Starting phenix.real_space_refine on Thu Sep 18 00:55:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6he4_0209/09_2025/6he4_0209.cif Found real_map, /net/cci-nas-00/data/ceres_data/6he4_0209/09_2025/6he4_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2025/6he4_0209.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2025/6he4_0209.map" model { file = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2025/6he4_0209.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6he4_0209/09_2025/6he4_0209.cif" } 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-2.0-5805/lib/python3.9/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: 3.30, per 1000 atoms: 0.26 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: 1.33 Conformation dependent library (CDL) restraints added in 785.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 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: 0.43 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: 2.04 Time building geometry restraints manager: 1.75 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: 7567 28.64 - 57.28: 358 57.28 - 85.92: 124 85.92 - 114.56: 15 114.56 - 143.20: 3 Dihedral angle restraints: 8067 sinusoidal: 3483 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 8064 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: 5.460 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.630 Find NCS groups from input model: 0.290 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:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 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 : 19.331 143.201 5103 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 aren 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 covalent geometry : bond 0.03563 (12881) covalent geometry : angle 3.64778 (17407) hydrogen bonds : bond 0.31085 ( 507) hydrogen bonds : angle 9.10549 ( 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 : 0.577 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: 0.6879 (m-80) cc_final: 0.6643 (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: 0.5084 (t80) cc_final: 0.4406 (t80) REVERT: H 363 ILE cc_start: 0.8560 (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: 0.8098 (mt) REVERT: I 127 VAL cc_start: 0.6647 (m) cc_final: 0.5639 (m) REVERT: I 150 ILE cc_start: 0.7193 (mt) cc_final: 0.6370 (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: 0.7158 (p) REVERT: I 207 VAL cc_start: 0.8451 (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: 0.8610 (m-30) cc_final: 0.8321 (t0) REVERT: I 297 ILE cc_start: 0.8608 (mp) cc_final: 0.7964 (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: 0.4448 (t) cc_final: 0.3679 (p) REVERT: I 371 THR cc_start: 0.6843 (p) cc_final: 0.5427 (p) REVERT: K 149 GLN cc_start: 0.9100 (mp10) cc_final: 0.8884 (mp10) REVERT: K 150 ILE cc_start: 0.8253 (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: 0.7513 (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: 0.7336 (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: 0.7056 (mt) REVERT: K 204 ILE cc_start: 0.7858 (mt) cc_final: 0.7619 (mt) REVERT: K 207 VAL cc_start: 0.8389 (t) cc_final: 0.7755 (m) REVERT: K 216 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5679 (pt) REVERT: K 243 LEU cc_start: 0.8507 (mt) cc_final: 0.7963 (mt) REVERT: K 255 THR cc_start: 0.6484 (OUTLIER) cc_final: 0.6210 (p) REVERT: K 269 LEU cc_start: 0.8562 (mt) cc_final: 0.8240 (mt) REVERT: K 287 THR cc_start: 0.8333 (t) cc_final: 0.7994 (m) REVERT: K 324 HIS cc_start: 0.7727 (m-70) cc_final: 0.7081 (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: 0.8994 (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: 0.8236 (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: 0.7157 (p) REVERT: L 260 GLU cc_start: 0.5091 (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: 0.6423 (tt) cc_final: 0.6192 (tt) REVERT: L 297 ILE cc_start: 0.6505 (tt) cc_final: 0.6079 (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: 0.6836 (m-80) cc_final: 0.6217 (m-80) REVERT: L 364 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6715 (mtt-85) REVERT: M 149 GLN cc_start: 0.8379 (mp10) cc_final: 0.7838 (mp10) REVERT: M 188 LYS cc_start: 0.5654 (mmtp) cc_final: 0.4881 (pttm) REVERT: M 199 THR cc_start: 0.8415 (p) cc_final: 0.7992 (t) REVERT: M 203 PHE cc_start: 0.7633 (t80) cc_final: 0.7020 (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: 0.8507 (mt) cc_final: 0.8232 (tp) REVERT: M 363 ILE cc_start: 0.8518 (mt) cc_final: 0.8317 (mm) REVERT: J 158 GLU cc_start: 0.7000 (mt-10) cc_final: 0.6772 (mt-10) REVERT: J 159 LEU cc_start: 0.7847 (tp) cc_final: 0.7290 (tp) REVERT: J 180 LEU cc_start: 0.7732 (mt) cc_final: 0.7273 (mt) REVERT: J 231 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8075 (mtmp) REVERT: J 272 LEU cc_start: 0.5189 (OUTLIER) cc_final: 0.4404 (tp) REVERT: J 321 PHE cc_start: 0.6740 (m-80) cc_final: 0.6164 (m-80) REVERT: J 324 HIS cc_start: 0.7010 (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: 0.8112 (mt) REVERT: J 364 ARG cc_start: 0.6975 (mtm-85) cc_final: 0.6714 (ptp-110) REVERT: J 374 ASP cc_start: 0.8187 (m-30) cc_final: 0.7364 (m-30) outliers start: 49 outliers final: 10 residues processed: 852 average time/residue: 0.1584 time to fit residues: 179.0917 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 : 0.478 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** L 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3866 r_free = 0.3866 target = 0.138464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111529 restraints weight = 32111.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.115143 restraints weight = 23661.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.118203 restraints weight = 18468.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120282 restraints weight = 14760.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.122568 restraints weight = 12289.102| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12881 Z= 0.266 Angle : 0.989 15.425 17407 Z= 0.539 Chirality : 0.052 0.274 2000 Planarity : 0.008 0.070 2243 Dihedral : 12.934 136.758 1881 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 21.09 Ramachandran Plot: Outliers : 0.82 % Allowed : 6.67 % Favored : 92.52 % Rotamer: Outliers : 0.67 % Allowed : 3.96 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % Twisted Proline : 3.33 % Twisted General : 0.66 % 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 aren not related in a simple way. whole: -1.39 (0.20), residues: 1590 helix: -0.03 (0.17), residues: 799 sheet: -0.93 (0.39), residues: 150 loop : -2.04 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG J 278 TYR 0.022 0.003 TYR M 215 PHE 0.038 0.004 PHE H 167 HIS 0.004 0.002 HIS J 324 Details of bonding type rmsd covalent geometry : bond 0.00536 (12881) covalent geometry : angle 0.98901 (17407) hydrogen bonds : bond 0.06966 ( 507) hydrogen bonds : angle 5.96406 ( 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 762 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 753 time to evaluate : 0.494 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: H 128 TYR cc_start: 0.8690 (t80) cc_final: 0.8380 (m-80) REVERT: H 130 PHE cc_start: 0.9418 (m-80) cc_final: 0.9100 (m-80) REVERT: H 141 GLU cc_start: 0.8668 (pm20) cc_final: 0.8308 (pm20) REVERT: H 154 ARG cc_start: 0.9120 (mtp85) cc_final: 0.8820 (mmm-85) REVERT: H 186 THR cc_start: 0.9472 (p) cc_final: 0.9210 (p) REVERT: H 227 PHE cc_start: 0.9417 (m-80) cc_final: 0.8842 (m-80) REVERT: H 231 LYS cc_start: 0.9724 (mtmm) cc_final: 0.9484 (mtmm) REVERT: H 241 ASP cc_start: 0.8921 (p0) cc_final: 0.8159 (p0) REVERT: H 267 GLN cc_start: 0.9377 (mt0) cc_final: 0.9099 (mt0) REVERT: H 269 LEU cc_start: 0.9144 (mt) cc_final: 0.8844 (mp) REVERT: H 315 GLU cc_start: 0.9440 (mp0) cc_final: 0.9203 (mp0) REVERT: H 321 PHE cc_start: 0.9387 (m-80) cc_final: 0.8861 (m-80) REVERT: H 324 HIS cc_start: 0.8789 (m90) cc_final: 0.7635 (m90) REVERT: H 338 GLU cc_start: 0.9146 (mm-30) cc_final: 0.8941 (mp0) REVERT: H 361 PHE cc_start: 0.9108 (t80) cc_final: 0.8619 (t80) REVERT: H 367 ARG cc_start: 0.7224 (mtm110) cc_final: 0.6386 (ttp-110) REVERT: H 372 MET cc_start: 0.8202 (mmm) cc_final: 0.7684 (mmm) REVERT: I 130 PHE cc_start: 0.8527 (m-80) cc_final: 0.8233 (m-80) REVERT: I 152 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9115 (mt-10) REVERT: I 186 THR cc_start: 0.9135 (p) cc_final: 0.8801 (p) REVERT: I 215 TYR cc_start: 0.7789 (m-80) cc_final: 0.7228 (m-80) REVERT: I 227 PHE cc_start: 0.8693 (t80) cc_final: 0.8399 (t80) REVERT: I 231 LYS cc_start: 0.9396 (mttm) cc_final: 0.9081 (mmmt) REVERT: I 260 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8727 (mt-10) REVERT: I 289 ARG cc_start: 0.6539 (mtt180) cc_final: 0.5721 (mtm-85) REVERT: I 307 ILE cc_start: 0.9354 (tp) cc_final: 0.8913 (tt) REVERT: I 309 VAL cc_start: 0.9611 (t) cc_final: 0.9246 (p) REVERT: I 311 LEU cc_start: 0.8654 (mm) cc_final: 0.8307 (mt) REVERT: I 318 ILE cc_start: 0.9115 (mt) cc_final: 0.8710 (mt) REVERT: I 321 PHE cc_start: 0.8215 (m-10) cc_final: 0.7818 (m-10) REVERT: I 326 ARG cc_start: 0.7934 (mtm110) cc_final: 0.7523 (mtm110) REVERT: I 327 LYS cc_start: 0.9308 (mmpt) cc_final: 0.8910 (mmpt) REVERT: I 333 ASP cc_start: 0.8719 (t0) cc_final: 0.8505 (t70) REVERT: I 351 ILE cc_start: 0.9311 (mt) cc_final: 0.9069 (mt) REVERT: I 361 PHE cc_start: 0.8532 (m-80) cc_final: 0.7966 (m-80) REVERT: I 372 MET cc_start: 0.9107 (mmm) cc_final: 0.8103 (mmm) REVERT: I 374 ASP cc_start: 0.9323 (m-30) cc_final: 0.9095 (m-30) REVERT: K 131 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7630 (tm-30) REVERT: K 149 GLN cc_start: 0.9737 (mp-120) cc_final: 0.9376 (mp10) REVERT: K 151 GLU cc_start: 0.9443 (mt-10) cc_final: 0.8936 (tp30) REVERT: K 154 ARG cc_start: 0.8380 (ttt-90) cc_final: 0.7369 (tmm160) REVERT: K 179 LEU cc_start: 0.9258 (tp) cc_final: 0.8762 (tp) REVERT: K 189 THR cc_start: 0.8475 (m) cc_final: 0.8183 (p) REVERT: K 190 LEU cc_start: 0.9102 (mt) cc_final: 0.8895 (mt) REVERT: K 193 LYS cc_start: 0.8898 (mtmm) cc_final: 0.8493 (mtmm) REVERT: K 206 VAL cc_start: 0.9513 (p) cc_final: 0.9279 (p) REVERT: K 243 LEU cc_start: 0.9306 (mt) cc_final: 0.8961 (mt) REVERT: K 287 THR cc_start: 0.8523 (t) cc_final: 0.8006 (m) REVERT: K 303 PHE cc_start: 0.9484 (m-80) cc_final: 0.9146 (m-80) REVERT: K 311 LEU cc_start: 0.8966 (mt) cc_final: 0.8548 (tt) REVERT: K 318 ILE cc_start: 0.8713 (mt) cc_final: 0.8124 (mt) REVERT: K 319 GLN cc_start: 0.9501 (mt0) cc_final: 0.9172 (mt0) REVERT: K 321 PHE cc_start: 0.8629 (m-80) cc_final: 0.8019 (m-80) REVERT: K 322 LYS cc_start: 0.9311 (mtmt) cc_final: 0.8842 (tptm) REVERT: K 351 ILE cc_start: 0.9339 (mm) cc_final: 0.8999 (mm) REVERT: K 372 MET cc_start: 0.5441 (mmm) cc_final: 0.4697 (mmm) REVERT: K 375 PHE cc_start: 0.9064 (m-80) cc_final: 0.8768 (m-10) REVERT: L 132 VAL cc_start: 0.8320 (p) cc_final: 0.6829 (p) REVERT: L 142 ASP cc_start: 0.9017 (m-30) cc_final: 0.8786 (m-30) REVERT: L 143 ILE cc_start: 0.9037 (tt) cc_final: 0.8785 (tt) REVERT: L 165 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8620 (pp20) REVERT: L 166 LEU cc_start: 0.9215 (mt) cc_final: 0.8690 (mt) REVERT: L 193 LYS cc_start: 0.9100 (tptt) cc_final: 0.8780 (tptt) REVERT: L 224 ARG cc_start: 0.8386 (mtm-85) cc_final: 0.7420 (mtm-85) REVERT: L 225 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8420 (mt-10) REVERT: L 228 GLN cc_start: 0.9102 (tp40) cc_final: 0.8780 (tp40) REVERT: L 231 LYS cc_start: 0.9256 (mmmt) cc_final: 0.9039 (mmtt) REVERT: L 232 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8720 (mm-30) REVERT: L 258 ASP cc_start: 0.7897 (p0) cc_final: 0.7616 (p0) REVERT: L 265 MET cc_start: 0.9075 (tmm) cc_final: 0.8831 (tmm) REVERT: L 273 ASP cc_start: 0.8938 (t70) cc_final: 0.8538 (t70) REVERT: L 281 VAL cc_start: 0.9381 (m) cc_final: 0.9052 (m) REVERT: L 284 ILE cc_start: 0.9141 (mm) cc_final: 0.8654 (mm) REVERT: L 317 ARG cc_start: 0.8919 (mmt-90) cc_final: 0.8589 (mmt-90) REVERT: L 320 ILE cc_start: 0.9306 (mt) cc_final: 0.9031 (mm) REVERT: L 337 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9239 (mmtm) REVERT: L 338 GLU cc_start: 0.9280 (pt0) cc_final: 0.8855 (pm20) REVERT: L 356 THR cc_start: 0.8845 (p) cc_final: 0.8179 (p) REVERT: L 364 ARG cc_start: 0.9057 (mtt90) cc_final: 0.8646 (mpp80) REVERT: L 372 MET cc_start: 0.5044 (mmm) cc_final: 0.4751 (mmm) REVERT: M 151 GLU cc_start: 0.9096 (mm-30) cc_final: 0.8621 (pt0) REVERT: M 152 GLU cc_start: 0.9478 (mp0) cc_final: 0.9236 (mp0) REVERT: M 155 GLU cc_start: 0.9525 (mp0) cc_final: 0.9246 (mp0) REVERT: M 228 GLN cc_start: 0.9390 (tp40) cc_final: 0.8777 (tp40) REVERT: M 280 ASP cc_start: 0.7925 (p0) cc_final: 0.7615 (p0) REVERT: M 294 ASP cc_start: 0.8907 (p0) cc_final: 0.8632 (p0) REVERT: M 306 ILE cc_start: 0.9510 (pt) cc_final: 0.9280 (pt) REVERT: M 321 PHE cc_start: 0.8490 (m-10) cc_final: 0.8019 (m-80) REVERT: M 357 GLU cc_start: 0.8726 (tm-30) cc_final: 0.7341 (tp30) REVERT: M 361 PHE cc_start: 0.8507 (m-80) cc_final: 0.8069 (m-10) REVERT: M 367 ARG cc_start: 0.7023 (ptt90) cc_final: 0.5671 (ptt-90) REVERT: M 372 MET cc_start: 0.8558 (tpt) cc_final: 0.7139 (mmm) REVERT: M 374 ASP cc_start: 0.8591 (m-30) cc_final: 0.7441 (m-30) REVERT: M 376 THR cc_start: 0.9660 (p) cc_final: 0.9354 (p) REVERT: J 149 GLN cc_start: 0.9528 (mp10) cc_final: 0.8993 (mp10) REVERT: J 159 LEU cc_start: 0.9214 (tp) cc_final: 0.8940 (tp) REVERT: J 190 LEU cc_start: 0.9266 (tp) cc_final: 0.9012 (tp) REVERT: J 206 VAL cc_start: 0.9133 (p) cc_final: 0.8780 (p) REVERT: J 214 LYS cc_start: 0.8721 (ptmm) cc_final: 0.8444 (ptmm) REVERT: J 228 GLN cc_start: 0.9239 (mt0) cc_final: 0.8919 (mm-40) REVERT: J 314 PHE cc_start: 0.8279 (t80) cc_final: 0.8053 (t80) REVERT: J 319 GLN cc_start: 0.9365 (mm110) cc_final: 0.8887 (mt0) REVERT: J 324 HIS cc_start: 0.8183 (m170) cc_final: 0.7908 (m-70) REVERT: J 326 ARG cc_start: 0.8528 (ppt170) cc_final: 0.8081 (ppt170) REVERT: J 327 LYS cc_start: 0.9341 (tttt) cc_final: 0.8994 (tptt) REVERT: J 338 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8984 (mm-30) REVERT: J 350 ASP cc_start: 0.9615 (m-30) cc_final: 0.9350 (m-30) REVERT: J 366 GLU cc_start: 0.8848 (tp30) cc_final: 0.8025 (tp30) REVERT: J 375 PHE cc_start: 0.9436 (m-10) cc_final: 0.9090 (m-80) outliers start: 9 outliers final: 2 residues processed: 757 average time/residue: 0.1603 time to fit residues: 159.9064 Evaluate side-chains 601 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 599 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 0.9990 chunk 17 optimal weight: 4.9990 chunk 130 optimal weight: 0.0030 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 0.9980 chunk 134 optimal weight: 0.7980 chunk 119 optimal weight: 0.0270 chunk 146 optimal weight: 0.3980 chunk 148 optimal weight: 0.4980 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.3448 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 262 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.108527 restraints weight = 31930.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.112133 restraints weight = 23966.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.115092 restraints weight = 18802.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.117543 restraints weight = 15259.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.119537 restraints weight = 12653.194| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6393 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= 0.194 Angle : 0.883 15.079 17407 Z= 0.474 Chirality : 0.051 0.320 2000 Planarity : 0.007 0.092 2243 Dihedral : 12.315 138.166 1881 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.42 % Favored : 92.70 % Rotamer: Outliers : 0.45 % Allowed : 4.19 % Favored : 95.37 % 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 aren not related in a simple way. whole: -1.32 (0.20), residues: 1590 helix: -0.13 (0.18), residues: 789 sheet: -0.99 (0.40), residues: 151 loop : -1.72 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 341 TYR 0.019 0.002 TYR K 140 PHE 0.034 0.003 PHE H 336 HIS 0.011 0.003 HIS H 324 Details of bonding type rmsd covalent geometry : bond 0.00424 (12881) covalent geometry : angle 0.88281 (17407) hydrogen bonds : bond 0.05335 ( 507) hydrogen bonds : angle 5.55331 ( 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 732 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 726 time to evaluate : 0.355 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 130 PHE cc_start: 0.9282 (m-80) cc_final: 0.8971 (m-80) REVERT: H 227 PHE cc_start: 0.9462 (m-80) cc_final: 0.8907 (m-80) REVERT: H 237 ILE cc_start: 0.6574 (mp) cc_final: 0.6328 (mp) REVERT: H 239 PHE cc_start: 0.7976 (t80) cc_final: 0.7674 (t80) REVERT: H 267 GLN cc_start: 0.9336 (mt0) cc_final: 0.9066 (mt0) REVERT: H 271 GLU cc_start: 0.9262 (mp0) cc_final: 0.9048 (mp0) REVERT: H 321 PHE cc_start: 0.9548 (m-80) cc_final: 0.9240 (m-80) REVERT: H 324 HIS cc_start: 0.8889 (m90) cc_final: 0.8680 (m90) REVERT: H 356 THR cc_start: 0.9559 (p) cc_final: 0.9312 (p) REVERT: H 364 ARG cc_start: 0.8878 (mtm180) cc_final: 0.8317 (mtm-85) REVERT: H 372 MET cc_start: 0.8465 (mmm) cc_final: 0.7776 (mmm) REVERT: I 127 VAL cc_start: 0.8614 (m) cc_final: 0.8261 (m) REVERT: I 130 PHE cc_start: 0.8481 (m-10) cc_final: 0.8237 (m-80) REVERT: I 190 LEU cc_start: 0.8668 (tp) cc_final: 0.8441 (tp) REVERT: I 227 PHE cc_start: 0.8898 (t80) cc_final: 0.8650 (t80) REVERT: I 231 LYS cc_start: 0.9650 (mttm) cc_final: 0.9392 (mmmt) REVERT: I 266 MET cc_start: 0.8489 (mtp) cc_final: 0.8251 (mtp) REVERT: I 282 LYS cc_start: 0.8289 (mmtp) cc_final: 0.8002 (mmmt) REVERT: I 294 ASP cc_start: 0.8627 (t0) cc_final: 0.8225 (t0) REVERT: I 302 ARG cc_start: 0.8182 (mmt180) cc_final: 0.7895 (mmt180) REVERT: I 303 PHE cc_start: 0.9004 (m-80) cc_final: 0.8645 (m-80) REVERT: I 311 LEU cc_start: 0.8833 (mm) cc_final: 0.8406 (mt) REVERT: I 318 ILE cc_start: 0.9055 (mt) cc_final: 0.8589 (mt) REVERT: I 321 PHE cc_start: 0.8450 (m-10) cc_final: 0.7770 (m-10) REVERT: I 326 ARG cc_start: 0.7836 (mtm110) cc_final: 0.7477 (mtm110) REVERT: I 327 LYS cc_start: 0.9131 (mmpt) cc_final: 0.8734 (mmpt) REVERT: I 341 ARG cc_start: 0.9045 (ttp80) cc_final: 0.8720 (ttp80) REVERT: I 342 ILE cc_start: 0.9171 (mt) cc_final: 0.8623 (mt) REVERT: I 351 ILE cc_start: 0.9342 (mt) cc_final: 0.9092 (mt) REVERT: I 357 GLU cc_start: 0.8749 (tp30) cc_final: 0.8193 (tp30) REVERT: I 372 MET cc_start: 0.9341 (mmm) cc_final: 0.8451 (mmm) REVERT: K 149 GLN cc_start: 0.9724 (mp-120) cc_final: 0.9232 (mp10) REVERT: K 154 ARG cc_start: 0.9101 (tmt170) cc_final: 0.8754 (tpt90) REVERT: K 160 PRO cc_start: 0.9292 (Cg_exo) cc_final: 0.8943 (Cg_endo) REVERT: K 179 LEU cc_start: 0.9235 (tp) cc_final: 0.9035 (tp) REVERT: K 189 THR cc_start: 0.8570 (m) cc_final: 0.8204 (p) REVERT: K 193 LYS cc_start: 0.9068 (mtmm) cc_final: 0.8685 (mtmm) REVERT: K 213 GLN cc_start: 0.8292 (mp-120) cc_final: 0.8001 (mp-120) REVERT: K 267 GLN cc_start: 0.8603 (tp40) cc_final: 0.7521 (tp40) REVERT: K 287 THR cc_start: 0.8879 (t) cc_final: 0.8439 (m) REVERT: K 288 ASN cc_start: 0.8808 (p0) cc_final: 0.8415 (t0) REVERT: K 290 ILE cc_start: 0.9033 (pt) cc_final: 0.8738 (tp) REVERT: K 319 GLN cc_start: 0.9500 (mt0) cc_final: 0.9062 (mt0) REVERT: K 321 PHE cc_start: 0.8721 (m-80) cc_final: 0.7722 (m-80) REVERT: K 338 GLU cc_start: 0.9153 (tp30) cc_final: 0.8509 (tp30) REVERT: K 372 MET cc_start: 0.6138 (mmm) cc_final: 0.5224 (mmm) REVERT: K 375 PHE cc_start: 0.9015 (m-80) cc_final: 0.8780 (m-10) REVERT: L 137 GLU cc_start: 0.9171 (pm20) cc_final: 0.8741 (pm20) REVERT: L 149 GLN cc_start: 0.9292 (mp10) cc_final: 0.8962 (mp10) REVERT: L 166 LEU cc_start: 0.9124 (mt) cc_final: 0.8593 (mt) REVERT: L 172 ILE cc_start: 0.7998 (tp) cc_final: 0.7358 (tp) REVERT: L 193 LYS cc_start: 0.9274 (tptt) cc_final: 0.9058 (tptt) REVERT: L 202 THR cc_start: 0.8383 (m) cc_final: 0.8021 (m) REVERT: L 204 ILE cc_start: 0.9403 (mm) cc_final: 0.8893 (tp) REVERT: L 222 LEU cc_start: 0.9465 (mt) cc_final: 0.9209 (mt) REVERT: L 225 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8128 (mt-10) REVERT: L 228 GLN cc_start: 0.9162 (tp40) cc_final: 0.8775 (tp40) REVERT: L 232 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8616 (mm-30) REVERT: L 265 MET cc_start: 0.8959 (tmm) cc_final: 0.8752 (tmm) REVERT: L 273 ASP cc_start: 0.9121 (t70) cc_final: 0.8672 (t70) REVERT: L 281 VAL cc_start: 0.9485 (m) cc_final: 0.9245 (m) REVERT: L 284 ILE cc_start: 0.8971 (mm) cc_final: 0.8490 (mm) REVERT: L 328 MET cc_start: 0.8550 (ppp) cc_final: 0.8230 (ppp) REVERT: L 337 LYS cc_start: 0.9507 (mmtm) cc_final: 0.9249 (mmtm) REVERT: L 360 MET cc_start: 0.9151 (ttp) cc_final: 0.8938 (ttp) REVERT: L 365 GLU cc_start: 0.8310 (pt0) cc_final: 0.7052 (mt-10) REVERT: L 382 VAL cc_start: 0.8677 (OUTLIER) cc_final: 0.8385 (t) REVERT: M 132 VAL cc_start: 0.9388 (t) cc_final: 0.9184 (t) REVERT: M 140 TYR cc_start: 0.9275 (p90) cc_final: 0.8882 (p90) REVERT: M 221 ARG cc_start: 0.8915 (ttp-110) cc_final: 0.8281 (ptm-80) REVERT: M 227 PHE cc_start: 0.8251 (t80) cc_final: 0.7952 (t80) REVERT: M 264 THR cc_start: 0.9178 (m) cc_final: 0.8892 (p) REVERT: M 271 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8413 (pp20) REVERT: M 303 PHE cc_start: 0.8502 (m-80) cc_final: 0.8249 (m-80) REVERT: M 305 ARG cc_start: 0.7553 (ptm160) cc_final: 0.7110 (ptm160) REVERT: M 306 ILE cc_start: 0.9474 (pt) cc_final: 0.9230 (pt) REVERT: M 307 ILE cc_start: 0.9450 (mt) cc_final: 0.8864 (tt) REVERT: M 310 PRO cc_start: 0.9056 (Cg_endo) cc_final: 0.8569 (Cg_exo) REVERT: M 321 PHE cc_start: 0.8761 (m-10) cc_final: 0.8348 (m-80) REVERT: M 333 ASP cc_start: 0.9279 (p0) cc_final: 0.8976 (p0) REVERT: M 367 ARG cc_start: 0.5886 (ptt90) cc_final: 0.5545 (ptt-90) REVERT: M 372 MET cc_start: 0.8955 (tpt) cc_final: 0.7821 (tpt) REVERT: M 375 PHE cc_start: 0.9214 (m-10) cc_final: 0.8956 (m-10) REVERT: M 379 ILE cc_start: 0.9570 (pt) cc_final: 0.9323 (pt) REVERT: J 149 GLN cc_start: 0.9603 (mp10) cc_final: 0.9159 (mp10) REVERT: J 159 LEU cc_start: 0.9160 (tp) cc_final: 0.8789 (tp) REVERT: J 172 ILE cc_start: 0.9149 (tp) cc_final: 0.8828 (tp) REVERT: J 190 LEU cc_start: 0.9083 (tp) cc_final: 0.8867 (tp) REVERT: J 198 GLN cc_start: 0.8313 (mt0) cc_final: 0.8024 (tt0) REVERT: J 214 LYS cc_start: 0.9242 (ptmm) cc_final: 0.9008 (ptmm) REVERT: J 228 GLN cc_start: 0.9291 (mt0) cc_final: 0.8963 (mm-40) REVERT: J 263 ARG cc_start: 0.9425 (mpp80) cc_final: 0.9224 (ptp-170) REVERT: J 307 ILE cc_start: 0.9523 (mp) cc_final: 0.9300 (mp) REVERT: J 314 PHE cc_start: 0.8252 (t80) cc_final: 0.8013 (t80) REVERT: J 319 GLN cc_start: 0.9484 (mm110) cc_final: 0.8920 (mt0) REVERT: J 321 PHE cc_start: 0.9378 (m-80) cc_final: 0.9020 (m-10) REVERT: J 324 HIS cc_start: 0.8396 (m170) cc_final: 0.7370 (m90) REVERT: J 326 ARG cc_start: 0.8312 (ppt170) cc_final: 0.7816 (ppt170) REVERT: J 328 MET cc_start: 0.7055 (ppp) cc_final: 0.6791 (ppp) REVERT: J 335 ASP cc_start: 0.9078 (t70) cc_final: 0.8451 (t0) REVERT: J 338 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8659 (mm-30) REVERT: J 372 MET cc_start: 0.8991 (mmp) cc_final: 0.8752 (mmm) outliers start: 6 outliers final: 0 residues processed: 729 average time/residue: 0.1520 time to fit residues: 146.4191 Evaluate side-chains 581 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 580 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 139 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** L 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN J 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.103650 restraints weight = 34321.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.107099 restraints weight = 25688.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109833 restraints weight = 20189.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.112077 restraints weight = 16451.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113935 restraints weight = 13716.456| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.7158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 12881 Z= 0.233 Angle : 0.910 14.832 17407 Z= 0.485 Chirality : 0.052 0.294 2000 Planarity : 0.006 0.072 2243 Dihedral : 12.081 133.409 1881 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 24.87 Ramachandran Plot: Outliers : 0.88 % Allowed : 6.42 % Favored : 92.70 % Rotamer: Outliers : 0.52 % Allowed : 4.19 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.89 % Cis-general : 1.20 % 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 aren not related in a simple way. whole: -1.27 (0.21), residues: 1590 helix: -0.24 (0.18), residues: 792 sheet: -1.00 (0.41), residues: 159 loop : -1.44 (0.26), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 221 TYR 0.037 0.002 TYR H 140 PHE 0.034 0.003 PHE H 361 HIS 0.015 0.005 HIS L 324 Details of bonding type rmsd covalent geometry : bond 0.00498 (12881) covalent geometry : angle 0.91024 (17407) hydrogen bonds : bond 0.04924 ( 507) hydrogen bonds : angle 5.73694 ( 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 700 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 693 time to evaluate : 0.506 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 130 PHE cc_start: 0.9297 (m-10) cc_final: 0.8966 (m-80) REVERT: H 140 TYR cc_start: 0.8529 (m-80) cc_final: 0.8313 (m-10) REVERT: H 154 ARG cc_start: 0.9086 (mtp-110) cc_final: 0.8877 (mtp-110) REVERT: H 221 ARG cc_start: 0.7926 (ppt170) cc_final: 0.7720 (ppt170) REVERT: H 227 PHE cc_start: 0.9543 (m-80) cc_final: 0.8977 (m-80) REVERT: H 233 LYS cc_start: 0.9346 (tptp) cc_final: 0.9128 (tptp) REVERT: H 239 PHE cc_start: 0.7985 (t80) cc_final: 0.7600 (t80) REVERT: H 263 ARG cc_start: 0.9409 (mtp180) cc_final: 0.9025 (mtp180) REVERT: H 290 ILE cc_start: 0.9407 (tp) cc_final: 0.9184 (tp) REVERT: H 321 PHE cc_start: 0.9562 (m-80) cc_final: 0.9282 (m-80) REVERT: H 356 THR cc_start: 0.9529 (p) cc_final: 0.9206 (p) REVERT: H 364 ARG cc_start: 0.9004 (mtt180) cc_final: 0.8779 (mtm-85) REVERT: H 372 MET cc_start: 0.8458 (mmm) cc_final: 0.7913 (mmm) REVERT: I 127 VAL cc_start: 0.8746 (m) cc_final: 0.8365 (m) REVERT: I 130 PHE cc_start: 0.8982 (m-10) cc_final: 0.8539 (m-80) REVERT: I 149 GLN cc_start: 0.9109 (tt0) cc_final: 0.8888 (tt0) REVERT: I 163 LYS cc_start: 0.9507 (ttmt) cc_final: 0.9031 (ttmm) REVERT: I 190 LEU cc_start: 0.8805 (tp) cc_final: 0.8596 (tp) REVERT: I 221 ARG cc_start: 0.9283 (ttp80) cc_final: 0.9069 (ttp-110) REVERT: I 227 PHE cc_start: 0.8846 (t80) cc_final: 0.8545 (t80) REVERT: I 260 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8743 (mt-10) REVERT: I 294 ASP cc_start: 0.8857 (t0) cc_final: 0.8313 (t0) REVERT: I 303 PHE cc_start: 0.9142 (m-80) cc_final: 0.8828 (m-80) REVERT: I 311 LEU cc_start: 0.8856 (mm) cc_final: 0.8436 (mt) REVERT: I 315 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8699 (tm-30) REVERT: I 318 ILE cc_start: 0.8967 (mt) cc_final: 0.8410 (mt) REVERT: I 321 PHE cc_start: 0.8481 (m-10) cc_final: 0.7708 (m-10) REVERT: I 326 ARG cc_start: 0.8081 (mtm110) cc_final: 0.7610 (mtm110) REVERT: I 327 LYS cc_start: 0.9159 (mmpt) cc_final: 0.8708 (mmpt) REVERT: I 342 ILE cc_start: 0.9172 (mt) cc_final: 0.8936 (mt) REVERT: I 351 ILE cc_start: 0.9413 (mt) cc_final: 0.9116 (mt) REVERT: I 357 GLU cc_start: 0.8713 (tp30) cc_final: 0.8399 (tp30) REVERT: I 372 MET cc_start: 0.9384 (mmm) cc_final: 0.8668 (mmm) REVERT: I 375 PHE cc_start: 0.9023 (m-80) cc_final: 0.8261 (m-80) REVERT: K 149 GLN cc_start: 0.9729 (mp-120) cc_final: 0.9310 (mp10) REVERT: K 151 GLU cc_start: 0.9442 (mt-10) cc_final: 0.8960 (tp30) REVERT: K 189 THR cc_start: 0.9144 (m) cc_final: 0.8497 (m) REVERT: K 190 LEU cc_start: 0.9379 (mt) cc_final: 0.9025 (mt) REVERT: K 193 LYS cc_start: 0.9097 (mtmm) cc_final: 0.8680 (mtmm) REVERT: K 211 PHE cc_start: 0.9238 (m-80) cc_final: 0.8570 (m-80) REVERT: K 213 GLN cc_start: 0.8343 (mp-120) cc_final: 0.8076 (mp10) REVERT: K 221 ARG cc_start: 0.8507 (mmp-170) cc_final: 0.8181 (mmp-170) REVERT: K 222 LEU cc_start: 0.9480 (tp) cc_final: 0.9188 (tp) REVERT: K 238 ILE cc_start: 0.9348 (mt) cc_final: 0.9144 (mt) REVERT: K 240 ILE cc_start: 0.8902 (tp) cc_final: 0.8633 (tp) REVERT: K 243 LEU cc_start: 0.9230 (mt) cc_final: 0.8987 (mt) REVERT: K 260 GLU cc_start: 0.9150 (tp30) cc_final: 0.8585 (tp30) REVERT: K 267 GLN cc_start: 0.8736 (tp40) cc_final: 0.7960 (tp40) REVERT: K 287 THR cc_start: 0.9229 (t) cc_final: 0.8595 (m) REVERT: K 288 ASN cc_start: 0.8874 (p0) cc_final: 0.8201 (t0) REVERT: K 311 LEU cc_start: 0.9214 (mt) cc_final: 0.8849 (tt) REVERT: K 315 GLU cc_start: 0.8986 (pm20) cc_final: 0.8549 (mp0) REVERT: K 318 ILE cc_start: 0.9127 (mt) cc_final: 0.8645 (mt) REVERT: K 319 GLN cc_start: 0.9557 (mt0) cc_final: 0.9275 (mm110) REVERT: K 321 PHE cc_start: 0.8686 (m-80) cc_final: 0.8097 (m-80) REVERT: K 322 LYS cc_start: 0.9274 (mtmm) cc_final: 0.8880 (tptm) REVERT: K 338 GLU cc_start: 0.9221 (tp30) cc_final: 0.8604 (tp30) REVERT: K 351 ILE cc_start: 0.9296 (mm) cc_final: 0.9051 (mm) REVERT: K 361 PHE cc_start: 0.9074 (m-80) cc_final: 0.8395 (m-80) REVERT: K 372 MET cc_start: 0.6466 (mmm) cc_final: 0.5368 (mmm) REVERT: K 375 PHE cc_start: 0.9158 (m-80) cc_final: 0.8779 (m-80) REVERT: L 132 VAL cc_start: 0.7879 (p) cc_final: 0.7674 (p) REVERT: L 137 GLU cc_start: 0.9190 (pm20) cc_final: 0.8730 (pm20) REVERT: L 143 ILE cc_start: 0.8964 (tt) cc_final: 0.8608 (tt) REVERT: L 193 LYS cc_start: 0.9236 (tptt) cc_final: 0.9036 (tptt) REVERT: L 202 THR cc_start: 0.8678 (m) cc_final: 0.8268 (p) REVERT: L 206 VAL cc_start: 0.9173 (m) cc_final: 0.8929 (t) REVERT: L 211 PHE cc_start: 0.8765 (m-80) cc_final: 0.8350 (m-80) REVERT: L 222 LEU cc_start: 0.9517 (mt) cc_final: 0.9285 (mt) REVERT: L 224 ARG cc_start: 0.8587 (mtm-85) cc_final: 0.8222 (mtm-85) REVERT: L 225 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8465 (mt-10) REVERT: L 228 GLN cc_start: 0.9208 (tp40) cc_final: 0.8720 (tp40) REVERT: L 232 GLU cc_start: 0.9018 (mm-30) cc_final: 0.8705 (mm-30) REVERT: L 233 LYS cc_start: 0.8951 (tppt) cc_final: 0.8612 (tppt) REVERT: L 273 ASP cc_start: 0.9221 (t70) cc_final: 0.8697 (t70) REVERT: L 281 VAL cc_start: 0.9496 (m) cc_final: 0.9265 (m) REVERT: L 284 ILE cc_start: 0.9177 (mm) cc_final: 0.8631 (mm) REVERT: L 328 MET cc_start: 0.8534 (ppp) cc_final: 0.8155 (ppp) REVERT: L 356 THR cc_start: 0.9076 (p) cc_final: 0.8773 (p) REVERT: L 364 ARG cc_start: 0.9138 (mtt90) cc_final: 0.8571 (mtt-85) REVERT: L 365 GLU cc_start: 0.8593 (pt0) cc_final: 0.7474 (mt-10) REVERT: M 140 TYR cc_start: 0.9318 (p90) cc_final: 0.8854 (p90) REVERT: M 229 LEU cc_start: 0.9614 (mt) cc_final: 0.9337 (mt) REVERT: M 246 ILE cc_start: 0.8706 (tt) cc_final: 0.8478 (tt) REVERT: M 259 ARG cc_start: 0.6821 (ttm110) cc_final: 0.5797 (ttm110) REVERT: M 264 THR cc_start: 0.9125 (m) cc_final: 0.8839 (p) REVERT: M 294 ASP cc_start: 0.8779 (p0) cc_final: 0.8556 (p0) REVERT: M 310 PRO cc_start: 0.9092 (Cg_endo) cc_final: 0.8738 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9148 (mm) cc_final: 0.8726 (mm) REVERT: M 333 ASP cc_start: 0.9253 (p0) cc_final: 0.8845 (p0) REVERT: M 361 PHE cc_start: 0.9065 (m-80) cc_final: 0.8354 (m-80) REVERT: M 372 MET cc_start: 0.8975 (tpt) cc_final: 0.8018 (tpt) REVERT: M 375 PHE cc_start: 0.9212 (m-10) cc_final: 0.8878 (m-10) REVERT: J 149 GLN cc_start: 0.9600 (mp10) cc_final: 0.9113 (mp10) REVERT: J 152 GLU cc_start: 0.9393 (OUTLIER) cc_final: 0.9191 (pm20) REVERT: J 167 PHE cc_start: 0.8136 (m-80) cc_final: 0.7777 (m-10) REVERT: J 172 ILE cc_start: 0.8993 (tp) cc_final: 0.8776 (tp) REVERT: J 186 THR cc_start: 0.9521 (p) cc_final: 0.9263 (p) REVERT: J 198 GLN cc_start: 0.8467 (mt0) cc_final: 0.8147 (tt0) REVERT: J 228 GLN cc_start: 0.9298 (mt0) cc_final: 0.8924 (mm-40) REVERT: J 328 MET cc_start: 0.7115 (ppp) cc_final: 0.6779 (ppp) REVERT: J 338 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8746 (mm-30) REVERT: J 356 THR cc_start: 0.8773 (m) cc_final: 0.8534 (m) REVERT: J 360 MET cc_start: 0.9454 (tmm) cc_final: 0.8628 (tmm) REVERT: J 372 MET cc_start: 0.9258 (mmp) cc_final: 0.8751 (mmm) REVERT: J 375 PHE cc_start: 0.9157 (m-80) cc_final: 0.8930 (m-80) outliers start: 7 outliers final: 2 residues processed: 694 average time/residue: 0.1532 time to fit residues: 141.4875 Evaluate side-chains 583 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 580 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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: 1.9990 chunk 129 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 138 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 18 optimal weight: 0.1980 chunk 114 optimal weight: 0.8980 chunk 20 optimal weight: 0.0770 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 198 GLN ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.130021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104008 restraints weight = 33373.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.107524 restraints weight = 24723.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.110272 restraints weight = 19223.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.112486 restraints weight = 15516.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114261 restraints weight = 12868.827| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.7636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 12881 Z= 0.194 Angle : 0.855 14.089 17407 Z= 0.456 Chirality : 0.051 0.305 2000 Planarity : 0.006 0.058 2243 Dihedral : 11.793 134.402 1881 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.73 % Favored : 92.52 % Rotamer: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.86 % 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 aren not related in a simple way. whole: -1.17 (0.21), residues: 1590 helix: -0.26 (0.17), residues: 800 sheet: -0.67 (0.42), residues: 146 loop : -1.33 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 278 TYR 0.032 0.002 TYR H 140 PHE 0.045 0.003 PHE L 321 HIS 0.006 0.002 HIS H 324 Details of bonding type rmsd covalent geometry : bond 0.00429 (12881) covalent geometry : angle 0.85549 (17407) hydrogen bonds : bond 0.04488 ( 507) hydrogen bonds : angle 5.58464 ( 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 674 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 673 time to evaluate : 0.323 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: 0.8219 (m-80) cc_final: 0.7937 (m-80) REVERT: H 130 PHE cc_start: 0.9321 (m-10) cc_final: 0.8923 (m-80) REVERT: H 161 LEU cc_start: 0.9474 (tp) cc_final: 0.9178 (tp) REVERT: H 181 TYR cc_start: 0.8706 (t80) cc_final: 0.8410 (t80) REVERT: H 221 ARG cc_start: 0.7916 (ppt170) cc_final: 0.7712 (ppt170) REVERT: H 227 PHE cc_start: 0.9549 (m-80) cc_final: 0.8966 (m-80) REVERT: H 233 LYS cc_start: 0.9259 (tptp) cc_final: 0.9030 (tptp) REVERT: H 239 PHE cc_start: 0.8048 (t80) cc_final: 0.7367 (t80) REVERT: H 263 ARG cc_start: 0.9422 (mtp180) cc_final: 0.9169 (mtp180) REVERT: H 321 PHE cc_start: 0.9557 (m-80) cc_final: 0.9332 (m-80) REVERT: H 361 PHE cc_start: 0.9077 (t80) cc_final: 0.8835 (t80) REVERT: H 372 MET cc_start: 0.8571 (mmm) cc_final: 0.7952 (mmm) REVERT: H 374 ASP cc_start: 0.9410 (m-30) cc_final: 0.8543 (m-30) REVERT: H 377 LYS cc_start: 0.9399 (ptpp) cc_final: 0.8801 (pttp) REVERT: I 127 VAL cc_start: 0.8716 (m) cc_final: 0.8337 (m) REVERT: I 130 PHE cc_start: 0.9027 (m-10) cc_final: 0.8580 (m-80) REVERT: I 163 LYS cc_start: 0.9533 (ttmt) cc_final: 0.9303 (ttmm) REVERT: I 207 VAL cc_start: 0.8112 (t) cc_final: 0.7885 (t) REVERT: I 221 ARG cc_start: 0.9515 (ttp80) cc_final: 0.9133 (ttp80) REVERT: I 224 ARG cc_start: 0.8363 (mtm-85) cc_final: 0.7948 (mpp80) REVERT: I 227 PHE cc_start: 0.8900 (t80) cc_final: 0.8660 (t80) REVERT: I 231 LYS cc_start: 0.9198 (mmmt) cc_final: 0.8901 (mmmt) REVERT: I 260 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8800 (mt-10) REVERT: I 276 ASP cc_start: 0.7730 (m-30) cc_final: 0.7376 (m-30) REVERT: I 294 ASP cc_start: 0.8899 (t0) cc_final: 0.8382 (t0) REVERT: I 303 PHE cc_start: 0.9195 (m-80) cc_final: 0.8922 (m-80) REVERT: I 311 LEU cc_start: 0.8866 (mm) cc_final: 0.8386 (mt) REVERT: I 318 ILE cc_start: 0.9071 (mt) cc_final: 0.8556 (mt) REVERT: I 321 PHE cc_start: 0.8381 (m-10) cc_final: 0.7742 (m-10) REVERT: I 323 ILE cc_start: 0.9576 (mm) cc_final: 0.9076 (tp) REVERT: I 326 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7638 (mtm110) REVERT: I 327 LYS cc_start: 0.9063 (mmpt) cc_final: 0.8724 (mmpt) REVERT: I 351 ILE cc_start: 0.9388 (mt) cc_final: 0.8890 (mt) REVERT: I 357 GLU cc_start: 0.8772 (tp30) cc_final: 0.8478 (tp30) REVERT: I 372 MET cc_start: 0.9496 (mmm) cc_final: 0.8851 (mmm) REVERT: I 375 PHE cc_start: 0.9040 (m-80) cc_final: 0.8313 (m-80) REVERT: K 149 GLN cc_start: 0.9695 (mp-120) cc_final: 0.9402 (mp10) REVERT: K 154 ARG cc_start: 0.9557 (tmt170) cc_final: 0.9216 (tmm160) REVERT: K 162 LEU cc_start: 0.9147 (mt) cc_final: 0.8423 (mt) REVERT: K 189 THR cc_start: 0.9163 (m) cc_final: 0.8547 (m) REVERT: K 190 LEU cc_start: 0.9407 (mt) cc_final: 0.9072 (mt) REVERT: K 193 LYS cc_start: 0.9174 (mtmm) cc_final: 0.8671 (mtmm) REVERT: K 211 PHE cc_start: 0.9224 (m-80) cc_final: 0.8552 (m-80) REVERT: K 221 ARG cc_start: 0.8556 (mmp-170) cc_final: 0.8251 (mmp-170) REVERT: K 222 LEU cc_start: 0.9433 (tp) cc_final: 0.9207 (tp) REVERT: K 224 ARG cc_start: 0.8558 (ttt180) cc_final: 0.8334 (ttt180) REVERT: K 243 LEU cc_start: 0.9248 (mt) cc_final: 0.9042 (mt) REVERT: K 260 GLU cc_start: 0.9160 (tp30) cc_final: 0.8710 (tp30) REVERT: K 266 MET cc_start: 0.8577 (mtm) cc_final: 0.8308 (mtm) REVERT: K 267 GLN cc_start: 0.8649 (tp40) cc_final: 0.7763 (tp40) REVERT: K 287 THR cc_start: 0.9136 (t) cc_final: 0.8726 (m) REVERT: K 308 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8231 (tm-30) REVERT: K 310 PRO cc_start: 0.8428 (Cg_endo) cc_final: 0.7931 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9209 (mt) cc_final: 0.8868 (tt) REVERT: K 318 ILE cc_start: 0.9099 (mt) cc_final: 0.8527 (mt) REVERT: K 319 GLN cc_start: 0.9607 (mt0) cc_final: 0.9262 (mm110) REVERT: K 321 PHE cc_start: 0.8664 (m-80) cc_final: 0.8023 (m-80) REVERT: K 322 LYS cc_start: 0.9229 (mtmm) cc_final: 0.8863 (tptm) REVERT: K 338 GLU cc_start: 0.9189 (tp30) cc_final: 0.8566 (tp30) REVERT: K 341 ARG cc_start: 0.9160 (ttp80) cc_final: 0.8877 (ttp80) REVERT: K 351 ILE cc_start: 0.9269 (mm) cc_final: 0.9024 (mm) REVERT: K 372 MET cc_start: 0.6584 (mmm) cc_final: 0.5337 (mmm) REVERT: K 375 PHE cc_start: 0.9216 (m-80) cc_final: 0.8875 (m-80) REVERT: L 137 GLU cc_start: 0.9261 (pm20) cc_final: 0.8864 (pm20) REVERT: L 165 GLU cc_start: 0.9188 (tp30) cc_final: 0.8729 (tp30) REVERT: L 169 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8786 (mt-10) REVERT: L 202 THR cc_start: 0.8783 (m) cc_final: 0.8413 (p) REVERT: L 204 ILE cc_start: 0.9318 (mm) cc_final: 0.9047 (mm) REVERT: L 206 VAL cc_start: 0.9197 (m) cc_final: 0.8882 (t) REVERT: L 211 PHE cc_start: 0.8822 (m-80) cc_final: 0.8449 (m-80) REVERT: L 222 LEU cc_start: 0.9546 (mt) cc_final: 0.9296 (mt) REVERT: L 225 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8439 (mt-10) REVERT: L 232 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8691 (mm-30) REVERT: L 233 LYS cc_start: 0.8965 (tppt) cc_final: 0.8538 (tppt) REVERT: L 240 ILE cc_start: 0.9284 (tp) cc_final: 0.8887 (tp) REVERT: L 263 ARG cc_start: 0.9129 (ptp90) cc_final: 0.8544 (mtt180) REVERT: L 273 ASP cc_start: 0.9104 (t70) cc_final: 0.8686 (t70) REVERT: L 282 LYS cc_start: 0.8812 (mppt) cc_final: 0.8597 (mmtm) REVERT: L 284 ILE cc_start: 0.9018 (mm) cc_final: 0.8578 (mm) REVERT: L 305 ARG cc_start: 0.9071 (ttm170) cc_final: 0.8552 (ttm170) REVERT: L 308 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8659 (tm-30) REVERT: L 364 ARG cc_start: 0.9138 (mtt90) cc_final: 0.8703 (mtm-85) REVERT: L 365 GLU cc_start: 0.8457 (pt0) cc_final: 0.7319 (mt-10) REVERT: M 140 TYR cc_start: 0.9339 (p90) cc_final: 0.8808 (p90) REVERT: M 179 LEU cc_start: 0.9459 (tp) cc_final: 0.9199 (tp) REVERT: M 210 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8344 (mt-10) REVERT: M 221 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8106 (ptm-80) REVERT: M 264 THR cc_start: 0.9114 (m) cc_final: 0.8795 (p) REVERT: M 306 ILE cc_start: 0.9564 (pt) cc_final: 0.9309 (pt) REVERT: M 307 ILE cc_start: 0.9370 (mp) cc_final: 0.9165 (mt) REVERT: M 310 PRO cc_start: 0.9112 (Cg_endo) cc_final: 0.8753 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9172 (mm) cc_final: 0.8932 (mm) REVERT: M 333 ASP cc_start: 0.9375 (p0) cc_final: 0.9036 (p0) REVERT: M 372 MET cc_start: 0.8941 (tpt) cc_final: 0.7973 (tpt) REVERT: M 375 PHE cc_start: 0.9291 (m-10) cc_final: 0.8893 (m-10) REVERT: J 149 GLN cc_start: 0.9601 (mp10) cc_final: 0.9220 (mp10) REVERT: J 159 LEU cc_start: 0.9252 (tp) cc_final: 0.8927 (tp) REVERT: J 167 PHE cc_start: 0.8548 (m-80) cc_final: 0.8217 (m-80) REVERT: J 172 ILE cc_start: 0.9228 (tp) cc_final: 0.9000 (tp) REVERT: J 214 LYS cc_start: 0.8623 (ptmt) cc_final: 0.8369 (ptmt) REVERT: J 215 TYR cc_start: 0.8557 (m-80) cc_final: 0.7969 (m-80) REVERT: J 224 ARG cc_start: 0.9366 (ptp-110) cc_final: 0.9055 (ptp-110) REVERT: J 228 GLN cc_start: 0.9302 (mt0) cc_final: 0.8915 (mm-40) REVERT: J 307 ILE cc_start: 0.9549 (mp) cc_final: 0.9196 (mp) REVERT: J 327 LYS cc_start: 0.9399 (tmtt) cc_final: 0.9060 (tmtt) REVERT: J 328 MET cc_start: 0.7223 (ppp) cc_final: 0.6618 (ppp) REVERT: J 354 ILE cc_start: 0.9692 (tt) cc_final: 0.9334 (tt) REVERT: J 356 THR cc_start: 0.8742 (m) cc_final: 0.8453 (m) REVERT: J 357 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8535 (pt0) REVERT: J 372 MET cc_start: 0.9027 (mmp) cc_final: 0.8621 (mmm) REVERT: J 375 PHE cc_start: 0.9132 (m-80) cc_final: 0.8895 (m-80) outliers start: 1 outliers final: 0 residues processed: 673 average time/residue: 0.1435 time to fit residues: 129.9054 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 : 0.494 ------------------------------------------------------------------------------- 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: 0.8980 chunk 94 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 53 optimal weight: 0.2980 chunk 145 optimal weight: 0.0670 chunk 101 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 252 ASN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN L 198 GLN ** L 262 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 = 0.3806 r_free = 0.3806 target = 0.133992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.107619 restraints weight = 34203.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.111232 restraints weight = 25265.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.114025 restraints weight = 19611.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.116313 restraints weight = 15814.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118173 restraints weight = 13123.485| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.7954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12881 Z= 0.182 Angle : 0.868 17.208 17407 Z= 0.459 Chirality : 0.051 0.238 2000 Planarity : 0.007 0.108 2243 Dihedral : 11.651 133.974 1881 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 23.15 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.67 % Favored : 92.58 % Rotamer: Outliers : 0.07 % Allowed : 2.47 % Favored : 97.46 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -1.13 (0.21), residues: 1590 helix: -0.28 (0.17), residues: 796 sheet: -0.65 (0.41), residues: 147 loop : -1.23 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG H 249 TYR 0.015 0.001 TYR M 181 PHE 0.036 0.002 PHE M 321 HIS 0.009 0.002 HIS H 324 Details of bonding type rmsd covalent geometry : bond 0.00406 (12881) covalent geometry : angle 0.86758 (17407) hydrogen bonds : bond 0.04416 ( 507) hydrogen bonds : angle 5.49105 ( 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 657 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 656 time to evaluate : 0.491 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: H 128 TYR cc_start: 0.8194 (m-80) cc_final: 0.7727 (m-80) REVERT: H 172 ILE cc_start: 0.8504 (pt) cc_final: 0.8163 (pt) REVERT: H 227 PHE cc_start: 0.9241 (m-80) cc_final: 0.8967 (m-80) REVERT: H 233 LYS cc_start: 0.9392 (tptp) cc_final: 0.9066 (tptp) REVERT: H 237 ILE cc_start: 0.7322 (tp) cc_final: 0.6403 (mp) REVERT: H 239 PHE cc_start: 0.8057 (t80) cc_final: 0.7651 (t80) REVERT: H 262 GLN cc_start: 0.8841 (pm20) cc_final: 0.8517 (pm20) REVERT: H 290 ILE cc_start: 0.9324 (tp) cc_final: 0.9070 (tp) REVERT: H 306 ILE cc_start: 0.9354 (tp) cc_final: 0.9132 (tp) REVERT: H 372 MET cc_start: 0.8844 (mmm) cc_final: 0.8230 (mmm) REVERT: H 374 ASP cc_start: 0.9444 (m-30) cc_final: 0.9206 (m-30) REVERT: H 377 LYS cc_start: 0.9295 (ptpp) cc_final: 0.8991 (pttp) REVERT: I 127 VAL cc_start: 0.8659 (m) cc_final: 0.8331 (m) REVERT: I 130 PHE cc_start: 0.9042 (m-10) cc_final: 0.8595 (m-80) REVERT: I 151 GLU cc_start: 0.9281 (pm20) cc_final: 0.8654 (pm20) REVERT: I 154 ARG cc_start: 0.9358 (ptm160) cc_final: 0.8517 (tmm-80) REVERT: I 163 LYS cc_start: 0.9502 (ttmt) cc_final: 0.9092 (ttmm) REVERT: I 207 VAL cc_start: 0.8252 (t) cc_final: 0.7966 (t) REVERT: I 221 ARG cc_start: 0.9573 (ttp80) cc_final: 0.9208 (ttp80) REVERT: I 227 PHE cc_start: 0.8866 (t80) cc_final: 0.8545 (t80) REVERT: I 229 LEU cc_start: 0.9432 (tp) cc_final: 0.9193 (tp) REVERT: I 260 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8796 (mt-10) REVERT: I 276 ASP cc_start: 0.7728 (m-30) cc_final: 0.7358 (m-30) REVERT: I 294 ASP cc_start: 0.9008 (t0) cc_final: 0.8656 (t0) REVERT: I 303 PHE cc_start: 0.9251 (m-80) cc_final: 0.8982 (m-80) REVERT: I 315 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8480 (tm-30) REVERT: I 318 ILE cc_start: 0.9115 (mt) cc_final: 0.8586 (mt) REVERT: I 321 PHE cc_start: 0.8378 (m-10) cc_final: 0.7800 (m-10) REVERT: I 323 ILE cc_start: 0.9544 (mm) cc_final: 0.9039 (tp) REVERT: I 326 ARG cc_start: 0.8253 (mtm110) cc_final: 0.7587 (mtm110) REVERT: I 327 LYS cc_start: 0.9040 (mmpt) cc_final: 0.8715 (mmpt) REVERT: I 351 ILE cc_start: 0.9305 (mt) cc_final: 0.8830 (mt) REVERT: I 357 GLU cc_start: 0.9065 (tp30) cc_final: 0.8542 (tp30) REVERT: I 360 MET cc_start: 0.9495 (mtm) cc_final: 0.9197 (mtm) REVERT: I 372 MET cc_start: 0.9519 (mmm) cc_final: 0.8855 (mmm) REVERT: I 375 PHE cc_start: 0.9060 (m-80) cc_final: 0.8394 (m-80) REVERT: K 149 GLN cc_start: 0.9731 (mp-120) cc_final: 0.9419 (mp10) REVERT: K 151 GLU cc_start: 0.9613 (mt-10) cc_final: 0.9349 (tp30) REVERT: K 152 GLU cc_start: 0.9736 (mp0) cc_final: 0.9448 (mp0) REVERT: K 154 ARG cc_start: 0.9560 (tmt170) cc_final: 0.8843 (tmm160) REVERT: K 159 LEU cc_start: 0.9356 (mm) cc_final: 0.8523 (mm) REVERT: K 189 THR cc_start: 0.9207 (m) cc_final: 0.8637 (p) REVERT: K 190 LEU cc_start: 0.9414 (mt) cc_final: 0.9027 (mt) REVERT: K 193 LYS cc_start: 0.9190 (mtmm) cc_final: 0.8722 (mtmm) REVERT: K 211 PHE cc_start: 0.9337 (m-80) cc_final: 0.8758 (m-80) REVERT: K 222 LEU cc_start: 0.9436 (tp) cc_final: 0.9173 (tp) REVERT: K 259 ARG cc_start: 0.8917 (tpp80) cc_final: 0.8704 (mmm160) REVERT: K 260 GLU cc_start: 0.9267 (tp30) cc_final: 0.8639 (tp30) REVERT: K 262 GLN cc_start: 0.7188 (OUTLIER) cc_final: 0.6336 (mt0) REVERT: K 263 ARG cc_start: 0.9239 (ttm110) cc_final: 0.8552 (mtm-85) REVERT: K 266 MET cc_start: 0.8607 (mtm) cc_final: 0.8294 (mtm) REVERT: K 287 THR cc_start: 0.9110 (t) cc_final: 0.8884 (m) REVERT: K 310 PRO cc_start: 0.8525 (Cg_endo) cc_final: 0.8291 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9226 (mt) cc_final: 0.8932 (tt) REVERT: K 318 ILE cc_start: 0.9113 (mt) cc_final: 0.8516 (mm) REVERT: K 319 GLN cc_start: 0.9619 (mt0) cc_final: 0.9275 (mm-40) REVERT: K 321 PHE cc_start: 0.8781 (m-80) cc_final: 0.8029 (m-80) REVERT: K 322 LYS cc_start: 0.9215 (mtmm) cc_final: 0.8829 (tptm) REVERT: K 351 ILE cc_start: 0.9308 (mm) cc_final: 0.9089 (mm) REVERT: K 372 MET cc_start: 0.6931 (mmm) cc_final: 0.5634 (mmm) REVERT: K 375 PHE cc_start: 0.9313 (m-80) cc_final: 0.8921 (m-80) REVERT: L 137 GLU cc_start: 0.9341 (pm20) cc_final: 0.8914 (pm20) REVERT: L 165 GLU cc_start: 0.9220 (tp30) cc_final: 0.8731 (tp30) REVERT: L 169 GLU cc_start: 0.9347 (mt-10) cc_final: 0.8764 (mt-10) REVERT: L 202 THR cc_start: 0.8858 (m) cc_final: 0.8563 (p) REVERT: L 204 ILE cc_start: 0.9358 (mm) cc_final: 0.9094 (mm) REVERT: L 206 VAL cc_start: 0.9299 (m) cc_final: 0.9097 (t) REVERT: L 211 PHE cc_start: 0.8995 (m-80) cc_final: 0.8399 (m-80) REVERT: L 222 LEU cc_start: 0.9534 (mt) cc_final: 0.9282 (mt) REVERT: L 225 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8506 (mt-10) REVERT: L 232 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8741 (mm-30) REVERT: L 233 LYS cc_start: 0.8973 (tppt) cc_final: 0.8441 (tppt) REVERT: L 240 ILE cc_start: 0.9349 (tp) cc_final: 0.9044 (tp) REVERT: L 263 ARG cc_start: 0.9226 (ptp90) cc_final: 0.8908 (mtt180) REVERT: L 273 ASP cc_start: 0.9208 (t70) cc_final: 0.8803 (t70) REVERT: L 284 ILE cc_start: 0.9025 (mm) cc_final: 0.8422 (mm) REVERT: L 308 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8702 (tm-30) REVERT: L 365 GLU cc_start: 0.8435 (pt0) cc_final: 0.7252 (mt-10) REVERT: M 140 TYR cc_start: 0.9339 (p90) cc_final: 0.8782 (p90) REVERT: M 179 LEU cc_start: 0.9353 (tp) cc_final: 0.9120 (tp) REVERT: M 221 ARG cc_start: 0.8850 (ttp-110) cc_final: 0.8366 (ptm160) REVERT: M 224 ARG cc_start: 0.9346 (tmt-80) cc_final: 0.8972 (tmt-80) REVERT: M 229 LEU cc_start: 0.9383 (mt) cc_final: 0.9179 (mt) REVERT: M 264 THR cc_start: 0.9057 (m) cc_final: 0.8833 (m) REVERT: M 265 MET cc_start: 0.8571 (mtt) cc_final: 0.8351 (mtp) REVERT: M 303 PHE cc_start: 0.8764 (m-80) cc_final: 0.8558 (m-80) REVERT: M 307 ILE cc_start: 0.9449 (mp) cc_final: 0.9221 (mt) REVERT: M 310 PRO cc_start: 0.9082 (Cg_endo) cc_final: 0.8734 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9162 (mm) cc_final: 0.8901 (mm) REVERT: M 321 PHE cc_start: 0.9064 (m-80) cc_final: 0.8856 (m-80) REVERT: M 333 ASP cc_start: 0.9352 (p0) cc_final: 0.8939 (p0) REVERT: M 361 PHE cc_start: 0.8979 (m-80) cc_final: 0.8254 (m-80) REVERT: M 372 MET cc_start: 0.9036 (tpt) cc_final: 0.7902 (tpt) REVERT: M 375 PHE cc_start: 0.9297 (m-10) cc_final: 0.8953 (m-10) REVERT: M 376 THR cc_start: 0.9435 (p) cc_final: 0.9170 (p) REVERT: J 149 GLN cc_start: 0.9579 (mp10) cc_final: 0.9219 (mp10) REVERT: J 153 ILE cc_start: 0.9285 (mt) cc_final: 0.9085 (mt) REVERT: J 186 THR cc_start: 0.9639 (p) cc_final: 0.9313 (p) REVERT: J 215 TYR cc_start: 0.8589 (m-80) cc_final: 0.8004 (m-80) REVERT: J 224 ARG cc_start: 0.9358 (ptp-110) cc_final: 0.9004 (ptp-110) REVERT: J 228 GLN cc_start: 0.9287 (mt0) cc_final: 0.8909 (mm-40) REVERT: J 262 GLN cc_start: 0.8754 (tt0) cc_final: 0.7346 (tt0) REVERT: J 305 ARG cc_start: 0.7914 (tpt-90) cc_final: 0.7532 (mmm-85) REVERT: J 319 GLN cc_start: 0.9156 (mm110) cc_final: 0.8887 (mt0) REVERT: J 328 MET cc_start: 0.7367 (ppp) cc_final: 0.7074 (ppp) REVERT: J 354 ILE cc_start: 0.9630 (tt) cc_final: 0.9122 (tt) REVERT: J 356 THR cc_start: 0.8713 (m) cc_final: 0.8465 (m) REVERT: J 357 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8403 (pt0) REVERT: J 372 MET cc_start: 0.9035 (mmm) cc_final: 0.8710 (mmm) REVERT: J 375 PHE cc_start: 0.9156 (m-80) cc_final: 0.8892 (m-80) outliers start: 1 outliers final: 0 residues processed: 657 average time/residue: 0.1431 time to fit residues: 127.6908 Evaluate side-chains 567 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 566 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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: 6.9990 chunk 95 optimal weight: 0.0870 chunk 145 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 98 optimal weight: 0.0870 chunk 43 optimal weight: 0.8980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 197 ASN ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 198 GLN L 262 GLN ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 262 GLN ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.107357 restraints weight = 33680.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.110632 restraints weight = 25174.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113590 restraints weight = 19969.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116000 restraints weight = 16166.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.117860 restraints weight = 13385.794| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.8174 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= 0.170 Angle : 0.839 16.201 17407 Z= 0.447 Chirality : 0.051 0.289 2000 Planarity : 0.006 0.053 2243 Dihedral : 11.428 132.360 1881 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 20.74 Ramachandran Plot: Outliers : 0.75 % Allowed : 6.60 % Favored : 92.64 % Rotamer: Outliers : 0.15 % Allowed : 1.79 % Favored : 98.06 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -1.05 (0.21), residues: 1590 helix: -0.17 (0.18), residues: 797 sheet: -0.51 (0.41), residues: 155 loop : -1.30 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 341 TYR 0.014 0.002 TYR M 140 PHE 0.045 0.002 PHE K 361 HIS 0.019 0.004 HIS J 324 Details of bonding type rmsd covalent geometry : bond 0.00373 (12881) covalent geometry : angle 0.83907 (17407) hydrogen bonds : bond 0.04233 ( 507) hydrogen bonds : angle 5.37291 ( 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 651 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 649 time to evaluate : 0.450 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: H 128 TYR cc_start: 0.8150 (m-80) cc_final: 0.7613 (m-80) REVERT: H 172 ILE cc_start: 0.8391 (pt) cc_final: 0.7974 (pt) REVERT: H 181 TYR cc_start: 0.8749 (t80) cc_final: 0.8368 (t80) REVERT: H 221 ARG cc_start: 0.7932 (ppt170) cc_final: 0.7638 (ppt170) REVERT: H 227 PHE cc_start: 0.9527 (m-80) cc_final: 0.8991 (m-80) REVERT: H 250 ARG cc_start: 0.8105 (ptt-90) cc_final: 0.7833 (ptt-90) REVERT: H 260 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9116 (mp0) REVERT: H 262 GLN cc_start: 0.8992 (pm20) cc_final: 0.8669 (pm20) REVERT: H 263 ARG cc_start: 0.9314 (mtp180) cc_final: 0.9034 (mtm-85) REVERT: H 265 MET cc_start: 0.9487 (tmm) cc_final: 0.9267 (tmm) REVERT: H 276 ASP cc_start: 0.8482 (m-30) cc_final: 0.8039 (m-30) REVERT: H 290 ILE cc_start: 0.9303 (tp) cc_final: 0.8929 (tp) REVERT: H 328 MET cc_start: 0.8331 (ptp) cc_final: 0.8107 (ptt) REVERT: H 372 MET cc_start: 0.8846 (mmm) cc_final: 0.8249 (mmm) REVERT: I 127 VAL cc_start: 0.8710 (m) cc_final: 0.8371 (m) REVERT: I 130 PHE cc_start: 0.9025 (m-10) cc_final: 0.8550 (m-80) REVERT: I 151 GLU cc_start: 0.9296 (pm20) cc_final: 0.8633 (pm20) REVERT: I 154 ARG cc_start: 0.9310 (ptm160) cc_final: 0.8508 (tmm-80) REVERT: I 207 VAL cc_start: 0.8289 (t) cc_final: 0.8059 (t) REVERT: I 221 ARG cc_start: 0.9521 (ttp80) cc_final: 0.9097 (ttp80) REVERT: I 224 ARG cc_start: 0.8350 (mtm-85) cc_final: 0.8003 (mpp80) REVERT: I 229 LEU cc_start: 0.9495 (tp) cc_final: 0.9241 (tp) REVERT: I 260 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8636 (mt-10) REVERT: I 276 ASP cc_start: 0.7355 (m-30) cc_final: 0.6990 (m-30) REVERT: I 284 ILE cc_start: 0.9674 (mt) cc_final: 0.9468 (mt) REVERT: I 294 ASP cc_start: 0.9122 (t0) cc_final: 0.8700 (t0) REVERT: I 303 PHE cc_start: 0.9268 (m-80) cc_final: 0.9029 (m-80) REVERT: I 318 ILE cc_start: 0.9119 (mt) cc_final: 0.8635 (mt) REVERT: I 321 PHE cc_start: 0.8367 (m-10) cc_final: 0.7748 (m-10) REVERT: I 323 ILE cc_start: 0.9546 (mm) cc_final: 0.8957 (tp) REVERT: I 326 ARG cc_start: 0.8166 (mtm110) cc_final: 0.7678 (mtm110) REVERT: I 327 LYS cc_start: 0.8983 (mmpt) cc_final: 0.8657 (mmpt) REVERT: I 351 ILE cc_start: 0.9282 (mt) cc_final: 0.8823 (mt) REVERT: I 357 GLU cc_start: 0.9154 (tp30) cc_final: 0.8495 (tp30) REVERT: I 360 MET cc_start: 0.9390 (mtm) cc_final: 0.9140 (mtm) REVERT: I 372 MET cc_start: 0.9469 (mmm) cc_final: 0.8754 (mmm) REVERT: I 375 PHE cc_start: 0.9030 (m-80) cc_final: 0.8348 (m-80) REVERT: K 131 GLU cc_start: 0.8467 (pp20) cc_final: 0.8238 (pp20) REVERT: K 149 GLN cc_start: 0.9724 (mp-120) cc_final: 0.9397 (mp10) REVERT: K 151 GLU cc_start: 0.9573 (mt-10) cc_final: 0.9359 (tp30) REVERT: K 158 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8493 (tm-30) REVERT: K 159 LEU cc_start: 0.9421 (mm) cc_final: 0.9010 (mm) REVERT: K 167 PHE cc_start: 0.7549 (m-80) cc_final: 0.7305 (m-80) REVERT: K 172 ILE cc_start: 0.6993 (mp) cc_final: 0.6639 (tt) REVERT: K 189 THR cc_start: 0.9232 (m) cc_final: 0.8667 (p) REVERT: K 190 LEU cc_start: 0.9430 (mt) cc_final: 0.9065 (mt) REVERT: K 193 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8739 (mtmm) REVERT: K 211 PHE cc_start: 0.9273 (m-80) cc_final: 0.8566 (m-80) REVERT: K 222 LEU cc_start: 0.9471 (tp) cc_final: 0.9182 (tp) REVERT: K 259 ARG cc_start: 0.8871 (tpp80) cc_final: 0.8488 (mmm160) REVERT: K 260 GLU cc_start: 0.9388 (tp30) cc_final: 0.8788 (tp30) REVERT: K 263 ARG cc_start: 0.9218 (ttm110) cc_final: 0.8851 (mtm-85) REVERT: K 287 THR cc_start: 0.9081 (t) cc_final: 0.8778 (m) REVERT: K 310 PRO cc_start: 0.8482 (Cg_endo) cc_final: 0.8253 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9204 (mt) cc_final: 0.8887 (tt) REVERT: K 319 GLN cc_start: 0.9568 (mt0) cc_final: 0.9144 (mt0) REVERT: K 321 PHE cc_start: 0.8851 (m-80) cc_final: 0.8237 (m-80) REVERT: K 351 ILE cc_start: 0.9335 (mm) cc_final: 0.9120 (mm) REVERT: K 372 MET cc_start: 0.7310 (mmm) cc_final: 0.6164 (mmm) REVERT: K 375 PHE cc_start: 0.9223 (m-80) cc_final: 0.8880 (m-80) REVERT: L 137 GLU cc_start: 0.9303 (pm20) cc_final: 0.8876 (pm20) REVERT: L 165 GLU cc_start: 0.9178 (tp30) cc_final: 0.8873 (tp30) REVERT: L 202 THR cc_start: 0.8844 (m) cc_final: 0.8628 (p) REVERT: L 204 ILE cc_start: 0.9397 (mm) cc_final: 0.9083 (mm) REVERT: L 211 PHE cc_start: 0.8976 (m-80) cc_final: 0.8305 (m-80) REVERT: L 222 LEU cc_start: 0.9578 (mt) cc_final: 0.9285 (mt) REVERT: L 225 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8422 (mt-10) REVERT: L 232 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8862 (mm-30) REVERT: L 233 LYS cc_start: 0.9099 (tppt) cc_final: 0.8556 (tppt) REVERT: L 240 ILE cc_start: 0.9329 (tp) cc_final: 0.8932 (tp) REVERT: L 265 MET cc_start: 0.9187 (tmm) cc_final: 0.8944 (tmm) REVERT: L 273 ASP cc_start: 0.9032 (t70) cc_final: 0.8659 (t70) REVERT: L 284 ILE cc_start: 0.8920 (mm) cc_final: 0.8446 (mm) REVERT: L 321 PHE cc_start: 0.9167 (m-80) cc_final: 0.8896 (m-80) REVERT: L 365 GLU cc_start: 0.8419 (pt0) cc_final: 0.7186 (mt-10) REVERT: M 140 TYR cc_start: 0.9218 (p90) cc_final: 0.8626 (p90) REVERT: M 221 ARG cc_start: 0.8786 (ttp-110) cc_final: 0.8332 (ptm160) REVERT: M 224 ARG cc_start: 0.9278 (tmt-80) cc_final: 0.8899 (tmt-80) REVERT: M 239 PHE cc_start: 0.9200 (t80) cc_final: 0.8707 (t80) REVERT: M 240 ILE cc_start: 0.9463 (mp) cc_final: 0.9238 (mp) REVERT: M 246 ILE cc_start: 0.8661 (tt) cc_final: 0.8428 (tt) REVERT: M 263 ARG cc_start: 0.9258 (tpp80) cc_final: 0.9023 (mmm160) REVERT: M 307 ILE cc_start: 0.9491 (mp) cc_final: 0.9072 (tt) REVERT: M 310 PRO cc_start: 0.9044 (Cg_endo) cc_final: 0.8703 (Cg_exo) REVERT: M 318 ILE cc_start: 0.9130 (mm) cc_final: 0.8880 (mm) REVERT: M 321 PHE cc_start: 0.9112 (m-80) cc_final: 0.8835 (m-80) REVERT: M 333 ASP cc_start: 0.9280 (p0) cc_final: 0.8860 (p0) REVERT: M 370 VAL cc_start: 0.8655 (t) cc_final: 0.7903 (t) REVERT: M 371 THR cc_start: 0.7689 (p) cc_final: 0.7152 (p) REVERT: M 372 MET cc_start: 0.9014 (tpt) cc_final: 0.8083 (tpt) REVERT: M 375 PHE cc_start: 0.9262 (m-10) cc_final: 0.9006 (m-10) REVERT: M 376 THR cc_start: 0.9519 (p) cc_final: 0.9291 (p) REVERT: J 149 GLN cc_start: 0.9529 (mp10) cc_final: 0.9174 (mp10) REVERT: J 159 LEU cc_start: 0.9658 (tp) cc_final: 0.9364 (tp) REVERT: J 172 ILE cc_start: 0.9145 (tp) cc_final: 0.8773 (tp) REVERT: J 214 LYS cc_start: 0.8580 (ptmt) cc_final: 0.8316 (ptmt) REVERT: J 215 TYR cc_start: 0.8517 (m-80) cc_final: 0.7922 (m-80) REVERT: J 228 GLN cc_start: 0.9287 (mt0) cc_final: 0.8956 (mm-40) REVERT: J 305 ARG cc_start: 0.7769 (tpt-90) cc_final: 0.7484 (mmm-85) REVERT: J 328 MET cc_start: 0.7265 (ppp) cc_final: 0.6869 (ppp) REVERT: J 335 ASP cc_start: 0.8759 (t70) cc_final: 0.8268 (t0) REVERT: J 338 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8437 (mm-30) REVERT: J 372 MET cc_start: 0.9158 (mmm) cc_final: 0.8827 (mmm) REVERT: J 375 PHE cc_start: 0.9115 (m-80) cc_final: 0.8830 (m-80) outliers start: 2 outliers final: 0 residues processed: 650 average time/residue: 0.1375 time to fit residues: 121.2213 Evaluate side-chains 553 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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: 0.7980 chunk 149 optimal weight: 0.5980 chunk 137 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 60 optimal weight: 0.2980 chunk 113 optimal weight: 0.0970 chunk 64 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 18 optimal weight: 0.2980 chunk 71 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 267 GLN K 262 GLN L 198 GLN L 262 GLN ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.131988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.105120 restraints weight = 34132.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.108659 restraints weight = 25650.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.111437 restraints weight = 20114.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.113731 restraints weight = 16341.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115645 restraints weight = 13612.043| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.8340 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= 0.177 Angle : 0.854 17.120 17407 Z= 0.457 Chirality : 0.050 0.270 2000 Planarity : 0.006 0.069 2243 Dihedral : 11.233 130.593 1881 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 22.06 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.42 % Favored : 91.89 % Rotamer: Outliers : 0.15 % Allowed : 1.57 % Favored : 98.28 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -0.97 (0.21), residues: 1590 helix: -0.14 (0.18), residues: 796 sheet: -0.38 (0.44), residues: 138 loop : -1.22 (0.27), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 341 TYR 0.014 0.001 TYR H 140 PHE 0.058 0.003 PHE K 361 HIS 0.023 0.004 HIS J 324 Details of bonding type rmsd covalent geometry : bond 0.00391 (12881) covalent geometry : angle 0.85385 (17407) hydrogen bonds : bond 0.04399 ( 507) hydrogen bonds : angle 5.44318 ( 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 644 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 642 time to evaluate : 0.495 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: H 128 TYR cc_start: 0.8120 (m-80) cc_final: 0.7863 (m-80) REVERT: H 130 PHE cc_start: 0.9007 (m-10) cc_final: 0.8634 (m-80) REVERT: H 172 ILE cc_start: 0.8351 (pt) cc_final: 0.8019 (pt) REVERT: H 181 TYR cc_start: 0.8618 (t80) cc_final: 0.8302 (t80) REVERT: H 207 VAL cc_start: 0.7732 (t) cc_final: 0.7458 (t) REVERT: H 221 ARG cc_start: 0.7941 (ppt170) cc_final: 0.7645 (ppt170) REVERT: H 227 PHE cc_start: 0.9471 (m-80) cc_final: 0.8923 (m-80) REVERT: H 228 GLN cc_start: 0.8757 (pp30) cc_final: 0.8415 (pp30) REVERT: H 233 LYS cc_start: 0.9388 (tptp) cc_final: 0.9058 (tptp) REVERT: H 249 ARG cc_start: 0.8654 (mpt180) cc_final: 0.8243 (mpt180) REVERT: H 260 GLU cc_start: 0.9344 (mm-30) cc_final: 0.9094 (mp0) REVERT: H 265 MET cc_start: 0.9432 (tmm) cc_final: 0.9225 (tmm) REVERT: H 276 ASP cc_start: 0.8459 (m-30) cc_final: 0.7994 (m-30) REVERT: H 290 ILE cc_start: 0.9218 (tp) cc_final: 0.8954 (tp) REVERT: H 293 LEU cc_start: 0.7327 (pt) cc_final: 0.6268 (pt) REVERT: H 306 ILE cc_start: 0.9317 (tp) cc_final: 0.9053 (tp) REVERT: H 328 MET cc_start: 0.8058 (ptp) cc_final: 0.7840 (ptp) REVERT: H 372 MET cc_start: 0.8810 (mmm) cc_final: 0.8260 (mmm) REVERT: I 127 VAL cc_start: 0.8768 (m) cc_final: 0.8426 (m) REVERT: I 130 PHE cc_start: 0.9025 (m-10) cc_final: 0.8567 (m-80) REVERT: I 154 ARG cc_start: 0.9383 (ptm160) cc_final: 0.8525 (tmm-80) REVERT: I 207 VAL cc_start: 0.8405 (t) cc_final: 0.8053 (t) REVERT: I 218 GLU cc_start: 0.7563 (tt0) cc_final: 0.7105 (tt0) REVERT: I 221 ARG cc_start: 0.9517 (ttp80) cc_final: 0.8911 (ttp80) REVERT: I 222 LEU cc_start: 0.9612 (mt) cc_final: 0.9234 (mt) REVERT: I 224 ARG cc_start: 0.8288 (mtm-85) cc_final: 0.7862 (mpp80) REVERT: I 229 LEU cc_start: 0.9472 (tp) cc_final: 0.9242 (tp) REVERT: I 237 ILE cc_start: 0.9650 (mp) cc_final: 0.9419 (mp) REVERT: I 276 ASP cc_start: 0.7331 (m-30) cc_final: 0.6985 (m-30) REVERT: I 294 ASP cc_start: 0.9121 (t0) cc_final: 0.8639 (t0) REVERT: I 303 PHE cc_start: 0.9235 (m-80) cc_final: 0.9008 (m-80) REVERT: I 318 ILE cc_start: 0.9107 (mt) cc_final: 0.8651 (mt) REVERT: I 321 PHE cc_start: 0.8335 (m-10) cc_final: 0.7766 (m-10) REVERT: I 322 LYS cc_start: 0.9637 (mmtm) cc_final: 0.9183 (mmmm) REVERT: I 323 ILE cc_start: 0.9557 (mm) cc_final: 0.9087 (tp) REVERT: I 326 ARG cc_start: 0.8189 (mtm110) cc_final: 0.7607 (mtm110) REVERT: I 327 LYS cc_start: 0.9033 (mmpt) cc_final: 0.8633 (mmpt) REVERT: I 351 ILE cc_start: 0.9275 (mt) cc_final: 0.8803 (mt) REVERT: I 357 GLU cc_start: 0.9052 (tp30) cc_final: 0.8707 (tp30) REVERT: I 360 MET cc_start: 0.9394 (mtm) cc_final: 0.9021 (mtm) REVERT: I 372 MET cc_start: 0.9406 (mmm) cc_final: 0.8754 (mmm) REVERT: I 373 LEU cc_start: 0.9707 (tt) cc_final: 0.8905 (tt) REVERT: I 374 ASP cc_start: 0.9203 (m-30) cc_final: 0.8969 (m-30) REVERT: I 375 PHE cc_start: 0.8929 (m-80) cc_final: 0.8290 (m-80) REVERT: K 131 GLU cc_start: 0.8357 (pp20) cc_final: 0.8112 (tt0) REVERT: K 149 GLN cc_start: 0.9705 (mp-120) cc_final: 0.9361 (mp10) REVERT: K 151 GLU cc_start: 0.9526 (mt-10) cc_final: 0.9235 (tp30) REVERT: K 159 LEU cc_start: 0.9399 (mm) cc_final: 0.9063 (mm) REVERT: K 165 GLU cc_start: 0.9269 (pm20) cc_final: 0.8988 (pm20) REVERT: K 189 THR cc_start: 0.9213 (m) cc_final: 0.8661 (p) REVERT: K 190 LEU cc_start: 0.9466 (mt) cc_final: 0.9066 (mt) REVERT: K 193 LYS cc_start: 0.9247 (mtmm) cc_final: 0.8766 (mtmm) REVERT: K 211 PHE cc_start: 0.9289 (m-80) cc_final: 0.8599 (m-80) REVERT: K 222 LEU cc_start: 0.9499 (tp) cc_final: 0.9218 (tp) REVERT: K 259 ARG cc_start: 0.8793 (tpp80) cc_final: 0.8431 (mmm160) REVERT: K 287 THR cc_start: 0.9149 (t) cc_final: 0.8858 (m) REVERT: K 290 ILE cc_start: 0.9353 (pt) cc_final: 0.9138 (tp) REVERT: K 310 PRO cc_start: 0.8475 (Cg_endo) cc_final: 0.8231 (Cg_exo) REVERT: K 311 LEU cc_start: 0.9182 (mt) cc_final: 0.8847 (tt) REVERT: K 315 GLU cc_start: 0.9109 (pm20) cc_final: 0.8644 (mp0) REVERT: K 319 GLN cc_start: 0.9558 (mt0) cc_final: 0.9268 (mt0) REVERT: K 321 PHE cc_start: 0.9029 (m-80) cc_final: 0.8386 (m-80) REVERT: K 337 LYS cc_start: 0.9489 (pptt) cc_final: 0.9116 (pptt) REVERT: K 357 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8385 (tm-30) REVERT: K 372 MET cc_start: 0.7336 (mmm) cc_final: 0.6035 (mmm) REVERT: K 375 PHE cc_start: 0.9136 (m-80) cc_final: 0.8837 (m-80) REVERT: L 137 GLU cc_start: 0.9215 (pm20) cc_final: 0.8636 (pm20) REVERT: L 165 GLU cc_start: 0.9171 (tp30) cc_final: 0.8834 (tp30) REVERT: L 202 THR cc_start: 0.8831 (m) cc_final: 0.8573 (p) REVERT: L 204 ILE cc_start: 0.9412 (mm) cc_final: 0.9109 (mm) REVERT: L 206 VAL cc_start: 0.9241 (t) cc_final: 0.9029 (t) REVERT: L 222 LEU cc_start: 0.9573 (mt) cc_final: 0.9276 (mt) REVERT: L 225 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8439 (mt-10) REVERT: L 232 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8879 (mm-30) REVERT: L 233 LYS cc_start: 0.9124 (tppt) cc_final: 0.8612 (tppt) REVERT: L 240 ILE cc_start: 0.9220 (tp) cc_final: 0.8853 (tp) REVERT: L 273 ASP cc_start: 0.9183 (t70) cc_final: 0.8855 (t70) REVERT: L 284 ILE cc_start: 0.9060 (mm) cc_final: 0.8425 (mm) REVERT: L 321 PHE cc_start: 0.9181 (m-80) cc_final: 0.8971 (m-10) REVERT: L 365 GLU cc_start: 0.8325 (pt0) cc_final: 0.7002 (mt-10) REVERT: M 140 TYR cc_start: 0.9232 (p90) cc_final: 0.8691 (p90) REVERT: M 154 ARG cc_start: 0.9308 (ptm160) cc_final: 0.9028 (ptt180) REVERT: M 179 LEU cc_start: 0.9458 (tp) cc_final: 0.9233 (tp) REVERT: M 210 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8859 (mt-10) REVERT: M 221 ARG cc_start: 0.8762 (ttp-110) cc_final: 0.8315 (ptm160) REVERT: M 224 ARG cc_start: 0.9301 (tmt-80) cc_final: 0.8907 (tmt-80) REVERT: M 306 ILE cc_start: 0.9582 (pt) cc_final: 0.9283 (pt) REVERT: M 307 ILE cc_start: 0.9545 (mp) cc_final: 0.9018 (tt) REVERT: M 310 PRO cc_start: 0.9018 (Cg_endo) cc_final: 0.8650 (Cg_exo) REVERT: M 318 ILE cc_start: 0.8986 (mm) cc_final: 0.8733 (mm) REVERT: M 333 ASP cc_start: 0.9228 (p0) cc_final: 0.8749 (p0) REVERT: M 361 PHE cc_start: 0.8851 (m-80) cc_final: 0.8313 (m-80) REVERT: M 370 VAL cc_start: 0.8401 (t) cc_final: 0.8078 (t) REVERT: M 371 THR cc_start: 0.7811 (p) cc_final: 0.7323 (p) REVERT: M 372 MET cc_start: 0.9008 (tpt) cc_final: 0.8319 (tpt) REVERT: M 375 PHE cc_start: 0.9214 (m-10) cc_final: 0.8967 (m-10) REVERT: M 376 THR cc_start: 0.9389 (p) cc_final: 0.9106 (p) REVERT: J 149 GLN cc_start: 0.9496 (mp10) cc_final: 0.8996 (mp10) REVERT: J 153 ILE cc_start: 0.9214 (mt) cc_final: 0.9006 (mt) REVERT: J 159 LEU cc_start: 0.9614 (tp) cc_final: 0.9354 (tp) REVERT: J 167 PHE cc_start: 0.8448 (m-80) cc_final: 0.7897 (m-80) REVERT: J 214 LYS cc_start: 0.8559 (ptmt) cc_final: 0.8238 (ptmt) REVERT: J 215 TYR cc_start: 0.8612 (m-80) cc_final: 0.7964 (m-80) REVERT: J 224 ARG cc_start: 0.9310 (ptp-110) cc_final: 0.8600 (ptp-170) REVERT: J 228 GLN cc_start: 0.9270 (mt0) cc_final: 0.8982 (mm-40) REVERT: J 262 GLN cc_start: 0.8927 (tt0) cc_final: 0.8644 (tt0) REVERT: J 275 PHE cc_start: 0.7983 (t80) cc_final: 0.7774 (t80) REVERT: J 319 GLN cc_start: 0.9431 (mm110) cc_final: 0.8866 (mt0) REVERT: J 328 MET cc_start: 0.7281 (ppp) cc_final: 0.6944 (ppp) REVERT: J 365 GLU cc_start: 0.8754 (pt0) cc_final: 0.8516 (tp30) REVERT: J 372 MET cc_start: 0.9043 (mmm) cc_final: 0.8706 (mmm) REVERT: J 375 PHE cc_start: 0.9047 (m-80) cc_final: 0.8826 (m-80) outliers start: 2 outliers final: 1 residues processed: 644 average time/residue: 0.1387 time to fit residues: 122.1703 Evaluate side-chains 559 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 558 time to evaluate : 0.636 ------------------------------------------------------------------------------- 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: 0.3980 chunk 150 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 0.3980 chunk 134 optimal weight: 0.0870 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 124 optimal weight: 0.0770 chunk 90 optimal weight: 0.4980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 262 GLN ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 197 ASN ** J 324 HIS ** 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 = 0.3817 r_free = 0.3817 target = 0.133141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.105956 restraints weight = 33650.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109340 restraints weight = 25148.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112073 restraints weight = 19876.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.114308 restraints weight = 16238.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116162 restraints weight = 13626.252| |-----------------------------------------------------------------------------| r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.8495 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= 0.174 Angle : 0.885 17.133 17407 Z= 0.470 Chirality : 0.051 0.276 2000 Planarity : 0.007 0.127 2243 Dihedral : 11.073 129.394 1881 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 21.75 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.23 % Favored : 92.08 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.13 % 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 aren not related in a simple way. whole: -1.03 (0.21), residues: 1590 helix: -0.22 (0.18), residues: 796 sheet: -0.53 (0.45), residues: 133 loop : -1.17 (0.27), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 341 TYR 0.025 0.001 TYR M 181 PHE 0.044 0.002 PHE K 361 HIS 0.022 0.003 HIS J 324 Details of bonding type rmsd covalent geometry : bond 0.00384 (12881) covalent geometry : angle 0.88488 (17407) hydrogen bonds : bond 0.04443 ( 507) hydrogen bonds : angle 5.50954 ( 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 637 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 637 time to evaluate : 0.507 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: H 128 TYR cc_start: 0.8119 (m-80) cc_final: 0.7869 (m-80) REVERT: H 130 PHE cc_start: 0.8993 (m-10) cc_final: 0.8646 (m-80) REVERT: H 181 TYR cc_start: 0.8600 (t80) cc_final: 0.8223 (t80) REVERT: H 207 VAL cc_start: 0.7603 (t) cc_final: 0.7356 (t) REVERT: H 227 PHE cc_start: 0.9499 (m-80) cc_final: 0.8920 (m-80) REVERT: H 228 GLN cc_start: 0.8747 (pp30) cc_final: 0.8408 (pp30) REVERT: H 233 LYS cc_start: 0.9385 (tptp) cc_final: 0.9037 (tptp) REVERT: H 265 MET cc_start: 0.9407 (tmm) cc_final: 0.9191 (tmm) REVERT: H 269 LEU cc_start: 0.8985 (mt) cc_final: 0.8781 (mt) REVERT: H 276 ASP cc_start: 0.8449 (m-30) cc_final: 0.8015 (m-30) REVERT: H 290 ILE cc_start: 0.9229 (tp) cc_final: 0.9010 (tp) REVERT: H 306 ILE cc_start: 0.9258 (tp) cc_final: 0.8974 (tp) REVERT: H 326 ARG cc_start: 0.8936 (ppt170) cc_final: 0.8729 (ppt170) REVERT: H 328 MET cc_start: 0.8243 (ptp) cc_final: 0.7953 (ptp) REVERT: H 360 MET cc_start: 0.9357 (ptp) cc_final: 0.9152 (ptp) REVERT: H 372 MET cc_start: 0.8748 (mmm) cc_final: 0.8127 (mmm) REVERT: H 383 LEU cc_start: 0.8759 (tp) cc_final: 0.8556 (tp) REVERT: I 127 VAL cc_start: 0.8751 (m) cc_final: 0.8436 (m) REVERT: I 130 PHE cc_start: 0.8982 (m-10) cc_final: 0.8576 (m-80) REVERT: I 207 VAL cc_start: 0.8523 (t) cc_final: 0.8239 (t) REVERT: I 215 TYR cc_start: 0.7785 (m-10) cc_final: 0.7422 (m-80) REVERT: I 221 ARG cc_start: 0.9512 (ttp80) cc_final: 0.9062 (ttp80) REVERT: I 222 LEU cc_start: 0.9606 (mt) cc_final: 0.9392 (mt) REVERT: I 229 LEU cc_start: 0.9471 (tp) cc_final: 0.9253 (tp) REVERT: I 260 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8530 (mt-10) REVERT: I 294 ASP cc_start: 0.9100 (t0) cc_final: 0.8597 (t0) REVERT: I 303 PHE cc_start: 0.9223 (m-80) cc_final: 0.8991 (m-80) REVERT: I 318 ILE cc_start: 0.9148 (mt) cc_final: 0.8706 (mt) REVERT: I 321 PHE cc_start: 0.8329 (m-10) cc_final: 0.7736 (m-10) REVERT: I 322 LYS cc_start: 0.9624 (mmtm) cc_final: 0.9168 (mmmm) REVERT: I 323 ILE cc_start: 0.9566 (mm) cc_final: 0.9116 (tp) REVERT: I 326 ARG cc_start: 0.8229 (mtm110) cc_final: 0.7677 (mtm110) REVERT: I 327 LYS cc_start: 0.9044 (mmpt) cc_final: 0.8637 (mmpt) REVERT: I 351 ILE cc_start: 0.9265 (mt) cc_final: 0.8796 (mt) REVERT: I 360 MET cc_start: 0.9270 (mtm) cc_final: 0.9042 (mtm) REVERT: I 361 PHE cc_start: 0.8649 (m-80) cc_final: 0.8051 (m-10) REVERT: I 372 MET cc_start: 0.9427 (mmm) cc_final: 0.8769 (mmm) REVERT: I 373 LEU cc_start: 0.9787 (tt) cc_final: 0.9466 (tt) REVERT: I 374 ASP cc_start: 0.9015 (m-30) cc_final: 0.8551 (m-30) REVERT: I 375 PHE cc_start: 0.8989 (m-80) cc_final: 0.8274 (m-80) REVERT: K 131 GLU cc_start: 0.7727 (pp20) cc_final: 0.7247 (tt0) REVERT: K 134 GLU cc_start: 0.8874 (tm-30) cc_final: 0.8217 (tm-30) REVERT: K 149 GLN cc_start: 0.9680 (mp-120) cc_final: 0.9398 (mp10) REVERT: K 151 GLU cc_start: 0.9561 (mt-10) cc_final: 0.9217 (tp30) REVERT: K 159 LEU cc_start: 0.9328 (mm) cc_final: 0.8967 (mm) REVERT: K 165 GLU cc_start: 0.9252 (pm20) cc_final: 0.8965 (pm20) REVERT: K 186 THR cc_start: 0.9055 (p) cc_final: 0.8810 (p) REVERT: K 189 THR cc_start: 0.9171 (m) cc_final: 0.8651 (p) REVERT: K 190 LEU cc_start: 0.9444 (mt) cc_final: 0.9060 (mt) REVERT: K 193 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8729 (mtmm) REVERT: K 211 PHE cc_start: 0.9218 (m-80) cc_final: 0.8538 (m-80) REVERT: K 222 LEU cc_start: 0.9524 (tp) cc_final: 0.9219 (tp) REVERT: K 237 ILE cc_start: 0.9305 (mm) cc_final: 0.8496 (tp) REVERT: K 311 LEU cc_start: 0.9199 (mt) cc_final: 0.8845 (tt) REVERT: K 315 GLU cc_start: 0.9115 (pm20) cc_final: 0.8748 (mp0) REVERT: K 337 LYS cc_start: 0.9482 (pptt) cc_final: 0.9100 (pptt) REVERT: K 341 ARG cc_start: 0.9000 (ttp80) cc_final: 0.8590 (ttp80) REVERT: K 357 GLU cc_start: 0.8868 (tm-30) cc_final: 0.8542 (tm-30) REVERT: K 361 PHE cc_start: 0.8660 (m-80) cc_final: 0.8300 (m-80) REVERT: K 372 MET cc_start: 0.7312 (mmm) cc_final: 0.5846 (mmm) REVERT: K 375 PHE cc_start: 0.9285 (m-80) cc_final: 0.8909 (m-80) REVERT: L 130 PHE cc_start: 0.8782 (m-80) cc_final: 0.8533 (m-80) REVERT: L 165 GLU cc_start: 0.9211 (tp30) cc_final: 0.8535 (tp30) REVERT: L 166 LEU cc_start: 0.9226 (mt) cc_final: 0.8914 (mt) REVERT: L 169 GLU cc_start: 0.9334 (mt-10) cc_final: 0.8700 (mt-10) REVERT: L 202 THR cc_start: 0.8786 (m) cc_final: 0.8578 (p) REVERT: L 204 ILE cc_start: 0.9387 (mm) cc_final: 0.9104 (mm) REVERT: L 206 VAL cc_start: 0.9423 (t) cc_final: 0.9206 (t) REVERT: L 211 PHE cc_start: 0.8945 (m-80) cc_final: 0.8700 (m-80) REVERT: L 222 LEU cc_start: 0.9524 (mt) cc_final: 0.9222 (mt) REVERT: L 225 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8431 (mt-10) REVERT: L 232 GLU cc_start: 0.9227 (mm-30) cc_final: 0.8931 (mm-30) REVERT: L 233 LYS cc_start: 0.9141 (tppt) cc_final: 0.8649 (tppt) REVERT: L 240 ILE cc_start: 0.9260 (tp) cc_final: 0.8916 (tp) REVERT: L 265 MET cc_start: 0.9035 (tmm) cc_final: 0.8804 (tmm) REVERT: L 273 ASP cc_start: 0.8987 (t70) cc_final: 0.8691 (t70) REVERT: L 282 LYS cc_start: 0.8542 (mptt) cc_final: 0.8172 (mmmt) REVERT: L 284 ILE cc_start: 0.8949 (mm) cc_final: 0.8452 (mm) REVERT: L 321 PHE cc_start: 0.9209 (m-80) cc_final: 0.8940 (m-10) REVERT: L 365 GLU cc_start: 0.8222 (pt0) cc_final: 0.6851 (mt-10) REVERT: M 140 TYR cc_start: 0.9261 (p90) cc_final: 0.8738 (p90) REVERT: M 154 ARG cc_start: 0.9290 (ptm160) cc_final: 0.9031 (ptt180) REVERT: M 179 LEU cc_start: 0.9520 (tp) cc_final: 0.9264 (tp) REVERT: M 221 ARG cc_start: 0.8726 (ttp-110) cc_final: 0.8293 (ptm160) REVERT: M 224 ARG cc_start: 0.9284 (tmt-80) cc_final: 0.8881 (tmt-80) REVERT: M 288 ASN cc_start: 0.9296 (m-40) cc_final: 0.8849 (m-40) REVERT: M 307 ILE cc_start: 0.9443 (mp) cc_final: 0.8931 (tt) REVERT: M 310 PRO cc_start: 0.9067 (Cg_endo) cc_final: 0.8693 (Cg_exo) REVERT: M 314 PHE cc_start: 0.9035 (t80) cc_final: 0.8606 (t80) REVERT: M 318 ILE cc_start: 0.8976 (mm) cc_final: 0.8642 (mm) REVERT: M 333 ASP cc_start: 0.9203 (p0) cc_final: 0.8759 (p0) REVERT: M 361 PHE cc_start: 0.8846 (m-80) cc_final: 0.8356 (m-80) REVERT: M 370 VAL cc_start: 0.8493 (t) cc_final: 0.8189 (t) REVERT: M 371 THR cc_start: 0.7821 (p) cc_final: 0.7287 (p) REVERT: M 372 MET cc_start: 0.8934 (tpt) cc_final: 0.8026 (tpt) REVERT: M 375 PHE cc_start: 0.9185 (m-10) cc_final: 0.8961 (m-10) REVERT: J 149 GLN cc_start: 0.9565 (mp10) cc_final: 0.9212 (mp10) REVERT: J 159 LEU cc_start: 0.9627 (tp) cc_final: 0.9404 (tp) REVERT: J 167 PHE cc_start: 0.8511 (m-80) cc_final: 0.7920 (m-80) REVERT: J 214 LYS cc_start: 0.8577 (ptmt) cc_final: 0.8253 (ptmt) REVERT: J 215 TYR cc_start: 0.8581 (m-80) cc_final: 0.7927 (m-80) REVERT: J 224 ARG cc_start: 0.9248 (ptp-110) cc_final: 0.8838 (ptp-170) REVERT: J 228 GLN cc_start: 0.9285 (mt0) cc_final: 0.9009 (mm-40) REVERT: J 242 GLU cc_start: 0.8358 (tm-30) cc_final: 0.7883 (tm-30) REVERT: J 262 GLN cc_start: 0.8857 (tt0) cc_final: 0.8582 (tt0) REVERT: J 315 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8465 (pp20) REVERT: J 328 MET cc_start: 0.7225 (ppp) cc_final: 0.6911 (ppp) REVERT: J 347 SER cc_start: 0.9400 (m) cc_final: 0.9043 (p) REVERT: J 350 ASP cc_start: 0.9457 (m-30) cc_final: 0.9239 (m-30) REVERT: J 352 LYS cc_start: 0.9250 (mmtt) cc_final: 0.8447 (mmtt) REVERT: J 372 MET cc_start: 0.9094 (mmm) cc_final: 0.8678 (mmm) REVERT: J 373 LEU cc_start: 0.9670 (tp) cc_final: 0.9286 (tp) REVERT: J 374 ASP cc_start: 0.8872 (m-30) cc_final: 0.8284 (m-30) REVERT: J 375 PHE cc_start: 0.9037 (m-80) cc_final: 0.8788 (m-80) REVERT: J 377 LYS cc_start: 0.9829 (mmpt) cc_final: 0.9474 (mttt) outliers start: 0 outliers final: 0 residues processed: 637 average time/residue: 0.1387 time to fit residues: 120.3360 Evaluate side-chains 560 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.571 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 143 optimal weight: 0.3980 chunk 112 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 84 optimal weight: 0.0570 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.132738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105499 restraints weight = 34002.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.109058 restraints weight = 25428.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.111887 restraints weight = 19911.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114168 restraints weight = 16154.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116119 restraints weight = 13443.690| |-----------------------------------------------------------------------------| r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.8686 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= 0.180 Angle : 0.904 17.192 17407 Z= 0.482 Chirality : 0.052 0.285 2000 Planarity : 0.006 0.087 2243 Dihedral : 10.978 128.135 1881 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.61 % Favored : 91.70 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -1.09 (0.21), residues: 1590 helix: -0.29 (0.18), residues: 799 sheet: -0.56 (0.45), residues: 134 loop : -1.17 (0.27), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG K 341 TYR 0.037 0.002 TYR H 140 PHE 0.044 0.002 PHE K 361 HIS 0.019 0.003 HIS J 324 Details of bonding type rmsd covalent geometry : bond 0.00402 (12881) covalent geometry : angle 0.90357 (17407) hydrogen bonds : bond 0.04409 ( 507) hydrogen bonds : angle 5.64635 ( 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 635 residues out of total 1338 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 635 time to evaluate : 0.536 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: H 128 TYR cc_start: 0.8111 (m-80) cc_final: 0.7872 (m-80) REVERT: H 130 PHE cc_start: 0.8943 (m-10) cc_final: 0.8656 (m-80) REVERT: H 172 ILE cc_start: 0.8715 (pt) cc_final: 0.8322 (pt) REVERT: H 181 TYR cc_start: 0.8663 (t80) cc_final: 0.8295 (t80) REVERT: H 207 VAL cc_start: 0.7504 (t) cc_final: 0.7288 (t) REVERT: H 227 PHE cc_start: 0.9486 (m-80) cc_final: 0.8862 (m-80) REVERT: H 228 GLN cc_start: 0.8757 (pp30) cc_final: 0.8424 (pp30) REVERT: H 233 LYS cc_start: 0.9383 (tptp) cc_final: 0.9027 (tptp) REVERT: H 260 GLU cc_start: 0.9099 (mp0) cc_final: 0.8835 (mp0) REVERT: H 262 GLN cc_start: 0.8982 (pm20) cc_final: 0.8598 (pm20) REVERT: H 269 LEU cc_start: 0.8974 (mt) cc_final: 0.8746 (mt) REVERT: H 276 ASP cc_start: 0.8485 (m-30) cc_final: 0.8046 (m-30) REVERT: H 290 ILE cc_start: 0.9259 (tp) cc_final: 0.9001 (tp) REVERT: H 306 ILE cc_start: 0.9258 (tp) cc_final: 0.9027 (tp) REVERT: H 311 LEU cc_start: 0.9153 (mm) cc_final: 0.8810 (mm) REVERT: H 328 MET cc_start: 0.8296 (ptp) cc_final: 0.8030 (ptp) REVERT: H 356 THR cc_start: 0.9573 (p) cc_final: 0.9313 (p) REVERT: H 360 MET cc_start: 0.9376 (ptp) cc_final: 0.9128 (ptp) REVERT: H 372 MET cc_start: 0.8866 (mmm) cc_final: 0.8372 (mmm) REVERT: H 383 LEU cc_start: 0.8702 (tp) cc_final: 0.8496 (tp) REVERT: I 127 VAL cc_start: 0.8794 (m) cc_final: 0.8501 (m) REVERT: I 130 PHE cc_start: 0.8845 (m-10) cc_final: 0.8395 (m-80) REVERT: I 154 ARG cc_start: 0.9338 (ptm160) cc_final: 0.8405 (tmm-80) REVERT: I 215 TYR cc_start: 0.7839 (m-10) cc_final: 0.7504 (m-80) REVERT: I 218 GLU cc_start: 0.7712 (tt0) cc_final: 0.7436 (tt0) REVERT: I 221 ARG cc_start: 0.9516 (ttp80) cc_final: 0.8931 (ttp80) REVERT: I 222 LEU cc_start: 0.9604 (mt) cc_final: 0.9378 (mt) REVERT: I 229 LEU cc_start: 0.9484 (tp) cc_final: 0.9269 (tp) REVERT: I 260 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8550 (mt-10) REVERT: I 282 LYS cc_start: 0.7645 (tptt) cc_final: 0.7232 (tptt) REVERT: I 283 VAL cc_start: 0.9189 (t) cc_final: 0.8825 (t) REVERT: I 284 ILE cc_start: 0.9702 (mt) cc_final: 0.9486 (mt) REVERT: I 294 ASP cc_start: 0.8956 (t0) cc_final: 0.8485 (t0) REVERT: I 303 PHE cc_start: 0.9197 (m-80) cc_final: 0.8963 (m-80) REVERT: I 318 ILE cc_start: 0.9121 (mt) cc_final: 0.8668 (mt) REVERT: I 321 PHE cc_start: 0.8309 (m-10) cc_final: 0.7714 (m-10) REVERT: I 322 LYS cc_start: 0.9606 (mmtm) cc_final: 0.9119 (mmmm) REVERT: I 323 ILE cc_start: 0.9572 (mm) cc_final: 0.9148 (tp) REVERT: I 326 ARG cc_start: 0.8250 (mtm110) cc_final: 0.7734 (mtm110) REVERT: I 327 LYS cc_start: 0.9060 (mmpt) cc_final: 0.8678 (mmpt) REVERT: I 351 ILE cc_start: 0.9272 (mt) cc_final: 0.8813 (mt) REVERT: I 360 MET cc_start: 0.9313 (mtm) cc_final: 0.9010 (mtm) REVERT: I 361 PHE cc_start: 0.8744 (m-80) cc_final: 0.8177 (m-10) REVERT: I 372 MET cc_start: 0.9436 (mmm) cc_final: 0.8889 (mmm) REVERT: I 373 LEU cc_start: 0.9799 (tt) cc_final: 0.9579 (tt) REVERT: I 374 ASP cc_start: 0.8981 (m-30) cc_final: 0.8592 (m-30) REVERT: I 375 PHE cc_start: 0.9001 (m-80) cc_final: 0.8244 (m-80) REVERT: K 151 GLU cc_start: 0.9572 (mt-10) cc_final: 0.9212 (tp30) REVERT: K 159 LEU cc_start: 0.9391 (mm) cc_final: 0.9002 (mm) REVERT: K 186 THR cc_start: 0.9146 (p) cc_final: 0.8896 (p) REVERT: K 189 THR cc_start: 0.9138 (m) cc_final: 0.8642 (p) REVERT: K 190 LEU cc_start: 0.9486 (mt) cc_final: 0.9122 (mt) REVERT: K 193 LYS cc_start: 0.9239 (mtmm) cc_final: 0.8828 (mtmm) REVERT: K 211 PHE cc_start: 0.9299 (m-80) cc_final: 0.8503 (m-80) REVERT: K 222 LEU cc_start: 0.9529 (tp) cc_final: 0.9226 (tp) REVERT: K 263 ARG cc_start: 0.8734 (mtm-85) cc_final: 0.8253 (mtm-85) REVERT: K 311 LEU cc_start: 0.9306 (mt) cc_final: 0.8935 (tt) REVERT: K 322 LYS cc_start: 0.8992 (mttp) cc_final: 0.8671 (mtmm) REVERT: K 337 LYS cc_start: 0.9473 (pptt) cc_final: 0.9089 (pptt) REVERT: K 341 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8633 (ttp80) REVERT: K 357 GLU cc_start: 0.8832 (tm-30) cc_final: 0.8305 (tm-30) REVERT: K 361 PHE cc_start: 0.8854 (m-80) cc_final: 0.8314 (m-80) REVERT: K 372 MET cc_start: 0.7326 (mmm) cc_final: 0.5874 (mmm) REVERT: K 375 PHE cc_start: 0.9332 (m-80) cc_final: 0.8935 (m-80) REVERT: L 130 PHE cc_start: 0.8807 (m-80) cc_final: 0.8522 (m-80) REVERT: L 165 GLU cc_start: 0.9215 (tp30) cc_final: 0.8812 (tp30) REVERT: L 193 LYS cc_start: 0.8998 (tptp) cc_final: 0.8788 (mmmt) REVERT: L 202 THR cc_start: 0.8798 (m) cc_final: 0.8569 (p) REVERT: L 204 ILE cc_start: 0.9418 (mm) cc_final: 0.9105 (mm) REVERT: L 206 VAL cc_start: 0.9399 (t) cc_final: 0.9164 (t) REVERT: L 211 PHE cc_start: 0.8981 (m-80) cc_final: 0.8655 (m-80) REVERT: L 222 LEU cc_start: 0.9521 (mt) cc_final: 0.9227 (mt) REVERT: L 225 GLU cc_start: 0.9017 (mt-10) cc_final: 0.8470 (mt-10) REVERT: L 232 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8922 (mm-30) REVERT: L 233 LYS cc_start: 0.9163 (tppt) cc_final: 0.8671 (tppt) REVERT: L 240 ILE cc_start: 0.9253 (tp) cc_final: 0.8901 (tp) REVERT: L 273 ASP cc_start: 0.9142 (t70) cc_final: 0.8862 (t70) REVERT: L 284 ILE cc_start: 0.9035 (mm) cc_final: 0.8488 (mm) REVERT: L 321 PHE cc_start: 0.9186 (m-80) cc_final: 0.8904 (m-10) REVERT: L 328 MET cc_start: 0.8460 (ppp) cc_final: 0.8192 (ppp) REVERT: L 365 GLU cc_start: 0.8210 (pt0) cc_final: 0.6846 (mt-10) REVERT: L 375 PHE cc_start: 0.8078 (m-80) cc_final: 0.7865 (m-80) REVERT: M 140 TYR cc_start: 0.9246 (p90) cc_final: 0.8716 (p90) REVERT: M 221 ARG cc_start: 0.8693 (ttp-110) cc_final: 0.8223 (ptm160) REVERT: M 224 ARG cc_start: 0.9304 (tmt-80) cc_final: 0.8869 (tmt-80) REVERT: M 225 GLU cc_start: 0.8746 (pp20) cc_final: 0.8513 (pp20) REVERT: M 227 PHE cc_start: 0.8064 (t80) cc_final: 0.7852 (t80) REVERT: M 264 THR cc_start: 0.9076 (m) cc_final: 0.8834 (p) REVERT: M 307 ILE cc_start: 0.9444 (mp) cc_final: 0.9146 (mt) REVERT: M 314 PHE cc_start: 0.9065 (t80) cc_final: 0.8630 (t80) REVERT: M 318 ILE cc_start: 0.9043 (mm) cc_final: 0.8728 (mm) REVERT: M 333 ASP cc_start: 0.9186 (p0) cc_final: 0.8721 (p0) REVERT: M 361 PHE cc_start: 0.8904 (m-80) cc_final: 0.8171 (m-10) REVERT: M 370 VAL cc_start: 0.8428 (t) cc_final: 0.8059 (t) REVERT: M 371 THR cc_start: 0.7833 (p) cc_final: 0.7322 (p) REVERT: M 372 MET cc_start: 0.8950 (tpt) cc_final: 0.8169 (tpt) REVERT: M 375 PHE cc_start: 0.9180 (m-10) cc_final: 0.8946 (m-10) REVERT: J 149 GLN cc_start: 0.9583 (mp10) cc_final: 0.9245 (mp10) REVERT: J 159 LEU cc_start: 0.9638 (tp) cc_final: 0.9412 (tp) REVERT: J 167 PHE cc_start: 0.8595 (m-80) cc_final: 0.8007 (m-80) REVERT: J 173 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8652 (mt-10) REVERT: J 224 ARG cc_start: 0.9401 (ptp-110) cc_final: 0.8842 (ptp-170) REVERT: J 228 GLN cc_start: 0.9274 (mt0) cc_final: 0.9047 (mm-40) REVERT: J 242 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7995 (tm-30) REVERT: J 262 GLN cc_start: 0.8850 (tt0) cc_final: 0.8551 (tt0) REVERT: J 267 GLN cc_start: 0.9459 (mm-40) cc_final: 0.8844 (mp10) REVERT: J 315 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8475 (pp20) REVERT: J 328 MET cc_start: 0.7050 (ppp) cc_final: 0.6775 (ppp) REVERT: J 347 SER cc_start: 0.9401 (m) cc_final: 0.9066 (p) REVERT: J 350 ASP cc_start: 0.9466 (m-30) cc_final: 0.9214 (m-30) REVERT: J 352 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8445 (mmtt) REVERT: J 366 GLU cc_start: 0.8960 (mp0) cc_final: 0.8657 (mp0) REVERT: J 372 MET cc_start: 0.9072 (mmm) cc_final: 0.8630 (mmm) REVERT: J 373 LEU cc_start: 0.9695 (tp) cc_final: 0.9277 (tp) REVERT: J 374 ASP cc_start: 0.8632 (m-30) cc_final: 0.8310 (m-30) REVERT: J 375 PHE cc_start: 0.9017 (m-80) cc_final: 0.8764 (m-80) REVERT: J 377 LYS cc_start: 0.9828 (mmpt) cc_final: 0.9469 (mttt) outliers start: 0 outliers final: 0 residues processed: 635 average time/residue: 0.1368 time to fit residues: 119.5661 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 : 0.493 ------------------------------------------------------------------------------- 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: 0.8980 chunk 111 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 109 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 chunk 84 optimal weight: 0.0060 overall best weight: 0.3374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 ASN ** J 267 GLN ** 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 = 0.3808 r_free = 0.3808 target = 0.132934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.106077 restraints weight = 33697.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.109501 restraints weight = 25243.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.112474 restraints weight = 19688.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.114660 restraints weight = 15969.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116491 restraints weight = 13336.251| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.8814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12881 Z= 0.178 Angle : 0.899 17.095 17407 Z= 0.479 Chirality : 0.051 0.294 2000 Planarity : 0.006 0.108 2243 Dihedral : 10.852 127.483 1881 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 22.41 Ramachandran Plot: Outliers : 0.69 % Allowed : 7.42 % Favored : 91.89 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.07 % 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 aren not related in a simple way. whole: -1.11 (0.21), residues: 1590 helix: -0.29 (0.18), residues: 797 sheet: -0.68 (0.45), residues: 135 loop : -1.17 (0.27), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG M 263 TYR 0.030 0.002 TYR H 140 PHE 0.043 0.002 PHE K 361 HIS 0.017 0.003 HIS J 324 Details of bonding type rmsd covalent geometry : bond 0.00395 (12881) covalent geometry : angle 0.89919 (17407) hydrogen bonds : bond 0.04412 ( 507) hydrogen bonds : angle 5.60778 ( 1518) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2976.65 seconds wall clock time: 52 minutes 3.42 seconds (3123.42 seconds total)