (mm) REVERT: L 328 MET cc_start: 0.8581 (ppp) cc_final: 0.7792 (ppp) REVERT: L 337 LYS cc_start: 0.9536 (mmtm) cc_final: 0.9230 (mmtm) REVERT: L 364 ARG cc_start: 0.9064 (mtt90) cc_final: 0.8479 (mpp80) REVERT: L 365 GLU cc_start: 0.8440 (pt0) cc_final: 0.7152 (mt-10) REVERT: M 126 MET cc_start: 0.4124 (tmm) cc_final: 0.3918 (ppp) REVERT: M 132 VAL cc_start: 0.9409 (t) cc_final: 0.9195 (t) REVERT: M 140 TYR cc_start: 0.9274 (p90) cc_final: 0.8918 (p90) REVERT: M 227 PHE cc_start: 0.8249 (t80) cc_final: 0.7847 (t80) REVERT: M 271 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8395 (pp20) REVERT: M 310 PRO cc_start: 0.9088 (Cg_endo) cc_final: 0.8696 (Cg_exo) REVERT: M 321 PHE cc_start: 0.8805 (m-10) cc_final: 0.8406 (m-80) REVERT: M 333 ASP cc_start: 0.9287 (p0) cc_final: 0.8838 (p0) REVERT: M 361 PHE cc_start: 0.8621 (m-80) cc_final: 0.7763 (m-10) REVERT: M 367 ARG cc_start: 0.5919 (ptt90) cc_final: 0.5644 (ptt-90) REVERT: M 372 MET cc_start: 0.8977 (tpt) cc_final: 0.7704 (mmm) REVERT: M 375 PHE cc_start: 0.9144 (m-10) cc_final: 0.8807 (m-10) REVERT: J 149 GLN cc_start: 0.9612 (mp10) cc_final: 0.9210 (mp10) REVERT: J 154 ARG cc_start: 0.8400 (mtp-110) cc_final: 0.8042 (mtp180) REVERT: J 159 LEU cc_start: 0.9119 (tp) cc_final: 0.8704 (tp) REVERT: J 172 ILE cc_start: 0.9080 (tp) cc_final: 0.8753 (tp) REVERT: J 214 LYS cc_start: 0.9107 (ptmm) cc_final: 0.8589 (ptmm) REVERT: J 215 TYR cc_start: 0.8199 (m-80) cc_final: 0.7980 (m-80) REVERT: J 228 GLN cc_start: 0.9265 (mt0) cc_final: 0.8917 (mm-40) REVERT: J 307 ILE cc_start: 0.9473 (mp) cc_final: 0.9246 (mp) REVERT: J 314 PHE cc_start: 0.8114 (t80) cc_final: 0.7881 (t80) REVERT: J 319 GLN cc_start: 0.9470 (mm110) cc_final: 0.9050 (mt0) REVERT: J 324 HIS cc_start: 0.8596 (m-70) cc_final: 0.8298 (m-70) REVERT: J 326 ARG cc_start: 0.8349 (ppt170) cc_final: 0.7829 (ppt170) REVERT: J 328 MET cc_start: 0.7040 (ppp) cc_final: 0.6756 (ppp) REVERT: J 335 ASP cc_start: 0.9223 (t70) cc_final: 0.8634 (t0) REVERT: J 338 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8729 (mm-30) REVERT: J 372 MET cc_start: 0.9006 (mmp) cc_final: 0.8575 (mmm) outliers start: 5 outliers final: 1 residues processed: 723 average time/residue: 0.1343 time to fit residues: 129.8156 Evaluate side-chains 586 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 584 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 68 optimal weight: 0.3980 chunk 13 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 130 optimal weight: 0.0670 chunk 53 optimal weight: 0.0010 chunk 139 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 150 optimal weight: 0.5980 chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 1.9990 overall best weight: 0.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** M 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.133923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105569 restraints weight = 32757.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.109193 restraints weight = 24663.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.112083 restraints weight = 19427.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114486 restraints weight = 15827.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.116250 restraints weight = 13204.119| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12881 Z= 0.182 Angle : 0.851 16.438 17407 Z= 0.453 Chirality : 0.050 0.301 2000 Planarity : 0.006 0.059 2243 Dihedral : 8.397 134.361 1757 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.67 % Favored : 92.52 % Rotamer: Outliers : 0.45 % Allowed : 4.04 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.05 (0.21), residues: 1590 helix: 0.01 (0.18), residues: 787 sheet: -0.96 (0.41), residues: 153 loop : -1.42 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 326 TYR 0.038 0.002 TYR H 140 PHE 0.030 0.003 PHE M 203 HIS 0.018 0.006 HIS L 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (12881) covalent geometry : angle 0.85121 / 0.45 (17407) hydrogen bonds : bond 0.04703 / 2.95 ( 507) hydrogen bonds : angle 5.44370 / 3.83 ( 1518) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 681 time to evaluate : 0.368 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 130 PHE cc_start: 0.9310 (m-10) cc_final: 0.8995 (m-80) REVERT: H 227 PHE cc_start: 0.9551 (m-80) cc_final: 0.8978 (m-80) REVERT: H 231 LYS cc_start: 0.9681 (mtmm) cc_final: 0.9385 (ptpt) REVERT: H 239 PHE cc_start: 0.8062 (t80) cc_final: 0.7662 (t80) REVERT: H 263 ARG cc_start: 0.9381 (mtp180) cc_final: 0.9171 (mtm-85) REVERT: H 290 ILE cc_start: 0.9349 (tp) cc_final: 0.9131 (tp) REVERT: H 320 ILE cc_start: 0.9607 (mt) cc_final: 0.9383 (tt) REVERT: H 321 PHE cc_start: 0.9609 (m-80) cc_final: 0.9381 (m-80) REVERT: H 324 HIS cc_start: 0.8501 (m170) cc_final: 0.7880 (m90) REVERT: H 328 MET cc_start: 0.8032 (ptp) cc_final: 0.7783 (ptp) REVERT: H 352 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9348 (mmmt) REVERT: H 366 GLU cc_start: 0.8880 (mp0) cc_final: 0.8563 (mp0) REVERT: H 372 MET cc_start: 0.8301 (mmm) cc_final: 0.7792 (mmm) REVERT: H 383 LEU cc_start: 0.8773 (tp) cc_final: 0.8525 (tp) REVERT: I 127 VAL cc_start: 0.8760 (m) cc_final: 0.8474 (m) REVERT: I 130 PHE cc_start: 0.9197 (m-10) cc_final: 0.8728 (m-80) REVERT: I 163 LYS cc_start: 0.9518 (ttmt) cc_final: 0.9028 (ttmm) REVERT: I 190 LEU cc_start: 0.8771 (tp) cc_final: 0.8562 (tp) REVERT: I 221 ARG cc_start: 0.9318 (ttp80) cc_final: 0.9094 (ttp80) REVERT: I 227 PHE cc_start: 0.9000 (t80) cc_final: 0.8679 (t80) REVERT: I 231 LYS cc_start: 0.9647 (mttm) cc_final: 0.9443 (mmmt) REVERT: I 242 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8569 (mm-30) REVERT: I 265 MET cc_start: 0.9324 (tpp) cc_final: 0.9098 (tpp) REVERT: I 266 MET cc_start: 0.8387 (mtp) cc_final: 0.8171 (mtp) REVERT: I 282 LYS cc_start: 0.8452 (mmtp) cc_final: 0.7911 (mmmt) REVERT: I 294 ASP cc_start: 0.9023 (t0) cc_final: 0.8518 (t0) REVERT: I 303 PHE cc_start: 0.9092 (m-80) cc_final: 0.8725 (m-80) REVERT: I 308 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8740 (tm-30) REVERT: I 310 PRO cc_start: 0.9414 (Cg_endo) cc_final: 0.8867 (Cg_exo) REVERT: I 311 LEU cc_start: 0.8839 (mm) cc_final: 0.8415 (mt) REVERT: I 318 ILE cc_start: 0.9105 (mt) cc_final: 0.8600 (mt) REVERT: I 321 PHE cc_start: 0.8435 (m-10) cc_final: 0.7782 (m-10) REVERT: I 323 ILE cc_start: 0.9515 (mm) cc_final: 0.8520 (tp) REVERT: I 326 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7514 (mtm110) REVERT: I 327 LYS cc_start: 0.9058 (mmpt) cc_final: 0.8580 (mmpt) REVERT: I 341 ARG cc_start: 0.9061 (ttp80) cc_final: 0.8635 (ttp80) REVERT: I 342 ILE cc_start: 0.9132 (mt) cc_final: 0.8609 (mt) REVERT: I 351 ILE cc_start: 0.9333 (mt) cc_final: 0.8835 (mt) REVERT: I 357 GLU cc_start: 0.8730 (tp30) cc_final: 0.8374 (tp30) REVERT: I 372 MET cc_start: 0.9359 (mmm) cc_final: 0.8613 (mmm) REVERT: K 149 GLN cc_start: 0.9699 (mp-120) cc_final: 0.9320 (mp10) REVERT: K 162 LEU cc_start: 0.9077 (mt) cc_final: 0.8486 (mt) REVERT: K 189 THR cc_start: 0.9082 (m) cc_final: 0.8412 (m) REVERT: K 190 LEU cc_start: 0.9280 (mt) cc_final: 0.8963 (mt) REVERT: K 193 LYS cc_start: 0.9091 (mtmm) cc_final: 0.8642 (mtmm) REVERT: K 260 GLU cc_start: 0.9180 (tp30) cc_final: 0.7849 (tp30) REVERT: K 267 GLN cc_start: 0.8692 (tp40) cc_final: 0.7578 (tp40) REVERT: K 287 THR cc_start: 0.9144 (t) cc_final: 0.8600 (m) REVERT: K 288 ASN cc_start: 0.8975 (p0) cc_final: 0.8139 (t0) REVERT: K 311 LEU cc_start: 0.9172 (mt) cc_final: 0.8804 (tt) REVERT: K 315 GLU cc_start: 0.8920 (pm20) cc_final: 0.8527 (mp0) REVERT: K 318 ILE cc_start: 0.8942 (mt) cc_final: 0.8317 (mt) REVERT: K 319 GLN cc_start: 0.9576 (mt0) cc_final: 0.9247 (mm110) REVERT: K 321 PHE cc_start: 0.8901 (m-80) cc_final: 0.8076 (m-80) REVERT: K 322 LYS cc_start: 0.9308 (mtmm) cc_final: 0.8948 (tptm) REVERT: K 337 LYS cc_start: 0.9621 (pptt) cc_final: 0.9347 (pptt) REVERT: K 338 GLU cc_start: 0.9168 (tp30) cc_final: 0.8654 (tp30) REVERT: K 351 ILE cc_start: 0.9264 (mm) cc_final: 0.8936 (mm) REVERT: K 357 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7901 (tm-30) REVERT: K 372 MET cc_start: 0.6877 (mmm) cc_final: 0.5653 (mmm) REVERT: K 375 PHE cc_start: 0.9147 (m-80) cc_final: 0.8803 (m-80) REVERT: L 137 GLU cc_start: 0.9193 (pm20) cc_final: 0.8563 (pm20) REVERT: L 193 LYS cc_start: 0.9037 (tptt) cc_final: 0.8789 (tptt) REVERT: L 202 THR cc_start: 0.8255 (m) cc_final: 0.8041 (m) REVERT: L 206 VAL cc_start: 0.8963 (m) cc_final: 0.8633 (t) REVERT: L 211 PHE cc_start: 0.8814 (m-80) cc_final: 0.8419 (m-80) REVERT: L 222 LEU cc_start: 0.9482 (mt) cc_final: 0.9268 (mt) REVERT: L 224 ARG cc_start: 0.8330 (mtm-85) cc_final: 0.8050 (mtm-85) REVERT: L 225 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8464 (mt-10) REVERT: L 232 GLU cc_start: 0.8979 (mm-30) cc_final: 0.8631 (mm-30) REVERT: L 263 ARG cc_start: 0.9027 (ptp90) cc_final: 0.8533 (mtt180) REVERT: L 273 ASP cc_start: 0.9155 (t70) cc_final: 0.8655 (t70) REVERT: L 281 VAL cc_start: 0.9485 (m) cc_final: 0.9276 (m) REVERT: L 284 ILE cc_start: 0.9020 (mm) cc_final: 0.8555 (mm) REVERT: L 328 MET cc_start: 0.8726 (ppp) cc_final: 0.7954 (ppp) REVERT: L 356 THR cc_start: 0.9093 (p) cc_final: 0.8857 (p) REVERT: L 364 ARG cc_start: 0.9172 (mtt90) cc_final: 0.8505 (mtt-85) REVERT: L 365 GLU cc_start: 0.8467 (pt0) cc_final: 0.7298 (mt-10) REVERT: M 140 TYR cc_start: 0.9300 (p90) cc_final: 0.8816 (p90) REVERT: M 179 LEU cc_start: 0.9480 (tp) cc_final: 0.9236 (tp) REVERT: M 210 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8616 (mt-10) REVERT: M 227 PHE cc_start: 0.8357 (t80) cc_final: 0.8095 (t80) REVERT: M 264 THR cc_start: 0.9106 (m) cc_final: 0.8865 (p) REVERT: M 271 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8433 (pp20) REVERT: M 294 ASP cc_start: 0.8795 (p0) cc_final: 0.8550 (p0) REVERT: M 305 ARG cc_start: 0.7726 (ptm160) cc_final: 0.7509 (ptm160) REVERT: M 306 ILE cc_start: 0.9556 (pt) cc_final: 0.9336 (pt) REVERT: M 307 ILE cc_start: 0.9337 (mp) cc_final: 0.8447 (mt) REVERT: M 310 PRO cc_start: 0.8976 (Cg_endo) cc_final: 0.8540 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9148 (mm) cc_final: 0.8691 (mm) REVERT: M 333 ASP cc_start: 0.9415 (p0) cc_final: 0.9084 (p0) REVERT: M 357 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8059 (tp30) REVERT: M 361 PHE cc_start: 0.8675 (m-80) cc_final: 0.8063 (m-10) REVERT: M 372 MET cc_start: 0.8904 (tpt) cc_final: 0.7930 (tpt) REVERT: M 375 PHE cc_start: 0.9224 (m-10) cc_final: 0.8941 (m-10) REVERT: J 149 GLN cc_start: 0.9596 (mp10) cc_final: 0.9245 (mp10) REVERT: J 154 ARG cc_start: 0.8710 (mtp-110) cc_final: 0.8451 (mmt180) REVERT: J 158 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7247 (mt-10) REVERT: J 215 TYR cc_start: 0.8301 (m-80) cc_final: 0.8087 (m-80) REVERT: J 228 GLN cc_start: 0.9281 (mt0) cc_final: 0.8926 (mm-40) REVERT: J 319 GLN cc_start: 0.9539 (mm110) cc_final: 0.8969 (mt0) REVERT: J 327 LYS cc_start: 0.9336 (tmtt) cc_final: 0.8941 (tptt) REVERT: J 328 MET cc_start: 0.7021 (ppp) cc_final: 0.6686 (ppp) REVERT: J 360 MET cc_start: 0.9428 (tmm) cc_final: 0.9036 (tmm) REVERT: J 366 GLU cc_start: 0.8991 (mp0) cc_final: 0.8576 (mp0) REVERT: J 372 MET cc_start: 0.9185 (mmp) cc_final: 0.8742 (mmm) REVERT: J 375 PHE cc_start: 0.9222 (m-80) cc_final: 0.8978 (m-80) outliers start: 6 outliers final: 3 residues processed: 684 average time/residue: 0.1287 time to fit residues: 119.2583 Evaluate side-chains 579 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 576 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 2 optimal weight: 0.4980 chunk 129 optimal weight: 0.6980 chunk 117 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 114 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** L 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.107664 restraints weight = 33715.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111323 restraints weight = 24731.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.114159 restraints weight = 19085.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.116484 restraints weight = 15313.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118429 restraints weight = 12618.812| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12881 Z= 0.196 Angle : 0.854 16.010 17407 Z= 0.454 Chirality : 0.050 0.290 2000 Planarity : 0.006 0.078 2243 Dihedral : 8.171 132.952 1757 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.73 % Favored : 92.52 % Rotamer: Outliers : 0.22 % Allowed : 3.14 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -1.10 (0.21), residues: 1590 helix: -0.09 (0.18), residues: 794 sheet: -0.80 (0.43), residues: 147 loop : -1.41 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG M 263 TYR 0.013 0.002 TYR M 140 PHE 0.052 0.003 PHE L 321 HIS 0.011 0.003 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.20 (12881) covalent geometry : angle 0.85352 / 0.45 (17407) hydrogen bonds : bond 0.04384 / 2.75 ( 507) hydrogen bonds : angle 5.51143 / 3.85 ( 1518) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 658 time to evaluate : 0.474 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: 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: 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: 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: H 128 TYR cc_start: 0.8220 (m-80) cc_final: 0.7745 (m-80) REVERT: H 181 TYR cc_start: 0.8749 (t80) cc_final: 0.8291 (t80) REVERT: H 221 ARG cc_start: 0.7777 (ppt170) cc_final: 0.7567 (ppt170) REVERT: H 227 PHE cc_start: 0.9315 (m-80) cc_final: 0.8826 (m-80) REVERT: H 233 LYS cc_start: 0.9337 (tptp) cc_final: 0.9050 (tmtt) REVERT: H 239 PHE cc_start: 0.8160 (t80) cc_final: 0.7635 (t80) REVERT: H 249 ARG cc_start: 0.7832 (ttm170) cc_final: 0.7555 (ttm170) REVERT: H 262 GLN cc_start: 0.8762 (pm20) cc_final: 0.8545 (pm20) REVERT: H 290 ILE cc_start: 0.9361 (tp) cc_final: 0.9059 (tp) REVERT: H 328 MET cc_start: 0.8350 (ptp) cc_final: 0.8109 (ptp) REVERT: H 352 LYS cc_start: 0.9711 (mmmt) cc_final: 0.9447 (mmmt) REVERT: H 372 MET cc_start: 0.8557 (mmm) cc_final: 0.7902 (mmm) REVERT: H 383 LEU cc_start: 0.8696 (tp) cc_final: 0.8430 (tp) REVERT: I 127 VAL cc_start: 0.8743 (m) cc_final: 0.8399 (m) REVERT: I 130 PHE cc_start: 0.9299 (m-10) cc_final: 0.8719 (m-80) REVERT: I 163 LYS cc_start: 0.9504 (ttmt) cc_final: 0.9075 (ttmm) REVERT: I 221 ARG cc_start: 0.9336 (ttp80) cc_final: 0.8849 (ttp80) REVERT: I 227 PHE cc_start: 0.8992 (t80) cc_final: 0.8581 (t80) REVERT: I 294 ASP cc_start: 0.8991 (t0) cc_final: 0.8421 (t0) REVERT: I 303 PHE cc_start: 0.9202 (m-80) cc_final: 0.8913 (m-80) REVERT: I 311 LEU cc_start: 0.8809 (mm) cc_final: 0.8351 (mt) REVERT: I 318 ILE cc_start: 0.9053 (mt) cc_final: 0.8592 (mt) REVERT: I 321 PHE cc_start: 0.8342 (m-10) cc_final: 0.7824 (m-10) REVERT: I 323 ILE cc_start: 0.9513 (mm) cc_final: 0.9065 (tp) REVERT: I 326 ARG cc_start: 0.8088 (mtm110) cc_final: 0.7608 (mtm110) REVERT: I 327 LYS cc_start: 0.9100 (mmpt) cc_final: 0.8759 (mmpt) REVERT: I 341 ARG cc_start: 0.9078 (ttp80) cc_final: 0.8723 (ttp80) REVERT: I 342 ILE cc_start: 0.9155 (mt) cc_final: 0.8635 (mt) REVERT: I 351 ILE cc_start: 0.9291 (mt) cc_final: 0.8860 (mt) REVERT: I 360 MET cc_start: 0.9282 (mtm) cc_final: 0.9080 (mtm) REVERT: I 370 VAL cc_start: 0.7480 (t) cc_final: 0.7131 (t) REVERT: I 372 MET cc_start: 0.9505 (mmm) cc_final: 0.8865 (mmm) REVERT: I 375 PHE cc_start: 0.9080 (m-80) cc_final: 0.8456 (m-80) REVERT: K 149 GLN cc_start: 0.9704 (mp-120) cc_final: 0.9405 (mp10) REVERT: K 151 GLU cc_start: 0.9520 (mt-10) cc_final: 0.9174 (tp30) REVERT: K 159 LEU cc_start: 0.9454 (mm) cc_final: 0.9180 (mm) REVERT: K 188 LYS cc_start: 0.9688 (mtmm) cc_final: 0.9383 (pttt) REVERT: K 189 THR cc_start: 0.9094 (m) cc_final: 0.8590 (m) REVERT: K 190 LEU cc_start: 0.9448 (mt) cc_final: 0.9059 (mt) REVERT: K 193 LYS cc_start: 0.9217 (mtmm) cc_final: 0.8723 (mtmm) REVERT: K 200 ARG cc_start: 0.9054 (pmt-80) cc_final: 0.8851 (pmt-80) REVERT: K 211 PHE cc_start: 0.9172 (m-80) cc_final: 0.8614 (m-80) REVERT: K 218 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8928 (mp0) REVERT: K 222 LEU cc_start: 0.9436 (tp) cc_final: 0.9193 (tp) REVERT: K 240 ILE cc_start: 0.8970 (tp) cc_final: 0.8705 (tp) REVERT: K 243 LEU cc_start: 0.9297 (mt) cc_final: 0.9076 (mt) REVERT: K 260 GLU cc_start: 0.8765 (tp30) cc_final: 0.8285 (tp30) REVERT: K 267 GLN cc_start: 0.8670 (tp40) cc_final: 0.7821 (tp40) REVERT: K 276 ASP cc_start: 0.8353 (m-30) cc_final: 0.7945 (m-30) REVERT: K 287 THR cc_start: 0.8947 (t) cc_final: 0.8550 (m) REVERT: K 311 LEU cc_start: 0.9259 (mt) cc_final: 0.8846 (tt) REVERT: K 315 GLU cc_start: 0.9022 (pm20) cc_final: 0.8561 (mp0) REVERT: K 318 ILE cc_start: 0.9014 (mt) cc_final: 0.8790 (mm) REVERT: K 319 GLN cc_start: 0.9593 (mt0) cc_final: 0.8975 (mm110) REVERT: K 321 PHE cc_start: 0.8971 (m-80) cc_final: 0.8249 (m-80) REVERT: K 322 LYS cc_start: 0.9254 (mtmm) cc_final: 0.8894 (mtmm) REVERT: K 337 LYS cc_start: 0.9633 (pptt) cc_final: 0.9387 (pptt) REVERT: K 338 GLU cc_start: 0.9378 (tp30) cc_final: 0.8845 (tp30) REVERT: K 351 ILE cc_start: 0.9314 (mm) cc_final: 0.9047 (mm) REVERT: K 357 GLU cc_start: 0.8794 (tm-30) cc_final: 0.7954 (tm-30) REVERT: K 361 PHE cc_start: 0.8526 (m-80) cc_final: 0.8142 (m-80) REVERT: K 372 MET cc_start: 0.7044 (mmm) cc_final: 0.5773 (mmm) REVERT: K 375 PHE cc_start: 0.9234 (m-80) cc_final: 0.8920 (m-80) REVERT: L 137 GLU cc_start: 0.9235 (pm20) cc_final: 0.8677 (pm20) REVERT: L 172 ILE cc_start: 0.8392 (tp) cc_final: 0.7705 (tp) REVERT: L 179 LEU cc_start: 0.9542 (tp) cc_final: 0.9323 (tp) REVERT: L 204 ILE cc_start: 0.9278 (mm) cc_final: 0.8984 (mm) REVERT: L 206 VAL cc_start: 0.9175 (m) cc_final: 0.8931 (t) REVERT: L 211 PHE cc_start: 0.8916 (m-80) cc_final: 0.8571 (m-80) REVERT: L 221 ARG cc_start: 0.8972 (tpp-160) cc_final: 0.8738 (tpp-160) REVERT: L 222 LEU cc_start: 0.9537 (mt) cc_final: 0.9264 (mt) REVERT: L 225 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8466 (mt-10) REVERT: L 232 GLU cc_start: 0.9078 (mm-30) cc_final: 0.8702 (mm-30) REVERT: L 240 ILE cc_start: 0.9319 (tp) cc_final: 0.9011 (tp) REVERT: L 273 ASP cc_start: 0.9144 (t70) cc_final: 0.8723 (t70) REVERT: L 284 ILE cc_start: 0.9073 (mm) cc_final: 0.8560 (mm) REVERT: L 308 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8678 (tm-30) REVERT: L 365 GLU cc_start: 0.8478 (pt0) cc_final: 0.7332 (mt-10) REVERT: M 140 TYR cc_start: 0.9239 (p90) cc_final: 0.8767 (p90) REVERT: M 210 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8622 (mt-10) REVERT: M 227 PHE cc_start: 0.8429 (t80) cc_final: 0.8184 (t80) REVERT: M 263 ARG cc_start: 0.9249 (tpp80) cc_final: 0.8991 (mmm160) REVERT: M 264 THR cc_start: 0.9083 (m) cc_final: 0.8818 (p) REVERT: M 271 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8457 (pp20) REVERT: M 294 ASP cc_start: 0.8835 (p0) cc_final: 0.8589 (p0) REVERT: M 310 PRO cc_start: 0.9045 (Cg_endo) cc_final: 0.8638 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9167 (mm) cc_final: 0.8936 (mm) REVERT: M 333 ASP cc_start: 0.9365 (p0) cc_final: 0.9023 (p0) REVERT: M 357 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8117 (tp30) REVERT: M 361 PHE cc_start: 0.8733 (m-80) cc_final: 0.8124 (m-10) REVERT: M 372 MET cc_start: 0.8919 (tpt) cc_final: 0.7968 (tpt) REVERT: M 375 PHE cc_start: 0.9277 (m-10) cc_final: 0.8966 (m-10) REVERT: J 149 GLN cc_start: 0.9616 (mp10) cc_final: 0.9234 (mp10) REVERT: J 153 ILE cc_start: 0.9299 (mt) cc_final: 0.9079 (mt) REVERT: J 154 ARG cc_start: 0.8848 (mtp-110) cc_final: 0.8515 (mmt180) REVERT: J 158 GLU cc_start: 0.8016 (mt-10) cc_final: 0.7551 (mt-10) REVERT: J 215 TYR cc_start: 0.8493 (m-80) cc_final: 0.8036 (m-80) REVERT: J 228 GLN cc_start: 0.9275 (mt0) cc_final: 0.8912 (mm-40) REVERT: J 319 GLN cc_start: 0.9532 (mm110) cc_final: 0.8899 (mt0) REVERT: J 326 ARG cc_start: 0.8224 (ppt170) cc_final: 0.7986 (ppt170) REVERT: J 327 LYS cc_start: 0.9346 (tmtt) cc_final: 0.9117 (tptp) REVERT: J 328 MET cc_start: 0.7216 (ppp) cc_final: 0.6988 (ppp) REVERT: J 347 SER cc_start: 0.9555 (m) cc_final: 0.9216 (p) REVERT: J 352 LYS cc_start: 0.9295 (mmtm) cc_final: 0.8710 (mmtt) REVERT: J 360 MET cc_start: 0.9243 (tmm) cc_final: 0.9038 (tmm) REVERT: J 372 MET cc_start: 0.8986 (mmp) cc_final: 0.8702 (mmm) REVERT: J 375 PHE cc_start: 0.9142 (m-80) cc_final: 0.8917 (m-80) outliers start: 3 outliers final: 1 residues processed: 659 average time/residue: 0.1357 time to fit residues: 121.0667 Evaluate side-chains 578 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 577 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 14 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 101 optimal weight: 0.7980 chunk 69 optimal weight: 0.4980 chunk 45 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN L 262 GLN J 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.134630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107502 restraints weight = 34087.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.111038 restraints weight = 25289.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.113869 restraints weight = 19692.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116131 restraints weight = 15939.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117978 restraints weight = 13241.530| |-----------------------------------------------------------------------------| r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.7961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12881 Z= 0.189 Angle : 0.839 15.415 17407 Z= 0.445 Chirality : 0.050 0.244 2000 Planarity : 0.006 0.056 2243 Dihedral : 8.028 133.374 1757 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 23.50 Ramachandran Plot: Outliers : 0.75 % Allowed : 7.11 % Favored : 92.14 % Rotamer: Outliers : 0.22 % Allowed : 1.94 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.13 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.01 (0.21), residues: 1590 helix: -0.13 (0.18), residues: 803 sheet: -0.72 (0.42), residues: 147 loop : -1.22 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG K 305 TYR 0.012 0.001 TYR H 215 PHE 0.035 0.002 PHE M 321 HIS 0.007 0.002 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (12881) covalent geometry : angle 0.83900 / 0.44 (17407) hydrogen bonds : bond 0.04078 / 2.57 ( 507) hydrogen bonds : angle 5.39957 / 3.79 ( 1518) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 671 time to evaluate : 0.477 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: 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: 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: 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: H 128 TYR cc_start: 0.8198 (m-80) cc_final: 0.7681 (m-80) REVERT: H 227 PHE cc_start: 0.9294 (m-80) cc_final: 0.8838 (m-80) REVERT: H 239 PHE cc_start: 0.8112 (t80) cc_final: 0.7884 (t80) REVERT: H 249 ARG cc_start: 0.7809 (ttm170) cc_final: 0.7476 (ttm170) REVERT: H 269 LEU cc_start: 0.9057 (mt) cc_final: 0.8853 (mt) REVERT: H 276 ASP cc_start: 0.8588 (m-30) cc_final: 0.8119 (m-30) REVERT: H 290 ILE cc_start: 0.9372 (tp) cc_final: 0.9127 (tp) REVERT: H 306 ILE cc_start: 0.9359 (tp) cc_final: 0.9126 (tp) REVERT: H 324 HIS cc_start: 0.9168 (m90) cc_final: 0.8536 (m-70) REVERT: H 352 LYS cc_start: 0.9719 (mmmt) cc_final: 0.9379 (mmmt) REVERT: H 372 MET cc_start: 0.8686 (mmm) cc_final: 0.8089 (mmm) REVERT: H 374 ASP cc_start: 0.9612 (m-30) cc_final: 0.9219 (m-30) REVERT: H 383 LEU cc_start: 0.8621 (tp) cc_final: 0.8349 (tp) REVERT: I 127 VAL cc_start: 0.8788 (m) cc_final: 0.8477 (m) REVERT: I 130 PHE cc_start: 0.9271 (m-10) cc_final: 0.8652 (m-80) REVERT: I 163 LYS cc_start: 0.9531 (ttmt) cc_final: 0.9236 (ttmm) REVERT: I 167 PHE cc_start: 0.8791 (m-10) cc_final: 0.8498 (m-80) REVERT: I 221 ARG cc_start: 0.9390 (ttp80) cc_final: 0.8986 (ttp80) REVERT: I 227 PHE cc_start: 0.8937 (t80) cc_final: 0.8612 (t80) REVERT: I 229 LEU cc_start: 0.9518 (tp) cc_final: 0.9254 (tp) REVERT: I 237 ILE cc_start: 0.9777 (mm) cc_final: 0.9556 (mm) REVERT: I 265 MET cc_start: 0.9393 (tpp) cc_final: 0.9190 (tpp) REVERT: I 294 ASP cc_start: 0.9082 (t0) cc_final: 0.8425 (t0) REVERT: I 302 ARG cc_start: 0.8729 (mmt90) cc_final: 0.8442 (mmt180) REVERT: I 303 PHE cc_start: 0.9244 (m-80) cc_final: 0.8979 (m-80) REVERT: I 318 ILE cc_start: 0.9055 (mt) cc_final: 0.8579 (mt) REVERT: I 321 PHE cc_start: 0.8442 (m-10) cc_final: 0.7857 (m-10) REVERT: I 323 ILE cc_start: 0.9504 (mm) cc_final: 0.9178 (mm) REVERT: I 326 ARG cc_start: 0.8131 (mtm110) cc_final: 0.7809 (ptp90) REVERT: I 341 ARG cc_start: 0.9181 (ttp80) cc_final: 0.8747 (ttp80) REVERT: I 342 ILE cc_start: 0.9158 (mt) cc_final: 0.8647 (mt) REVERT: I 351 ILE cc_start: 0.9306 (mt) cc_final: 0.8824 (mt) REVERT: I 356 THR cc_start: 0.9836 (m) cc_final: 0.9634 (p) REVERT: I 361 PHE cc_start: 0.8783 (m-80) cc_final: 0.8012 (m-10) REVERT: I 370 VAL cc_start: 0.7449 (t) cc_final: 0.6878 (t) REVERT: I 372 MET cc_start: 0.9486 (mmm) cc_final: 0.8819 (mmm) REVERT: I 375 PHE cc_start: 0.9046 (m-80) cc_final: 0.8451 (m-80) REVERT: K 149 GLN cc_start: 0.9763 (mp-120) cc_final: 0.9442 (mp10) REVERT: K 159 LEU cc_start: 0.9394 (mm) cc_final: 0.9106 (mm) REVERT: K 167 PHE cc_start: 0.7677 (m-80) cc_final: 0.7400 (m-80) REVERT: K 172 ILE cc_start: 0.7433 (mp) cc_final: 0.6476 (mp) REVERT: K 189 THR cc_start: 0.9121 (m) cc_final: 0.8581 (m) REVERT: K 190 LEU cc_start: 0.9466 (mt) cc_final: 0.9100 (mt) REVERT: K 193 LYS cc_start: 0.9210 (mtmm) cc_final: 0.8684 (mtmm) REVERT: K 200 ARG cc_start: 0.8851 (pmt-80) cc_final: 0.8627 (pmt-80) REVERT: K 211 PHE cc_start: 0.9127 (m-80) cc_final: 0.8458 (m-80) REVERT: K 222 LEU cc_start: 0.9427 (tp) cc_final: 0.9176 (tp) REVERT: K 243 LEU cc_start: 0.9305 (mt) cc_final: 0.9094 (mt) REVERT: K 260 GLU cc_start: 0.8753 (tp30) cc_final: 0.8144 (tp30) REVERT: K 267 GLN cc_start: 0.8795 (tp40) cc_final: 0.7967 (tp40) REVERT: K 276 ASP cc_start: 0.8353 (m-30) cc_final: 0.7898 (m-30) REVERT: K 287 THR cc_start: 0.8986 (t) cc_final: 0.8593 (m) REVERT: K 310 PRO cc_start: 0.8520 (Cg_endo) cc_final: 0.8296 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9245 (mt) cc_final: 0.8894 (tt) REVERT: K 315 GLU cc_start: 0.9053 (pm20) cc_final: 0.8846 (pm20) REVERT: K 319 GLN cc_start: 0.9620 (mt0) cc_final: 0.9185 (mt0) REVERT: K 337 LYS cc_start: 0.9655 (pptt) cc_final: 0.9422 (pptt) REVERT: K 338 GLU cc_start: 0.9327 (tp30) cc_final: 0.8819 (tp30) REVERT: K 341 ARG cc_start: 0.9218 (ttp80) cc_final: 0.8792 (ttp80) REVERT: K 351 ILE cc_start: 0.9365 (mm) cc_final: 0.9164 (mm) REVERT: K 357 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8071 (tm-30) REVERT: K 361 PHE cc_start: 0.8973 (m-80) cc_final: 0.8201 (m-10) REVERT: K 372 MET cc_start: 0.7169 (mmm) cc_final: 0.5880 (mmm) REVERT: K 375 PHE cc_start: 0.9290 (m-80) cc_final: 0.8945 (m-80) REVERT: L 165 GLU cc_start: 0.9306 (tp30) cc_final: 0.8954 (tp30) REVERT: L 206 VAL cc_start: 0.9210 (m) cc_final: 0.8909 (t) REVERT: L 211 PHE cc_start: 0.9081 (m-80) cc_final: 0.8501 (m-80) REVERT: L 221 ARG cc_start: 0.8983 (tpp-160) cc_final: 0.8685 (tpp-160) REVERT: L 222 LEU cc_start: 0.9558 (mt) cc_final: 0.9244 (mt) REVERT: L 225 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8465 (mt-10) REVERT: L 231 LYS cc_start: 0.9493 (mmmt) cc_final: 0.9232 (mmtt) REVERT: L 232 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8785 (mm-30) REVERT: L 233 LYS cc_start: 0.9196 (tptt) cc_final: 0.8978 (tppt) REVERT: L 240 ILE cc_start: 0.9336 (tp) cc_final: 0.8914 (tp) REVERT: L 263 ARG cc_start: 0.9111 (ptp90) cc_final: 0.8735 (mtt180) REVERT: L 265 MET cc_start: 0.9250 (tmm) cc_final: 0.9048 (tmm) REVERT: L 273 ASP cc_start: 0.9215 (t70) cc_final: 0.8880 (t70) REVERT: L 284 ILE cc_start: 0.9002 (mm) cc_final: 0.8575 (mm) REVERT: L 305 ARG cc_start: 0.9006 (ttm170) cc_final: 0.8617 (ttm170) REVERT: L 308 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8678 (tm-30) REVERT: L 328 MET cc_start: 0.8567 (ppp) cc_final: 0.8359 (ppp) REVERT: L 365 GLU cc_start: 0.8439 (pt0) cc_final: 0.7223 (mt-10) REVERT: M 140 TYR cc_start: 0.9317 (p90) cc_final: 0.8806 (p90) REVERT: M 210 GLU cc_start: 0.9190 (mt-10) cc_final: 0.8725 (mt-10) REVERT: M 221 ARG cc_start: 0.8458 (ttp-110) cc_final: 0.7680 (ptm-80) REVERT: M 227 PHE cc_start: 0.8384 (t80) cc_final: 0.8167 (t80) REVERT: M 264 THR cc_start: 0.9236 (m) cc_final: 0.8943 (p) REVERT: M 265 MET cc_start: 0.8349 (mtt) cc_final: 0.7982 (mtp) REVERT: M 271 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8433 (pp20) REVERT: M 310 PRO cc_start: 0.9035 (Cg_endo) cc_final: 0.8618 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9170 (mm) cc_final: 0.8924 (mm) REVERT: M 321 PHE cc_start: 0.9128 (m-80) cc_final: 0.8828 (m-80) REVERT: M 333 ASP cc_start: 0.9354 (p0) cc_final: 0.8982 (p0) REVERT: M 357 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8894 (tm-30) REVERT: M 371 THR cc_start: 0.7680 (p) cc_final: 0.6985 (p) REVERT: M 372 MET cc_start: 0.8969 (tpt) cc_final: 0.7925 (tpt) REVERT: M 375 PHE cc_start: 0.9242 (m-10) cc_final: 0.8953 (m-10) REVERT: J 149 GLN cc_start: 0.9549 (mp10) cc_final: 0.9158 (mp10) REVERT: J 215 TYR cc_start: 0.8543 (m-80) cc_final: 0.8096 (m-80) REVERT: J 228 GLN cc_start: 0.9282 (mt0) cc_final: 0.8930 (mm-40) REVERT: J 275 PHE cc_start: 0.8088 (t80) cc_final: 0.7864 (t80) REVERT: J 307 ILE cc_start: 0.9546 (mp) cc_final: 0.8991 (mp) REVERT: J 315 GLU cc_start: 0.9143 (mp0) cc_final: 0.8771 (mp0) REVERT: J 319 GLN cc_start: 0.9533 (mm110) cc_final: 0.8890 (mt0) REVERT: J 326 ARG cc_start: 0.8105 (ppt170) cc_final: 0.7806 (ppt170) REVERT: J 327 LYS cc_start: 0.9329 (tmtt) cc_final: 0.9095 (tptp) REVERT: J 328 MET cc_start: 0.7260 (ppp) cc_final: 0.6947 (ppp) REVERT: J 335 ASP cc_start: 0.9105 (t70) cc_final: 0.7858 (t0) REVERT: J 338 GLU cc_start: 0.8781 (mm-30) cc_final: 0.8554 (mm-30) REVERT: J 347 SER cc_start: 0.9440 (m) cc_final: 0.9018 (p) REVERT: J 352 LYS cc_start: 0.9324 (mmtm) cc_final: 0.8771 (mmtm) REVERT: J 357 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8663 (mm-30) REVERT: J 360 MET cc_start: 0.9168 (tmm) cc_final: 0.8332 (tmm) REVERT: J 372 MET cc_start: 0.9055 (mmm) cc_final: 0.8821 (mmm) REVERT: J 375 PHE cc_start: 0.9172 (m-80) cc_final: 0.8867 (m-80) outliers start: 3 outliers final: 0 residues processed: 672 average time/residue: 0.1356 time to fit residues: 124.0917 Evaluate side-chains 568 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 120 optimal weight: 7.9990 chunk 95 optimal weight: 0.4980 chunk 145 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 146 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 98 optimal weight: 0.0070 chunk 43 optimal weight: 0.2980 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 262 GLN L 288 ASN ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.135192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.108103 restraints weight = 33750.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.111670 restraints weight = 25346.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.114554 restraints weight = 19815.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116886 restraints weight = 16069.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.118728 restraints weight = 13371.338| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.8242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12881 Z= 0.176 Angle : 0.843 15.563 17407 Z= 0.449 Chirality : 0.049 0.278 2000 Planarity : 0.007 0.091 2243 Dihedral : 7.916 132.669 1757 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.69 % Allowed : 6.73 % Favored : 92.58 % Rotamer: Outliers : 0.15 % Allowed : 2.39 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.01 (0.21), residues: 1590 helix: -0.15 (0.18), residues: 811 sheet: -0.62 (0.41), residues: 155 loop : -1.23 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 305 TYR 0.011 0.001 TYR H 215 PHE 0.033 0.002 PHE L 375 HIS 0.005 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (12881) covalent geometry : angle 0.84261 / 0.45 (17407) hydrogen bonds : bond 0.04287 / 2.77 ( 507) hydrogen bonds : angle 5.46353 / 3.83 ( 1518) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 659 time to evaluate : 0.549 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: 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: 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: 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: H 128 TYR cc_start: 0.8140 (m-80) cc_final: 0.7583 (m-80) REVERT: H 172 ILE cc_start: 0.8483 (pt) cc_final: 0.8017 (pt) REVERT: H 181 TYR cc_start: 0.8826 (t80) cc_final: 0.8465 (t80) REVERT: H 204 ILE cc_start: 0.8863 (mt) cc_final: 0.8658 (mt) REVERT: H 227 PHE cc_start: 0.9278 (m-80) cc_final: 0.8847 (m-80) REVERT: H 233 LYS cc_start: 0.9186 (tptt) cc_final: 0.8979 (tmtt) REVERT: H 249 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7566 (ttm170) REVERT: H 250 ARG cc_start: 0.8385 (ptt-90) cc_final: 0.7906 (ptt-90) REVERT: H 262 GLN cc_start: 0.8798 (pm20) cc_final: 0.8545 (pm20) REVERT: H 269 LEU cc_start: 0.9003 (mt) cc_final: 0.8789 (mt) REVERT: H 276 ASP cc_start: 0.8483 (m-30) cc_final: 0.8051 (m-30) REVERT: H 290 ILE cc_start: 0.9349 (tp) cc_final: 0.9100 (tp) REVERT: H 352 LYS cc_start: 0.9743 (mmmt) cc_final: 0.9424 (mmmt) REVERT: H 372 MET cc_start: 0.8715 (mmm) cc_final: 0.8216 (mmm) REVERT: H 383 LEU cc_start: 0.8717 (tp) cc_final: 0.8430 (tp) REVERT: I 127 VAL cc_start: 0.8756 (m) cc_final: 0.8436 (m) REVERT: I 130 PHE cc_start: 0.9233 (m-10) cc_final: 0.8635 (m-80) REVERT: I 163 LYS cc_start: 0.9472 (ttmt) cc_final: 0.9154 (ttmm) REVERT: I 167 PHE cc_start: 0.8741 (m-10) cc_final: 0.8476 (m-80) REVERT: I 221 ARG cc_start: 0.9358 (ttp80) cc_final: 0.8913 (ttp80) REVERT: I 222 LEU cc_start: 0.9651 (mt) cc_final: 0.9446 (mt) REVERT: I 229 LEU cc_start: 0.9504 (tp) cc_final: 0.9245 (tp) REVERT: I 260 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8797 (mt-10) REVERT: I 265 MET cc_start: 0.9360 (tpp) cc_final: 0.9155 (tpp) REVERT: I 294 ASP cc_start: 0.9122 (t0) cc_final: 0.8555 (t0) REVERT: I 303 PHE cc_start: 0.9189 (m-80) cc_final: 0.8973 (m-80) REVERT: I 318 ILE cc_start: 0.9166 (mt) cc_final: 0.8814 (mt) REVERT: I 319 GLN cc_start: 0.9642 (mm110) cc_final: 0.9439 (mm-40) REVERT: I 321 PHE cc_start: 0.8433 (m-10) cc_final: 0.7830 (m-10) REVERT: I 322 LYS cc_start: 0.9657 (mmtm) cc_final: 0.9187 (mmmm) REVERT: I 323 ILE cc_start: 0.9533 (mm) cc_final: 0.8976 (tp) REVERT: I 326 ARG cc_start: 0.8181 (mtm110) cc_final: 0.7689 (mtm110) REVERT: I 327 LYS cc_start: 0.9071 (mmpt) cc_final: 0.8681 (mmpt) REVERT: I 341 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8757 (ttp80) REVERT: I 342 ILE cc_start: 0.9135 (mt) cc_final: 0.8606 (mt) REVERT: I 351 ILE cc_start: 0.9275 (mt) cc_final: 0.8816 (mt) REVERT: I 356 THR cc_start: 0.9840 (m) cc_final: 0.9588 (p) REVERT: I 360 MET cc_start: 0.9413 (mtm) cc_final: 0.9070 (mtm) REVERT: I 361 PHE cc_start: 0.8806 (m-80) cc_final: 0.8008 (m-10) REVERT: I 372 MET cc_start: 0.9499 (mmm) cc_final: 0.8846 (mmm) REVERT: I 373 LEU cc_start: 0.9737 (tt) cc_final: 0.9003 (tt) REVERT: I 374 ASP cc_start: 0.9157 (m-30) cc_final: 0.8891 (m-30) REVERT: K 134 GLU cc_start: 0.8808 (tm-30) cc_final: 0.8472 (tm-30) REVERT: K 149 GLN cc_start: 0.9669 (mp-120) cc_final: 0.9449 (mp10) REVERT: K 151 GLU cc_start: 0.9502 (mt-10) cc_final: 0.9202 (mt-10) REVERT: K 167 PHE cc_start: 0.7599 (m-80) cc_final: 0.7393 (m-80) REVERT: K 172 ILE cc_start: 0.7579 (mp) cc_final: 0.7303 (tt) REVERT: K 189 THR cc_start: 0.9229 (m) cc_final: 0.8661 (m) REVERT: K 190 LEU cc_start: 0.9425 (mt) cc_final: 0.9043 (mt) REVERT: K 193 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8695 (mtmm) REVERT: K 211 PHE cc_start: 0.9301 (m-80) cc_final: 0.8688 (m-80) REVERT: K 222 LEU cc_start: 0.9440 (tp) cc_final: 0.9197 (tp) REVERT: K 260 GLU cc_start: 0.8889 (tp30) cc_final: 0.8193 (tp30) REVERT: K 266 MET cc_start: 0.8565 (mtm) cc_final: 0.8345 (mtm) REVERT: K 267 GLN cc_start: 0.8794 (tp40) cc_final: 0.8089 (tp40) REVERT: K 276 ASP cc_start: 0.8380 (m-30) cc_final: 0.7956 (m-30) REVERT: K 287 THR cc_start: 0.8985 (t) cc_final: 0.8731 (m) REVERT: K 310 PRO cc_start: 0.8438 (Cg_endo) cc_final: 0.8170 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9277 (mt) cc_final: 0.8939 (tt) REVERT: K 319 GLN cc_start: 0.9627 (mt0) cc_final: 0.9350 (mt0) REVERT: K 337 LYS cc_start: 0.9673 (pptt) cc_final: 0.9353 (pptt) REVERT: K 351 ILE cc_start: 0.9350 (mm) cc_final: 0.9145 (mm) REVERT: K 357 GLU cc_start: 0.8939 (tm-30) cc_final: 0.8133 (tm-30) REVERT: K 361 PHE cc_start: 0.8526 (m-80) cc_final: 0.8162 (m-10) REVERT: K 372 MET cc_start: 0.7340 (mmm) cc_final: 0.6026 (mmm) REVERT: K 375 PHE cc_start: 0.9269 (m-80) cc_final: 0.8944 (m-80) REVERT: L 165 GLU cc_start: 0.9331 (tp30) cc_final: 0.8921 (tp30) REVERT: L 202 THR cc_start: 0.8910 (t) cc_final: 0.8504 (t) REVERT: L 206 VAL cc_start: 0.9256 (m) cc_final: 0.9012 (t) REVERT: L 211 PHE cc_start: 0.9011 (m-80) cc_final: 0.8469 (m-80) REVERT: L 221 ARG cc_start: 0.8982 (tpp-160) cc_final: 0.8629 (tpp-160) REVERT: L 222 LEU cc_start: 0.9568 (mt) cc_final: 0.9270 (mt) REVERT: L 225 GLU cc_start: 0.8990 (mt-10) cc_final: 0.8372 (mt-10) REVERT: L 232 GLU cc_start: 0.9176 (mm-30) cc_final: 0.8811 (mm-30) REVERT: L 233 LYS cc_start: 0.9335 (tptt) cc_final: 0.8976 (tppt) REVERT: L 240 ILE cc_start: 0.9261 (tp) cc_final: 0.8825 (tp) REVERT: L 263 ARG cc_start: 0.9123 (ptp90) cc_final: 0.8664 (mtt180) REVERT: L 265 MET cc_start: 0.9230 (tmm) cc_final: 0.9029 (tmm) REVERT: L 273 ASP cc_start: 0.9165 (t70) cc_final: 0.8862 (t70) REVERT: L 284 ILE cc_start: 0.9076 (mm) cc_final: 0.8542 (mm) REVERT: L 308 GLU cc_start: 0.8873 (tm-30) cc_final: 0.8627 (tm-30) REVERT: L 321 PHE cc_start: 0.9204 (m-80) cc_final: 0.8917 (m-80) REVERT: L 328 MET cc_start: 0.8658 (ppp) cc_final: 0.8301 (ppp) REVERT: L 365 GLU cc_start: 0.8325 (pt0) cc_final: 0.7031 (mt-10) REVERT: M 140 TYR cc_start: 0.9268 (p90) cc_final: 0.8740 (p90) REVERT: M 210 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8696 (mt-10) REVERT: M 221 ARG cc_start: 0.8340 (ttp-110) cc_final: 0.7874 (ptm-80) REVERT: M 224 ARG cc_start: 0.9348 (tmt-80) cc_final: 0.8911 (tmt-80) REVERT: M 229 LEU cc_start: 0.9381 (mt) cc_final: 0.9174 (mt) REVERT: M 240 ILE cc_start: 0.9423 (mp) cc_final: 0.9190 (mp) REVERT: M 246 ILE cc_start: 0.8826 (tt) cc_final: 0.8532 (tt) REVERT: M 264 THR cc_start: 0.9195 (m) cc_final: 0.8928 (p) REVERT: M 271 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8338 (pp20) REVERT: M 310 PRO cc_start: 0.9088 (Cg_endo) cc_final: 0.8694 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9119 (mm) cc_final: 0.8893 (mm) REVERT: M 333 ASP cc_start: 0.9300 (p0) cc_final: 0.8939 (p0) REVERT: M 372 MET cc_start: 0.8858 (tpt) cc_final: 0.7906 (tpt) REVERT: M 375 PHE cc_start: 0.9270 (m-10) cc_final: 0.8970 (m-10) REVERT: J 149 GLN cc_start: 0.9546 (mp10) cc_final: 0.9201 (mp10) REVERT: J 215 TYR cc_start: 0.8459 (m-80) cc_final: 0.7952 (m-80) REVERT: J 228 GLN cc_start: 0.9288 (mt0) cc_final: 0.8945 (mm-40) REVERT: J 315 GLU cc_start: 0.9103 (mp0) cc_final: 0.8709 (mp0) REVERT: J 319 GLN cc_start: 0.9529 (mm110) cc_final: 0.8872 (mt0) REVERT: J 321 PHE cc_start: 0.8767 (m-10) cc_final: 0.8413 (m-80) REVERT: J 326 ARG cc_start: 0.8213 (ppt170) cc_final: 0.7878 (ppt170) REVERT: J 327 LYS cc_start: 0.9304 (tmtt) cc_final: 0.9064 (tptp) REVERT: J 328 MET cc_start: 0.7288 (ppp) cc_final: 0.6848 (ppp) REVERT: J 347 SER cc_start: 0.9413 (m) cc_final: 0.8984 (p) REVERT: J 357 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8766 (mm-30) REVERT: J 360 MET cc_start: 0.9195 (tmm) cc_final: 0.8403 (tmm) REVERT: J 372 MET cc_start: 0.9241 (mmm) cc_final: 0.8799 (mmm) REVERT: J 375 PHE cc_start: 0.9169 (m-80) cc_final: 0.8832 (m-80) REVERT: J 383 LEU cc_start: 0.9266 (mm) cc_final: 0.9059 (mm) outliers start: 2 outliers final: 2 residues processed: 660 average time/residue: 0.1346 time to fit residues: 121.5732 Evaluate side-chains 567 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 565 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 48 optimal weight: 0.0980 chunk 149 optimal weight: 0.0770 chunk 137 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 chunk 90 optimal weight: 0.0770 chunk 18 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN L 213 GLN ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.136155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.109157 restraints weight = 33679.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.112675 restraints weight = 25154.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115497 restraints weight = 19716.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.117769 restraints weight = 16008.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.119663 restraints weight = 13330.269| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.8408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 12881 Z= 0.170 Angle : 0.858 15.207 17407 Z= 0.452 Chirality : 0.050 0.252 2000 Planarity : 0.007 0.085 2243 Dihedral : 7.793 131.118 1757 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.30 % Favored : 92.01 % Rotamer: Outliers : 0.07 % Allowed : 1.20 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.96 (0.22), residues: 1590 helix: -0.14 (0.18), residues: 821 sheet: -0.36 (0.43), residues: 152 loop : -1.27 (0.27), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG H 259 TYR 0.017 0.001 TYR K 140 PHE 0.080 0.002 PHE M 321 HIS 0.006 0.002 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.17 (12881) covalent geometry : angle 0.85785 / 0.45 (17407) hydrogen bonds : bond 0.04201 / 2.68 ( 507) hydrogen bonds : angle 5.32644 / 3.74 ( 1518) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 661 time to evaluate : 0.453 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 128 TYR cc_start: 0.8123 (m-80) cc_final: 0.7564 (m-80) REVERT: H 172 ILE cc_start: 0.8335 (pt) cc_final: 0.7868 (pt) REVERT: H 181 TYR cc_start: 0.8643 (t80) cc_final: 0.8342 (t80) REVERT: H 227 PHE cc_start: 0.9267 (m-80) cc_final: 0.8836 (m-80) REVERT: H 233 LYS cc_start: 0.9190 (tptt) cc_final: 0.8986 (tmtt) REVERT: H 249 ARG cc_start: 0.7761 (ttm170) cc_final: 0.7227 (ttm170) REVERT: H 250 ARG cc_start: 0.8469 (ptt-90) cc_final: 0.7870 (ptt-90) REVERT: H 259 ARG cc_start: 0.9336 (mpt90) cc_final: 0.9056 (mmt90) REVERT: H 263 ARG cc_start: 0.9463 (mtp180) cc_final: 0.9218 (ptp-110) REVERT: H 276 ASP cc_start: 0.8492 (m-30) cc_final: 0.7951 (m-30) REVERT: H 290 ILE cc_start: 0.9233 (tp) cc_final: 0.8959 (tp) REVERT: H 352 LYS cc_start: 0.9742 (mmmt) cc_final: 0.9433 (mmmt) REVERT: H 372 MET cc_start: 0.8704 (mmm) cc_final: 0.8241 (mmm) REVERT: H 383 LEU cc_start: 0.8733 (tp) cc_final: 0.8417 (tp) REVERT: I 127 VAL cc_start: 0.8802 (m) cc_final: 0.8483 (m) REVERT: I 130 PHE cc_start: 0.9160 (m-10) cc_final: 0.8557 (m-80) REVERT: I 163 LYS cc_start: 0.9457 (ttmt) cc_final: 0.9147 (ttmm) REVERT: I 167 PHE cc_start: 0.8706 (m-10) cc_final: 0.8476 (m-80) REVERT: I 221 ARG cc_start: 0.9386 (ttp80) cc_final: 0.8907 (ttp80) REVERT: I 222 LEU cc_start: 0.9646 (mt) cc_final: 0.9423 (mt) REVERT: I 229 LEU cc_start: 0.9515 (tp) cc_final: 0.9246 (tp) REVERT: I 265 MET cc_start: 0.9300 (tpp) cc_final: 0.9075 (tpp) REVERT: I 284 ILE cc_start: 0.9673 (mt) cc_final: 0.9467 (mt) REVERT: I 302 ARG cc_start: 0.8701 (mmt90) cc_final: 0.8499 (mmt180) REVERT: I 318 ILE cc_start: 0.9158 (mt) cc_final: 0.8762 (mt) REVERT: I 319 GLN cc_start: 0.9622 (mm110) cc_final: 0.9396 (mm-40) REVERT: I 321 PHE cc_start: 0.8401 (m-10) cc_final: 0.7813 (m-10) REVERT: I 322 LYS cc_start: 0.9650 (mmtm) cc_final: 0.9133 (mmmm) REVERT: I 323 ILE cc_start: 0.9486 (mm) cc_final: 0.8927 (tp) REVERT: I 326 ARG cc_start: 0.8161 (mtm110) cc_final: 0.7671 (mtm110) REVERT: I 327 LYS cc_start: 0.9071 (mmpt) cc_final: 0.8687 (mmpt) REVERT: I 341 ARG cc_start: 0.9168 (ttp80) cc_final: 0.8579 (ttp80) REVERT: I 342 ILE cc_start: 0.9150 (mt) cc_final: 0.8530 (mt) REVERT: I 351 ILE cc_start: 0.9244 (mt) cc_final: 0.8767 (mt) REVERT: I 356 THR cc_start: 0.9838 (m) cc_final: 0.9561 (p) REVERT: I 360 MET cc_start: 0.9341 (mtm) cc_final: 0.8885 (mtm) REVERT: I 361 PHE cc_start: 0.8635 (m-80) cc_final: 0.7911 (m-10) REVERT: I 372 MET cc_start: 0.9426 (mmm) cc_final: 0.8720 (mmm) REVERT: I 373 LEU cc_start: 0.9785 (tt) cc_final: 0.9485 (tt) REVERT: I 374 ASP cc_start: 0.9023 (m-30) cc_final: 0.8586 (m-30) REVERT: K 131 GLU cc_start: 0.8399 (pp20) cc_final: 0.8034 (tt0) REVERT: K 134 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8202 (tm-30) REVERT: K 148 VAL cc_start: 0.9572 (p) cc_final: 0.9303 (p) REVERT: K 151 GLU cc_start: 0.9538 (mt-10) cc_final: 0.8973 (mt-10) REVERT: K 152 GLU cc_start: 0.9500 (pm20) cc_final: 0.8865 (mp0) REVERT: K 167 PHE cc_start: 0.7571 (m-80) cc_final: 0.7309 (m-80) REVERT: K 172 ILE cc_start: 0.7451 (mp) cc_final: 0.6714 (mp) REVERT: K 189 THR cc_start: 0.9204 (m) cc_final: 0.8616 (m) REVERT: K 190 LEU cc_start: 0.9403 (mt) cc_final: 0.9007 (mt) REVERT: K 193 LYS cc_start: 0.9201 (mtmm) cc_final: 0.8720 (mtmm) REVERT: K 200 ARG cc_start: 0.8779 (pmt-80) cc_final: 0.8574 (pmt-80) REVERT: K 211 PHE cc_start: 0.9135 (m-80) cc_final: 0.8558 (m-80) REVERT: K 222 LEU cc_start: 0.9450 (tp) cc_final: 0.9230 (tp) REVERT: K 260 GLU cc_start: 0.8853 (tp30) cc_final: 0.8157 (tp30) REVERT: K 263 ARG cc_start: 0.8710 (mtm-85) cc_final: 0.7859 (mtm-85) REVERT: K 310 PRO cc_start: 0.8405 (Cg_endo) cc_final: 0.8085 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9239 (mt) cc_final: 0.8893 (tt) REVERT: K 315 GLU cc_start: 0.9049 (pm20) cc_final: 0.8376 (mp0) REVERT: K 319 GLN cc_start: 0.9609 (mt0) cc_final: 0.9348 (mt0) REVERT: K 337 LYS cc_start: 0.9677 (pptt) cc_final: 0.9329 (pptt) REVERT: K 351 ILE cc_start: 0.9322 (mm) cc_final: 0.9121 (mm) REVERT: K 357 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8198 (tm-30) REVERT: K 361 PHE cc_start: 0.8690 (m-80) cc_final: 0.8136 (m-10) REVERT: K 372 MET cc_start: 0.7264 (mmm) cc_final: 0.5934 (mmm) REVERT: K 375 PHE cc_start: 0.9245 (m-80) cc_final: 0.8958 (m-80) REVERT: L 131 GLU cc_start: 0.7568 (pp20) cc_final: 0.7365 (pp20) REVERT: L 165 GLU cc_start: 0.9285 (tp30) cc_final: 0.8891 (tp30) REVERT: L 172 ILE cc_start: 0.8657 (tp) cc_final: 0.8431 (tp) REVERT: L 202 THR cc_start: 0.8882 (t) cc_final: 0.8492 (t) REVERT: L 211 PHE cc_start: 0.9007 (m-80) cc_final: 0.8442 (m-80) REVERT: L 221 ARG cc_start: 0.9017 (tpp-160) cc_final: 0.8710 (tpp-160) REVERT: L 222 LEU cc_start: 0.9585 (mt) cc_final: 0.9283 (mt) REVERT: L 225 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8323 (mt-10) REVERT: L 232 GLU cc_start: 0.9202 (mm-30) cc_final: 0.8853 (mm-30) REVERT: L 233 LYS cc_start: 0.9360 (tptt) cc_final: 0.8991 (tppt) REVERT: L 240 ILE cc_start: 0.9262 (tp) cc_final: 0.8816 (tp) REVERT: L 265 MET cc_start: 0.9197 (tmm) cc_final: 0.8973 (tmm) REVERT: L 273 ASP cc_start: 0.9072 (t70) cc_final: 0.8840 (t70) REVERT: L 284 ILE cc_start: 0.9035 (mm) cc_final: 0.8592 (mm) REVERT: L 308 GLU cc_start: 0.8779 (tm-30) cc_final: 0.8541 (tm-30) REVERT: L 321 PHE cc_start: 0.9140 (m-80) cc_final: 0.8852 (m-80) REVERT: L 365 GLU cc_start: 0.8278 (pt0) cc_final: 0.6930 (mt-10) REVERT: L 372 MET cc_start: 0.4667 (mmm) cc_final: 0.4105 (mmm) REVERT: M 140 TYR cc_start: 0.9229 (p90) cc_final: 0.8689 (p90) REVERT: M 154 ARG cc_start: 0.9140 (ptm160) cc_final: 0.8913 (ptt180) REVERT: M 210 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8642 (mt-10) REVERT: M 221 ARG cc_start: 0.8362 (ttp-110) cc_final: 0.7844 (ptm-80) REVERT: M 224 ARG cc_start: 0.9324 (tmt-80) cc_final: 0.8861 (tmt-80) REVERT: M 264 THR cc_start: 0.9144 (m) cc_final: 0.8868 (p) REVERT: M 265 MET cc_start: 0.8408 (mtp) cc_final: 0.8029 (mtp) REVERT: M 305 ARG cc_start: 0.7290 (ptm160) cc_final: 0.7014 (ptm160) REVERT: M 310 PRO cc_start: 0.9110 (Cg_endo) cc_final: 0.8797 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9146 (mm) cc_final: 0.8909 (mm) REVERT: M 333 ASP cc_start: 0.9264 (p0) cc_final: 0.8897 (p0) REVERT: M 357 GLU cc_start: 0.9412 (tp30) cc_final: 0.8950 (tp30) REVERT: M 363 ILE cc_start: 0.9474 (mm) cc_final: 0.9167 (mm) REVERT: M 364 ARG cc_start: 0.8812 (mmp80) cc_final: 0.8416 (mpp80) REVERT: M 370 VAL cc_start: 0.8482 (t) cc_final: 0.8022 (t) REVERT: M 372 MET cc_start: 0.8840 (tpt) cc_final: 0.7919 (tpt) REVERT: J 149 GLN cc_start: 0.9542 (mp10) cc_final: 0.9286 (mp10) REVERT: J 215 TYR cc_start: 0.8373 (m-80) cc_final: 0.7859 (m-80) REVERT: J 228 GLN cc_start: 0.9231 (mt0) cc_final: 0.8949 (mm-40) REVERT: J 251 THR cc_start: 0.8223 (p) cc_final: 0.7970 (p) REVERT: J 315 GLU cc_start: 0.9075 (mp0) cc_final: 0.8702 (mp0) REVERT: J 319 GLN cc_start: 0.9515 (mm110) cc_final: 0.8845 (mt0) REVERT: J 321 PHE cc_start: 0.8725 (m-10) cc_final: 0.8349 (m-80) REVERT: J 326 ARG cc_start: 0.8186 (ppt170) cc_final: 0.7856 (ppt170) REVERT: J 328 MET cc_start: 0.7127 (ppp) cc_final: 0.6793 (ppp) REVERT: J 347 SER cc_start: 0.9405 (m) cc_final: 0.8940 (p) REVERT: J 356 THR cc_start: 0.8761 (m) cc_final: 0.8555 (m) REVERT: J 357 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8766 (mm-30) REVERT: J 360 MET cc_start: 0.9132 (tmm) cc_final: 0.8383 (tmm) REVERT: J 372 MET cc_start: 0.9117 (mmm) cc_final: 0.8779 (mmm) REVERT: J 375 PHE cc_start: 0.9089 (m-80) cc_final: 0.8822 (m-80) outliers start: 1 outliers final: 0 residues processed: 662 average time/residue: 0.1332 time to fit residues: 119.9446 Evaluate side-chains 578 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 105 optimal weight: 0.0000 chunk 150 optimal weight: 0.8980 chunk 137 optimal weight: 0.5980 chunk 81 optimal weight: 0.0470 chunk 66 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 90 optimal weight: 0.8980 overall best weight: 0.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.108135 restraints weight = 32917.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111692 restraints weight = 24612.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114506 restraints weight = 19236.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116786 restraints weight = 15604.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118691 restraints weight = 12998.927| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.8568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12881 Z= 0.177 Angle : 0.893 13.465 17407 Z= 0.469 Chirality : 0.051 0.231 2000 Planarity : 0.007 0.149 2243 Dihedral : 7.752 129.413 1757 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.04 % Favored : 92.26 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.95 (0.22), residues: 1590 helix: -0.14 (0.18), residues: 817 sheet: -0.31 (0.46), residues: 135 loop : -1.22 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.045 0.001 ARG K 224 TYR 0.010 0.001 TYR L 140 PHE 0.030 0.002 PHE H 361 HIS 0.004 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.18 (12881) covalent geometry : angle 0.89252 / 0.47 (17407) hydrogen bonds : bond 0.04237 / 2.71 ( 507) hydrogen bonds : angle 5.35265 / 3.76 ( 1518) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 0.397 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: 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: 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: symmetry clash REVERT: H 128 TYR cc_start: 0.8143 (m-80) cc_final: 0.7777 (m-80) REVERT: H 130 PHE cc_start: 0.9123 (m-80) cc_final: 0.8721 (m-80) REVERT: H 172 ILE cc_start: 0.8363 (pt) cc_final: 0.7880 (pt) REVERT: H 181 TYR cc_start: 0.8644 (t80) cc_final: 0.8228 (t80) REVERT: H 221 ARG cc_start: 0.7582 (ppt170) cc_final: 0.7331 (ppt170) REVERT: H 227 PHE cc_start: 0.9267 (m-80) cc_final: 0.8833 (m-80) REVERT: H 233 LYS cc_start: 0.9295 (tptt) cc_final: 0.9055 (tmtt) REVERT: H 250 ARG cc_start: 0.8086 (ptt-90) cc_final: 0.7850 (ptt-90) REVERT: H 262 GLN cc_start: 0.8809 (pm20) cc_final: 0.8431 (pm20) REVERT: H 269 LEU cc_start: 0.9033 (mt) cc_final: 0.8736 (mt) REVERT: H 276 ASP cc_start: 0.8489 (m-30) cc_final: 0.8000 (m-30) REVERT: H 290 ILE cc_start: 0.9159 (tp) cc_final: 0.8841 (tp) REVERT: H 347 SER cc_start: 0.8361 (p) cc_final: 0.8009 (p) REVERT: H 372 MET cc_start: 0.8690 (mmm) cc_final: 0.8238 (mmm) REVERT: H 383 LEU cc_start: 0.8837 (tp) cc_final: 0.8539 (tp) REVERT: I 127 VAL cc_start: 0.8849 (m) cc_final: 0.8491 (m) REVERT: I 130 PHE cc_start: 0.9127 (m-10) cc_final: 0.8482 (m-80) REVERT: I 163 LYS cc_start: 0.9456 (ttmt) cc_final: 0.9136 (ttmm) REVERT: I 167 PHE cc_start: 0.8747 (m-10) cc_final: 0.8327 (m-80) REVERT: I 215 TYR cc_start: 0.8034 (m-10) cc_final: 0.7807 (m-10) REVERT: I 229 LEU cc_start: 0.9483 (tp) cc_final: 0.9240 (tp) REVERT: I 249 ARG cc_start: 0.8641 (ptm-80) cc_final: 0.8232 (ptm-80) REVERT: I 260 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8717 (mt-10) REVERT: I 265 MET cc_start: 0.9341 (tpp) cc_final: 0.9111 (tpp) REVERT: I 282 LYS cc_start: 0.7667 (tptt) cc_final: 0.7264 (tptt) REVERT: I 318 ILE cc_start: 0.9163 (mt) cc_final: 0.8766 (mt) REVERT: I 319 GLN cc_start: 0.9631 (mm110) cc_final: 0.9410 (mm-40) REVERT: I 321 PHE cc_start: 0.8451 (m-10) cc_final: 0.7861 (m-10) REVERT: I 322 LYS cc_start: 0.9625 (mmtm) cc_final: 0.9107 (mmmm) REVERT: I 323 ILE cc_start: 0.9512 (mm) cc_final: 0.8970 (tp) REVERT: I 326 ARG cc_start: 0.8152 (mtm110) cc_final: 0.7694 (mtm110) REVERT: I 327 LYS cc_start: 0.9124 (mmpt) cc_final: 0.8755 (mmpt) REVERT: I 341 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8740 (ttp80) REVERT: I 342 ILE cc_start: 0.9103 (mt) cc_final: 0.8441 (mt) REVERT: I 351 ILE cc_start: 0.9290 (mt) cc_final: 0.8812 (mt) REVERT: I 356 THR cc_start: 0.9830 (m) cc_final: 0.9526 (p) REVERT: I 360 MET cc_start: 0.9266 (mtm) cc_final: 0.8858 (mtm) REVERT: I 361 PHE cc_start: 0.8733 (m-80) cc_final: 0.8081 (m-10) REVERT: I 372 MET cc_start: 0.9507 (mmm) cc_final: 0.8896 (mmm) REVERT: I 373 LEU cc_start: 0.9778 (tt) cc_final: 0.9510 (tt) REVERT: I 374 ASP cc_start: 0.9054 (m-30) cc_final: 0.8738 (m-30) REVERT: I 375 PHE cc_start: 0.8799 (m-80) cc_final: 0.8315 (m-80) REVERT: K 134 GLU cc_start: 0.8986 (tm-30) cc_final: 0.8747 (tm-30) REVERT: K 149 GLN cc_start: 0.9625 (mp10) cc_final: 0.9359 (mp10) REVERT: K 151 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9222 (mt-10) REVERT: K 167 PHE cc_start: 0.7635 (m-80) cc_final: 0.7306 (m-80) REVERT: K 172 ILE cc_start: 0.7149 (mp) cc_final: 0.6001 (mp) REVERT: K 189 THR cc_start: 0.9211 (m) cc_final: 0.8636 (m) REVERT: K 190 LEU cc_start: 0.9411 (mt) cc_final: 0.9015 (mt) REVERT: K 193 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8704 (mtmm) REVERT: K 211 PHE cc_start: 0.9185 (m-80) cc_final: 0.8277 (m-80) REVERT: K 222 LEU cc_start: 0.9418 (tp) cc_final: 0.9120 (tp) REVERT: K 267 GLN cc_start: 0.8032 (tp40) cc_final: 0.7747 (tp40) REVERT: K 310 PRO cc_start: 0.8364 (Cg_endo) cc_final: 0.8127 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9283 (mt) cc_final: 0.8921 (tt) REVERT: K 315 GLU cc_start: 0.9124 (pm20) cc_final: 0.8912 (pm20) REVERT: K 319 GLN cc_start: 0.9638 (mt0) cc_final: 0.9381 (mt0) REVERT: K 337 LYS cc_start: 0.9665 (pptt) cc_final: 0.9332 (pptt) REVERT: K 357 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8031 (tm-30) REVERT: K 361 PHE cc_start: 0.8697 (m-80) cc_final: 0.8039 (m-10) REVERT: K 372 MET cc_start: 0.7316 (mmm) cc_final: 0.5914 (mmm) REVERT: K 375 PHE cc_start: 0.9360 (m-80) cc_final: 0.8959 (m-80) REVERT: L 123 LYS cc_start: 0.4193 (mptt) cc_final: 0.3638 (mttp) REVERT: L 165 GLU cc_start: 0.9321 (tp30) cc_final: 0.8902 (tp30) REVERT: L 202 THR cc_start: 0.8840 (t) cc_final: 0.8485 (t) REVERT: L 206 VAL cc_start: 0.9215 (t) cc_final: 0.9000 (t) REVERT: L 221 ARG cc_start: 0.9049 (tpp-160) cc_final: 0.8663 (tpp-160) REVERT: L 222 LEU cc_start: 0.9585 (mt) cc_final: 0.9268 (mt) REVERT: L 225 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8310 (mt-10) REVERT: L 232 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8919 (mm-30) REVERT: L 233 LYS cc_start: 0.9327 (tptt) cc_final: 0.8972 (tppt) REVERT: L 240 ILE cc_start: 0.9153 (tp) cc_final: 0.8640 (tp) REVERT: L 265 MET cc_start: 0.9016 (tmm) cc_final: 0.8809 (tmm) REVERT: L 273 ASP cc_start: 0.9104 (t70) cc_final: 0.8881 (t70) REVERT: L 284 ILE cc_start: 0.9102 (mm) cc_final: 0.8554 (mm) REVERT: L 308 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8555 (tm-30) REVERT: M 140 TYR cc_start: 0.9271 (p90) cc_final: 0.8745 (p90) REVERT: M 154 ARG cc_start: 0.9128 (ptm160) cc_final: 0.8887 (ptt180) REVERT: M 210 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8635 (mt-10) REVERT: M 221 ARG cc_start: 0.8459 (ttp-110) cc_final: 0.7954 (ptm-80) REVERT: M 224 ARG cc_start: 0.9335 (tmt-80) cc_final: 0.8860 (tmt-80) REVERT: M 271 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8331 (pp20) REVERT: M 292 ILE cc_start: 0.8314 (pt) cc_final: 0.8101 (pt) REVERT: M 305 ARG cc_start: 0.7305 (ptm160) cc_final: 0.6943 (ptm160) REVERT: M 310 PRO cc_start: 0.9085 (Cg_endo) cc_final: 0.8873 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9131 (mm) cc_final: 0.8826 (mm) REVERT: M 333 ASP cc_start: 0.9345 (p0) cc_final: 0.8895 (p0) REVERT: M 357 GLU cc_start: 0.9418 (tp30) cc_final: 0.9089 (tp30) REVERT: M 371 THR cc_start: 0.7500 (p) cc_final: 0.7099 (p) REVERT: M 372 MET cc_start: 0.8886 (tpt) cc_final: 0.7988 (tpt) REVERT: M 375 PHE cc_start: 0.9243 (m-10) cc_final: 0.8974 (m-10) REVERT: J 149 GLN cc_start: 0.9596 (mp10) cc_final: 0.9269 (mp10) REVERT: J 167 PHE cc_start: 0.8612 (m-80) cc_final: 0.8165 (m-80) REVERT: J 215 TYR cc_start: 0.8384 (m-80) cc_final: 0.7945 (m-80) REVERT: J 224 ARG cc_start: 0.9386 (ptp-110) cc_final: 0.9012 (ptp-110) REVERT: J 249 ARG cc_start: 0.8341 (ptt-90) cc_final: 0.7886 (ptt-90) REVERT: J 315 GLU cc_start: 0.9078 (mp0) cc_final: 0.8710 (mp0) REVERT: J 319 GLN cc_start: 0.9485 (mm110) cc_final: 0.8872 (mt0) REVERT: J 321 PHE cc_start: 0.8687 (m-10) cc_final: 0.8282 (m-80) REVERT: J 326 ARG cc_start: 0.8129 (ppt170) cc_final: 0.7818 (ppt170) REVERT: J 327 LYS cc_start: 0.9117 (tmtt) cc_final: 0.8443 (tptp) REVERT: J 328 MET cc_start: 0.7185 (ppp) cc_final: 0.6781 (ppp) REVERT: J 338 GLU cc_start: 0.8265 (tp30) cc_final: 0.7794 (tp30) REVERT: J 347 SER cc_start: 0.9371 (m) cc_final: 0.8936 (p) REVERT: J 357 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8757 (mm-30) REVERT: J 360 MET cc_start: 0.9209 (tmm) cc_final: 0.8513 (tmm) REVERT: J 372 MET cc_start: 0.8979 (mmm) cc_final: 0.8590 (mmm) REVERT: J 375 PHE cc_start: 0.9122 (m-80) cc_final: 0.8850 (m-80) outliers start: 0 outliers final: 0 residues processed: 640 average time/residue: 0.1275 time to fit residues: 112.3586 Evaluate side-chains 554 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 554 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.6980 chunk 124 optimal weight: 0.0870 chunk 94 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 98 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 112 optimal weight: 0.0970 chunk 151 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 84 optimal weight: 0.9980 overall best weight: 0.3356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN J 198 GLN J 228 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.135062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.108182 restraints weight = 32814.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111718 restraints weight = 24405.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.114582 restraints weight = 19015.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.116879 restraints weight = 15387.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118774 restraints weight = 12783.076| |-----------------------------------------------------------------------------| r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.8752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12881 Z= 0.181 Angle : 0.904 13.758 17407 Z= 0.477 Chirality : 0.052 0.235 2000 Planarity : 0.008 0.149 2243 Dihedral : 7.749 128.264 1757 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 23.08 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.55 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.01 (0.22), residues: 1590 helix: -0.18 (0.18), residues: 810 sheet: -0.38 (0.46), residues: 135 loop : -1.25 (0.27), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 259 TYR 0.018 0.002 TYR K 140 PHE 0.032 0.002 PHE M 321 HIS 0.004 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (12881) covalent geometry : angle 0.90351 / 0.48 (17407) hydrogen bonds : bond 0.04466 / 2.85 ( 507) hydrogen bonds : angle 5.40042 / 3.75 ( 1518) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 636 time to evaluate : 0.538 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: 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: 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: H 128 TYR cc_start: 0.8157 (m-80) cc_final: 0.7650 (m-80) REVERT: H 172 ILE cc_start: 0.8495 (pt) cc_final: 0.8124 (pt) REVERT: H 181 TYR cc_start: 0.8635 (t80) cc_final: 0.8196 (t80) REVERT: H 227 PHE cc_start: 0.9307 (m-80) cc_final: 0.8863 (m-80) REVERT: H 233 LYS cc_start: 0.9296 (tptt) cc_final: 0.9046 (tmtt) REVERT: H 250 ARG cc_start: 0.8157 (ptt-90) cc_final: 0.7767 (ptt-90) REVERT: H 260 GLU cc_start: 0.9104 (mp0) cc_final: 0.8852 (mp0) REVERT: H 262 GLN cc_start: 0.8950 (pm20) cc_final: 0.8725 (pm20) REVERT: H 269 LEU cc_start: 0.9071 (mt) cc_final: 0.8780 (mt) REVERT: H 276 ASP cc_start: 0.8479 (m-30) cc_final: 0.7944 (m-30) REVERT: H 290 ILE cc_start: 0.9172 (tp) cc_final: 0.8878 (tp) REVERT: H 306 ILE cc_start: 0.9318 (tp) cc_final: 0.8969 (tp) REVERT: H 372 MET cc_start: 0.8714 (mmm) cc_final: 0.8313 (mmm) REVERT: H 383 LEU cc_start: 0.8885 (tp) cc_final: 0.8576 (tp) REVERT: I 127 VAL cc_start: 0.8821 (m) cc_final: 0.8478 (m) REVERT: I 130 PHE cc_start: 0.9081 (m-10) cc_final: 0.8478 (m-80) REVERT: I 163 LYS cc_start: 0.9496 (ttmt) cc_final: 0.9172 (ttmm) REVERT: I 167 PHE cc_start: 0.8742 (m-10) cc_final: 0.8495 (m-80) REVERT: I 221 ARG cc_start: 0.9402 (ttp80) cc_final: 0.8833 (ttp80) REVERT: I 222 LEU cc_start: 0.9642 (mt) cc_final: 0.9241 (mt) REVERT: I 229 LEU cc_start: 0.9502 (tp) cc_final: 0.9265 (tp) REVERT: I 249 ARG cc_start: 0.8739 (ptm-80) cc_final: 0.8381 (ptm-80) REVERT: I 260 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8813 (mt-10) REVERT: I 265 MET cc_start: 0.9344 (tpp) cc_final: 0.9106 (tpp) REVERT: I 276 ASP cc_start: 0.7372 (m-30) cc_final: 0.7052 (m-30) REVERT: I 282 LYS cc_start: 0.7730 (tptt) cc_final: 0.7252 (tttt) REVERT: I 284 ILE cc_start: 0.9687 (mt) cc_final: 0.9485 (mt) REVERT: I 318 ILE cc_start: 0.9157 (mt) cc_final: 0.8780 (mt) REVERT: I 319 GLN cc_start: 0.9618 (mm110) cc_final: 0.9414 (mm-40) REVERT: I 321 PHE cc_start: 0.8438 (m-10) cc_final: 0.7845 (m-10) REVERT: I 322 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9077 (mmmm) REVERT: I 323 ILE cc_start: 0.9526 (mm) cc_final: 0.9049 (tp) REVERT: I 327 LYS cc_start: 0.9194 (mmpt) cc_final: 0.8980 (mmmt) REVERT: I 341 ARG cc_start: 0.9163 (ttp80) cc_final: 0.8739 (ttp80) REVERT: I 342 ILE cc_start: 0.9137 (mt) cc_final: 0.8445 (mt) REVERT: I 351 ILE cc_start: 0.9286 (mt) cc_final: 0.8802 (mt) REVERT: I 356 THR cc_start: 0.9838 (m) cc_final: 0.9533 (p) REVERT: I 360 MET cc_start: 0.9277 (mtm) cc_final: 0.8878 (mtm) REVERT: I 361 PHE cc_start: 0.8791 (m-80) cc_final: 0.8136 (m-10) REVERT: I 372 MET cc_start: 0.9480 (mmm) cc_final: 0.8912 (mmm) REVERT: I 373 LEU cc_start: 0.9820 (tt) cc_final: 0.9592 (tt) REVERT: I 374 ASP cc_start: 0.9214 (m-30) cc_final: 0.8784 (m-30) REVERT: I 375 PHE cc_start: 0.8830 (m-80) cc_final: 0.8309 (m-80) REVERT: K 149 GLN cc_start: 0.9637 (mp10) cc_final: 0.9412 (mp10) REVERT: K 151 GLU cc_start: 0.9585 (mt-10) cc_final: 0.9219 (tp30) REVERT: K 167 PHE cc_start: 0.7641 (m-80) cc_final: 0.7283 (m-80) REVERT: K 172 ILE cc_start: 0.7199 (mp) cc_final: 0.6027 (mp) REVERT: K 189 THR cc_start: 0.9266 (m) cc_final: 0.8678 (m) REVERT: K 190 LEU cc_start: 0.9426 (mt) cc_final: 0.9017 (mt) REVERT: K 193 LYS cc_start: 0.9179 (mtmm) cc_final: 0.8676 (mtmm) REVERT: K 200 ARG cc_start: 0.8711 (pmt-80) cc_final: 0.8446 (pmt-80) REVERT: K 211 PHE cc_start: 0.9002 (m-80) cc_final: 0.8086 (m-80) REVERT: K 222 LEU cc_start: 0.9411 (tp) cc_final: 0.9192 (tp) REVERT: K 263 ARG cc_start: 0.9253 (mtm-85) cc_final: 0.8962 (mtm-85) REVERT: K 311 LEU cc_start: 0.9316 (mt) cc_final: 0.8960 (tt) REVERT: K 337 LYS cc_start: 0.9657 (pptt) cc_final: 0.9329 (pptt) REVERT: K 357 GLU cc_start: 0.8894 (tm-30) cc_final: 0.7956 (tm-30) REVERT: K 361 PHE cc_start: 0.8743 (m-80) cc_final: 0.8056 (m-10) REVERT: K 372 MET cc_start: 0.7324 (mmm) cc_final: 0.5847 (mmm) REVERT: K 373 LEU cc_start: 0.9406 (mm) cc_final: 0.9204 (mm) REVERT: K 375 PHE cc_start: 0.9431 (m-80) cc_final: 0.8910 (m-80) REVERT: L 165 GLU cc_start: 0.9320 (tp30) cc_final: 0.8853 (tp30) REVERT: L 198 GLN cc_start: 0.9285 (mp-120) cc_final: 0.8774 (mm-40) REVERT: L 202 THR cc_start: 0.8956 (t) cc_final: 0.8610 (t) REVERT: L 206 VAL cc_start: 0.9192 (t) cc_final: 0.8983 (t) REVERT: L 211 PHE cc_start: 0.8838 (m-80) cc_final: 0.8586 (m-80) REVERT: L 221 ARG cc_start: 0.9017 (tpp-160) cc_final: 0.8644 (tpp-160) REVERT: L 222 LEU cc_start: 0.9537 (mt) cc_final: 0.9206 (mt) REVERT: L 225 GLU cc_start: 0.9061 (mt-10) cc_final: 0.8341 (mt-10) REVERT: L 232 GLU cc_start: 0.9241 (mm-30) cc_final: 0.8913 (mm-30) REVERT: L 233 LYS cc_start: 0.9312 (tptt) cc_final: 0.8990 (tppt) REVERT: L 240 ILE cc_start: 0.9137 (tp) cc_final: 0.8497 (tp) REVERT: L 262 GLN cc_start: 0.8444 (mm-40) cc_final: 0.7878 (mm-40) REVERT: L 265 MET cc_start: 0.9012 (tmm) cc_final: 0.8809 (tmm) REVERT: L 284 ILE cc_start: 0.9011 (mm) cc_final: 0.8551 (mm) REVERT: M 140 TYR cc_start: 0.9304 (p90) cc_final: 0.8756 (p90) REVERT: M 152 GLU cc_start: 0.8986 (pt0) cc_final: 0.8616 (pt0) REVERT: M 221 ARG cc_start: 0.8494 (ttp-110) cc_final: 0.7898 (ptm-80) REVERT: M 224 ARG cc_start: 0.9328 (tmt-80) cc_final: 0.8870 (tmt-80) REVERT: M 225 GLU cc_start: 0.8743 (pp20) cc_final: 0.8532 (pp20) REVERT: M 263 ARG cc_start: 0.8991 (tpp80) cc_final: 0.8679 (tpp80) REVERT: M 305 ARG cc_start: 0.7387 (ptm160) cc_final: 0.7047 (ptm160) REVERT: M 310 PRO cc_start: 0.9120 (Cg_endo) cc_final: 0.8819 (Cg_exo) REVERT: M 314 PHE cc_start: 0.9120 (t80) cc_final: 0.8699 (t80) REVERT: M 318 ILE cc_start: 0.9052 (mm) cc_final: 0.8831 (mm) REVERT: M 333 ASP cc_start: 0.9328 (p0) cc_final: 0.8941 (p0) REVERT: M 357 GLU cc_start: 0.9371 (tp30) cc_final: 0.8866 (tp30) REVERT: M 363 ILE cc_start: 0.9510 (mm) cc_final: 0.9203 (mm) REVERT: M 364 ARG cc_start: 0.8757 (mmp80) cc_final: 0.8321 (mpp80) REVERT: M 372 MET cc_start: 0.8847 (tpt) cc_final: 0.8011 (tpt) REVERT: M 375 PHE cc_start: 0.9231 (m-10) cc_final: 0.8982 (m-10) REVERT: J 149 GLN cc_start: 0.9571 (mp10) cc_final: 0.9271 (mp10) REVERT: J 159 LEU cc_start: 0.9506 (tp) cc_final: 0.9281 (tp) REVERT: J 167 PHE cc_start: 0.8679 (m-80) cc_final: 0.8216 (m-80) REVERT: J 186 THR cc_start: 0.9514 (p) cc_final: 0.9243 (p) REVERT: J 193 LYS cc_start: 0.8565 (tptp) cc_final: 0.8174 (tmtt) REVERT: J 249 ARG cc_start: 0.8430 (ptt-90) cc_final: 0.7937 (ptt-90) REVERT: J 314 PHE cc_start: 0.8662 (t80) cc_final: 0.8444 (t80) REVERT: J 315 GLU cc_start: 0.9080 (mp0) cc_final: 0.8723 (mp0) REVERT: J 319 GLN cc_start: 0.9457 (mm110) cc_final: 0.8828 (mt0) REVERT: J 326 ARG cc_start: 0.8128 (ppt170) cc_final: 0.7868 (ppt170) REVERT: J 327 LYS cc_start: 0.9087 (tmtt) cc_final: 0.8434 (tptp) REVERT: J 328 MET cc_start: 0.7183 (ppp) cc_final: 0.6781 (ppp) REVERT: J 347 SER cc_start: 0.9384 (m) cc_final: 0.8957 (p) REVERT: J 357 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8786 (mm-30) REVERT: J 360 MET cc_start: 0.9216 (tmm) cc_final: 0.8497 (tmm) REVERT: J 372 MET cc_start: 0.8987 (mmm) cc_final: 0.8646 (mmm) REVERT: J 375 PHE cc_start: 0.9067 (m-80) cc_final: 0.8794 (m-80) outliers start: 0 outliers final: 0 residues processed: 636 average time/residue: 0.1274 time to fit residues: 111.4118 Evaluate side-chains 550 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 87 optimal weight: 0.0980 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 11 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 145 optimal weight: 0.0670 chunk 88 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 0.0370 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 overall best weight: 0.2396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN J 198 GLN ** J 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.139182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110728 restraints weight = 33026.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.114331 restraints weight = 24794.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.117263 restraints weight = 19555.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.119703 restraints weight = 15872.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.121651 restraints weight = 13203.705| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.8841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12881 Z= 0.175 Angle : 0.901 13.688 17407 Z= 0.477 Chirality : 0.051 0.222 2000 Planarity : 0.007 0.126 2243 Dihedral : 7.722 127.401 1757 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.36 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -1.06 (0.22), residues: 1590 helix: -0.25 (0.18), residues: 816 sheet: -0.49 (0.44), residues: 141 loop : -1.22 (0.27), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 341 TYR 0.018 0.002 TYR L 140 PHE 0.035 0.002 PHE H 321 HIS 0.003 0.001 HIS H 324 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (12881) covalent geometry : angle 0.90058 / 0.48 (17407) hydrogen bonds : bond 0.04376 / 2.83 ( 507) hydrogen bonds : angle 5.35111 / 3.71 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2737.27 seconds wall clock time: 47 minutes 53.92 seconds (2873.92 seconds total)