Starting phenix.real_space_refine on Sun Feb 18 12:50:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spx_40689/02_2024/8spx_40689_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spx_40689/02_2024/8spx_40689.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spx_40689/02_2024/8spx_40689.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spx_40689/02_2024/8spx_40689.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spx_40689/02_2024/8spx_40689_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8spx_40689/02_2024/8spx_40689_updated.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.029 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 18 5.49 5 Mg 6 5.21 5 S 68 5.16 5 C 13845 2.51 5 N 3826 2.21 5 O 4237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 364": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22000 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3650 Classifications: {'peptide': 476} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 453} Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 474, 3636 Classifications: {'peptide': 474} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 451} Chain: "C" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3644 Classifications: {'peptide': 475} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 452} Chain: "D" Number of atoms: 3631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3631 Classifications: {'peptide': 471} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 447} Chain: "E" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "F" Number of atoms: 3623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3623 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 446} Chain: "A" 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 11.19, per 1000 atoms: 0.51 Number of scatterers: 22000 At special positions: 0 Unit cell: (109.2, 119.28, 125.16, 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 68 16.00 P 18 15.00 Mg 6 11.99 O 4237 8.00 N 3826 7.00 C 13845 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 - 3.50 Amino acid : False - 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: 8.47 Conformation dependent library (CDL) restraints added in 3.8 seconds 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 100 helices and 20 sheets defined 39.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.72 Creating SS restraints... Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 202 through 214 Processing helix chain 'A' and resid 218 through 220 No H-bonds generated for 'chain 'A' and resid 218 through 220' Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.757A pdb=" N LEU A 237 " --> pdb=" O LEU A 234 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA A 238 " --> pdb=" O LEU A 235 " (cutoff:3.500A) Proline residue: A 239 - end of helix removed outlier: 3.664A pdb=" N GLU A 247 " --> pdb=" O ALA A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 277 removed outlier: 3.514A pdb=" N LEU A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 300 removed outlier: 3.969A pdb=" N PHE A 291 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU A 299 " --> pdb=" O ARG A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 324 No H-bonds generated for 'chain 'A' and resid 322 through 324' Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.703A pdb=" N ILE A 337 " --> pdb=" O ASN A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 382 through 398 Processing helix chain 'A' and resid 404 through 420 removed outlier: 3.693A pdb=" N VAL A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 removed outlier: 3.807A pdb=" N VAL A 434 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE A 436 " --> pdb=" O LYS A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 466 removed outlier: 4.549A pdb=" N ARG A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 478 Processing helix chain 'A' and resid 484 through 497 Processing helix chain 'B' and resid 101 through 103 No H-bonds generated for 'chain 'B' and resid 101 through 103' Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 176 through 187 removed outlier: 4.415A pdb=" N LYS B 187 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 214 Processing helix chain 'B' and resid 217 through 220 Processing helix chain 'B' and resid 232 through 252 Proline residue: B 239 - end of helix removed outlier: 3.716A pdb=" N MET B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 290 through 300 removed outlier: 4.470A pdb=" N ARG B 300 " --> pdb=" O ARG B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 324 No H-bonds generated for 'chain 'B' and resid 322 through 324' Processing helix chain 'B' and resid 329 through 337 Processing helix chain 'B' and resid 346 through 351 removed outlier: 3.675A pdb=" N SER B 351 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 396 removed outlier: 4.109A pdb=" N THR B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU B 392 " --> pdb=" O ALA B 388 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA B 394 " --> pdb=" O ARG B 390 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE B 395 " --> pdb=" O GLU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 419 removed outlier: 3.817A pdb=" N ALA B 408 " --> pdb=" O LYS B 404 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS B 409 " --> pdb=" O ALA B 405 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 410 " --> pdb=" O THR B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 450 through 466 removed outlier: 4.303A pdb=" N ARG B 454 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ARG B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS B 458 " --> pdb=" O ARG B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 478 Processing helix chain 'B' and resid 484 through 497 removed outlier: 3.525A pdb=" N PHE B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS B 496 " --> pdb=" O GLU B 492 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) Processing helix chain 'C' and resid 151 through 156 Processing helix chain 'C' and resid 175 through 187 removed outlier: 4.097A pdb=" N LYS C 187 " --> pdb=" O ILE C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 215 Processing helix chain 'C' and resid 232 through 252 Proline residue: C 239 - end of helix removed outlier: 3.927A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 277 removed outlier: 3.513A pdb=" N GLU C 272 " --> pdb=" O ALA C 268 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 300 removed outlier: 3.528A pdb=" N LEU C 293 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU C 297 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU C 298 " --> pdb=" O SER C 295 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU C 299 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 329 through 337 Processing helix chain 'C' and resid 373 through 378 Processing helix chain 'C' and resid 382 through 398 removed outlier: 4.127A pdb=" N ALA C 387 " --> pdb=" O ARG C 383 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA C 394 " --> pdb=" O ARG C 390 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE C 398 " --> pdb=" O ALA C 394 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 420 Processing helix chain 'C' and resid 430 through 442 Processing helix chain 'C' and resid 444 through 446 No H-bonds generated for 'chain 'C' and resid 444 through 446' Processing helix chain 'C' and resid 451 through 466 removed outlier: 4.128A pdb=" N ARG C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 478 Processing helix chain 'C' and resid 484 through 497 Processing helix chain 'D' and resid 140 through 145 Processing helix chain 'D' and resid 164 through 179 removed outlier: 3.663A pdb=" N GLU D 178 " --> pdb=" O ASN D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 205 removed outlier: 3.716A pdb=" N ASN D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 222 through 241 removed outlier: 4.816A pdb=" N ALA D 229 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU D 230 " --> pdb=" O MET D 226 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TYR D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N PHE D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 268 removed outlier: 3.645A pdb=" N GLN D 259 " --> pdb=" O ARG D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 289 removed outlier: 3.695A pdb=" N LEU D 288 " --> pdb=" O GLU D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 316 through 324 removed outlier: 3.930A pdb=" N SER D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N HIS D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 337 No H-bonds generated for 'chain 'D' and resid 334 through 337' Processing helix chain 'D' and resid 361 through 386 removed outlier: 3.842A pdb=" N LYS D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N ASP D 382 " --> pdb=" O LYS D 378 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ILE D 383 " --> pdb=" O GLU D 379 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 390 No H-bonds generated for 'chain 'D' and resid 388 through 390' Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.776A pdb=" N ARG D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE D 408 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE D 409 " --> pdb=" O ARG D 405 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU D 410 " --> pdb=" O ILE D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 441 Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.754A pdb=" N VAL D 463 " --> pdb=" O ILE D 459 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 91 No H-bonds generated for 'chain 'E' and resid 89 through 91' Processing helix chain 'E' and resid 125 through 127 No H-bonds generated for 'chain 'E' and resid 125 through 127' Processing helix chain 'E' and resid 140 through 145 Processing helix chain 'E' and resid 164 through 178 Processing helix chain 'E' and resid 192 through 205 removed outlier: 3.854A pdb=" N ASN E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 210 Processing helix chain 'E' and resid 222 through 241 removed outlier: 4.944A pdb=" N ALA E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU E 230 " --> pdb=" O MET E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 268 removed outlier: 3.571A pdb=" N GLN E 259 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 260 " --> pdb=" O PHE E 257 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL E 264 " --> pdb=" O GLY E 261 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA E 266 " --> pdb=" O GLU E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 291 removed outlier: 3.999A pdb=" N ARG E 291 " --> pdb=" O GLN E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 316 through 324 removed outlier: 4.064A pdb=" N SER E 323 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N HIS E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 356 through 359 No H-bonds generated for 'chain 'E' and resid 356 through 359' Processing helix chain 'E' and resid 361 through 387 removed outlier: 4.299A pdb=" N ASP E 382 " --> pdb=" O LYS E 378 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE E 386 " --> pdb=" O ASP E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 394 through 409 removed outlier: 3.681A pdb=" N PHE E 408 " --> pdb=" O ARG E 404 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE E 409 " --> pdb=" O ARG E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 removed outlier: 4.192A pdb=" N GLN E 419 " --> pdb=" O VAL E 416 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR E 421 " --> pdb=" O GLU E 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 430 through 441 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 459 through 469 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 140 through 145 Processing helix chain 'F' and resid 164 through 178 Processing helix chain 'F' and resid 192 through 205 Processing helix chain 'F' and resid 222 through 241 removed outlier: 4.877A pdb=" N ALA F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N LEU F 230 " --> pdb=" O MET F 226 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE F 239 " --> pdb=" O MET F 235 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 268 Processing helix chain 'F' and resid 282 through 289 Processing helix chain 'F' and resid 316 through 323 removed outlier: 3.581A pdb=" N SER F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 356 through 359 No H-bonds generated for 'chain 'F' and resid 356 through 359' Processing helix chain 'F' and resid 361 through 387 removed outlier: 4.378A pdb=" N ASP F 382 " --> pdb=" O LYS F 378 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE F 383 " --> pdb=" O GLU F 379 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE F 386 " --> pdb=" O ASP F 382 " (cutoff:3.500A) Processing helix chain 'F' and resid 394 through 409 removed outlier: 3.894A pdb=" N ARG F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 415 through 421 removed outlier: 3.828A pdb=" N GLU F 418 " --> pdb=" O HIS F 415 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 419 " --> pdb=" O VAL F 416 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR F 421 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'F' and resid 430 through 442 Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 459 through 469 Processing sheet with id= A, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.838A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 99 Processing sheet with id= C, first strand: chain 'A' and resid 107 through 109 removed outlier: 8.955A pdb=" N VAL A 108 " --> pdb=" O THR A 221 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL A 223 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N SER A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N VAL A 224 " --> pdb=" O SER A 193 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N SER A 312 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL A 258 " --> pdb=" O SER A 312 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N THR A 314 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N TYR A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU A 316 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.836A pdb=" N LEU A 166 " --> pdb=" O ILE A 342 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N LEU A 344 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 168 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 319 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY A 169 " --> pdb=" O VAL A 319 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.543A pdb=" N ARG B 40 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL B 34 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B 74 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N ALA B 63 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 96 through 99 Processing sheet with id= G, first strand: chain 'B' and resid 340 through 344 Processing sheet with id= H, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.977A pdb=" N SER B 193 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N VAL B 224 " --> pdb=" O SER B 193 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR B 195 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA B 226 " --> pdb=" O TYR B 195 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ALA B 197 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER B 312 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL B 258 " --> pdb=" O SER B 312 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N THR B 314 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N TYR B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 29 through 35 removed outlier: 6.568A pdb=" N ARG C 40 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL C 34 " --> pdb=" O ILE C 38 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 65 " --> pdb=" O GLY C 72 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU C 76 " --> pdb=" O GLY C 61 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N GLY C 61 " --> pdb=" O LEU C 76 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 99 Processing sheet with id= K, first strand: chain 'C' and resid 341 through 344 removed outlier: 6.810A pdb=" N LEU C 166 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 344 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE C 168 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 312 through 316 removed outlier: 3.680A pdb=" N TYR C 260 " --> pdb=" O LEU C 316 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE C 222 " --> pdb=" O TYR C 195 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ALA C 197 " --> pdb=" O ILE C 222 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL C 224 " --> pdb=" O ALA C 197 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N GLY C 199 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ALA C 226 " --> pdb=" O GLY C 199 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 removed outlier: 6.873A pdb=" N ASP D 15 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N VAL D 9 " --> pdb=" O VAL D 13 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N VAL D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL D 14 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ILE D 62 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N VAL D 50 " --> pdb=" O ILE D 62 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE D 44 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS D 34 " --> pdb=" O ILE D 44 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 327 through 330 removed outlier: 8.071A pdb=" N ILE D 154 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER D 302 " --> pdb=" O ILE D 154 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N LEU D 156 " --> pdb=" O SER D 302 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLN D 304 " --> pdb=" O LEU D 156 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLY D 158 " --> pdb=" O GLN D 304 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ILE D 306 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N VAL D 247 " --> pdb=" O THR D 301 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE D 303 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU D 249 " --> pdb=" O ILE D 303 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ALA D 305 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ILE D 251 " --> pdb=" O ALA D 305 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N TYR D 307 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ILE D 182 " --> pdb=" O LEU D 248 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N PHE D 250 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL D 184 " --> pdb=" O PHE D 250 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 75 through 77 removed outlier: 6.695A pdb=" N ASP E 15 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL E 9 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL E 13 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE E 62 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N VAL E 50 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE E 44 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 84 through 86 Processing sheet with id= Q, first strand: chain 'E' and resid 327 through 331 removed outlier: 6.951A pdb=" N VAL E 247 " --> pdb=" O THR E 301 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ILE E 303 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU E 249 " --> pdb=" O ILE E 303 " (cutoff:3.500A) removed outlier: 8.140A pdb=" N ALA E 305 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE E 251 " --> pdb=" O ALA E 305 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N TYR E 307 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 182 " --> pdb=" O LEU E 248 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N PHE E 250 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL E 184 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N ASP E 252 " --> pdb=" O VAL E 184 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA E 186 " --> pdb=" O ASP E 252 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 75 through 77 removed outlier: 3.594A pdb=" N ARG F 5 " --> pdb=" O LYS F 17 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ASP F 15 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N VAL F 9 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL F 13 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE F 62 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N VAL F 50 " --> pdb=" O ILE F 62 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE F 44 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'F' and resid 84 through 87 removed outlier: 3.738A pdb=" N ARG F 114 " --> pdb=" O VAL F 87 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 327 through 330 removed outlier: 6.599A pdb=" N SER F 302 " --> pdb=" O ILE F 154 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N LEU F 156 " --> pdb=" O SER F 302 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLN F 304 " --> pdb=" O LEU F 156 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N GLY F 158 " --> pdb=" O GLN F 304 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ILE F 306 " --> pdb=" O GLY F 158 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE F 303 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE F 251 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 305 " --> pdb=" O ILE F 251 " (cutoff:3.500A) 793 hydrogen bonds defined for protein. 2112 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: 7.54 Time building geometry restraints manager: 9.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7384 1.34 - 1.46: 2455 1.46 - 1.57: 12373 1.57 - 1.69: 23 1.69 - 1.81: 136 Bond restraints: 22371 Sorted by residual: bond pdb=" O3 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.569 1.506 0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" O4 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.568 1.506 0.062 2.00e-02 2.50e+03 9.67e+00 bond pdb=" O2 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.567 1.506 0.061 2.00e-02 2.50e+03 9.32e+00 bond pdb=" O1 PO4 F 503 " pdb=" P PO4 F 503 " ideal model delta sigma weight residual 1.565 1.508 0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" CA PRO A 280 " pdb=" C PRO A 280 " ideal model delta sigma weight residual 1.517 1.505 0.012 6.70e-03 2.23e+04 3.43e+00 ... (remaining 22366 not shown) Histogram of bond angle deviations from ideal: 99.58 - 107.80: 887 107.80 - 116.01: 14097 116.01 - 124.23: 14940 124.23 - 132.45: 406 132.45 - 140.66: 15 Bond angle restraints: 30345 Sorted by residual: angle pdb=" C ALA F 274 " pdb=" CA ALA F 274 " pdb=" CB ALA F 274 " ideal model delta sigma weight residual 116.54 110.46 6.08 1.15e+00 7.56e-01 2.79e+01 angle pdb=" C TYR B 329 " pdb=" N ILE B 330 " pdb=" CA ILE B 330 " ideal model delta sigma weight residual 120.33 124.43 -4.10 8.00e-01 1.56e+00 2.62e+01 angle pdb=" C GLN E 217 " pdb=" N MET E 218 " pdb=" CA MET E 218 " ideal model delta sigma weight residual 120.38 124.79 -4.41 1.37e+00 5.33e-01 1.04e+01 angle pdb=" N GLY A 360 " pdb=" CA GLY A 360 " pdb=" C GLY A 360 " ideal model delta sigma weight residual 112.64 116.41 -3.77 1.21e+00 6.83e-01 9.70e+00 angle pdb=" N ILE E 292 " pdb=" CA ILE E 292 " pdb=" C ILE E 292 " ideal model delta sigma weight residual 106.21 109.39 -3.18 1.07e+00 8.73e-01 8.84e+00 ... (remaining 30340 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 12490 17.65 - 35.30: 891 35.30 - 52.95: 199 52.95 - 70.60: 54 70.60 - 88.25: 26 Dihedral angle restraints: 13660 sinusoidal: 5602 harmonic: 8058 Sorted by residual: dihedral pdb=" CA PRO C 145 " pdb=" C PRO C 145 " pdb=" N LEU C 146 " pdb=" CA LEU C 146 " ideal model delta harmonic sigma weight residual 180.00 155.71 24.29 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ASP D 45 " pdb=" C ASP D 45 " pdb=" N LEU D 46 " pdb=" CA LEU D 46 " ideal model delta harmonic sigma weight residual -180.00 -156.72 -23.28 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C4' ADP F 502 " pdb=" C5' ADP F 502 " pdb=" O5' ADP F 502 " pdb=" PA ADP F 502 " ideal model delta sinusoidal sigma weight residual -180.00 -95.60 -84.40 1 2.00e+01 2.50e-03 2.17e+01 ... (remaining 13657 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1972 0.031 - 0.061: 927 0.061 - 0.091: 350 0.091 - 0.122: 190 0.122 - 0.152: 46 Chirality restraints: 3485 Sorted by residual: chirality pdb=" CA ILE D 71 " pdb=" N ILE D 71 " pdb=" C ILE D 71 " pdb=" CB ILE D 71 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE B 38 " pdb=" N ILE B 38 " pdb=" C ILE B 38 " pdb=" CB ILE B 38 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CA PRO E 222 " pdb=" N PRO E 222 " pdb=" C PRO E 222 " pdb=" CB PRO E 222 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.22e-01 ... (remaining 3482 not shown) Planarity restraints: 3962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 81 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO D 82 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 82 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO D 82 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER B 177 " 0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C SER B 177 " -0.036 2.00e-02 2.50e+03 pdb=" O SER B 177 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL B 178 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 120 " -0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO E 121 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.027 5.00e-02 4.00e+02 ... (remaining 3959 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 67 2.50 - 3.10: 15867 3.10 - 3.70: 31971 3.70 - 4.30: 48277 4.30 - 4.90: 80165 Nonbonded interactions: 176347 Sorted by model distance: nonbonded pdb="MG MG F 501 " pdb=" O3 PO4 F 503 " model vdw 1.895 2.170 nonbonded pdb="MG MG F 501 " pdb=" O2B ADP F 502 " model vdw 1.933 2.170 nonbonded pdb=" O1G ATP D 500 " pdb="MG MG D 501 " model vdw 1.981 2.170 nonbonded pdb=" OG1 THR D 165 " pdb="MG MG D 501 " model vdw 1.996 2.170 nonbonded pdb=" O LYS B 201 " pdb=" OG1 THR B 204 " model vdw 2.169 2.440 ... (remaining 176342 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'B' and (resid 27 through 499 or resid 600 through 601)) selection = (chain 'C' and (resid 27 through 499 or resid 600 through 601)) } ncs_group { reference = (chain 'D' and resid 2 through 470) selection = (chain 'E' and resid 2 through 470) selection = (chain 'F' and resid 2 through 470) } 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 individual isotropic 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: 0.770 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: 4.960 Check model and map are aligned: 0.370 Set scattering table: 0.240 Process input model: 57.370 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.140 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: 0.010 Load rotamer database and sin/cos tables:13.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6293 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 22371 Z= 0.247 Angle : 0.635 6.916 30345 Z= 0.360 Chirality : 0.045 0.152 3485 Planarity : 0.005 0.061 3962 Dihedral : 13.883 88.245 8510 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.03 % Allowed : 8.19 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2824 helix: 0.27 (0.15), residues: 1077 sheet: 0.08 (0.23), residues: 461 loop : -0.57 (0.17), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS F 363 PHE 0.021 0.002 PHE A 236 TYR 0.020 0.002 TYR A 248 ARG 0.004 0.001 ARG C 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 567 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 375 MET cc_start: 0.6720 (ttp) cc_final: 0.6047 (tpp) REVERT: E 235 MET cc_start: 0.6801 (mtt) cc_final: 0.6508 (mtp) REVERT: F 240 ARG cc_start: 0.6194 (OUTLIER) cc_final: 0.5963 (ptt90) outliers start: 47 outliers final: 13 residues processed: 598 average time/residue: 1.3008 time to fit residues: 884.6239 Evaluate side-chains 344 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 330 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 252 ASP Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 411 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 118 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 221 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 256 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 371 GLN A 467 ASN B 172 GLN B 230 GLN B 322 GLN B 333 ASN B 483 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 255 HIS C 358 ASN C 422 GLN C 426 GLN C 474 HIS D 34 HIS D 174 ASN D 259 GLN ** D 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 324 HIS D 330 ASN D 381 GLN ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 259 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 HIS E 412 GLN E 447 HIS F 33 GLN F 38 ASN F 174 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.3192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 22371 Z= 0.391 Angle : 0.786 12.701 30345 Z= 0.410 Chirality : 0.052 0.181 3485 Planarity : 0.007 0.063 3962 Dihedral : 9.517 85.295 3285 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 7.33 % Allowed : 17.37 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.15), residues: 2824 helix: -0.25 (0.15), residues: 1079 sheet: 0.14 (0.23), residues: 469 loop : -1.02 (0.17), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS F 200 PHE 0.028 0.003 PHE A 318 TYR 0.026 0.003 TYR F 199 ARG 0.008 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 346 time to evaluate : 2.258 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: A 93 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6779 (mtp180) REVERT: C 190 ASN cc_start: 0.5979 (OUTLIER) cc_final: 0.5154 (p0) REVERT: C 271 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.7219 (ttm170) REVERT: C 299 GLU cc_start: 0.6347 (OUTLIER) cc_final: 0.5572 (mt-10) REVERT: C 375 MET cc_start: 0.6402 (ttp) cc_final: 0.5848 (tpp) REVERT: C 454 ARG cc_start: 0.4200 (OUTLIER) cc_final: 0.2561 (mmt180) REVERT: C 470 HIS cc_start: 0.6860 (p-80) cc_final: 0.6629 (p-80) REVERT: D 271 MET cc_start: 0.6908 (mtp) cc_final: 0.6685 (mtm) REVERT: E 347 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6473 (mp) REVERT: E 413 ASN cc_start: 0.7123 (OUTLIER) cc_final: 0.6703 (p0) REVERT: F 213 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.5819 (mtt) REVERT: F 326 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6955 (m-30) REVERT: F 333 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6541 (tpp-160) REVERT: F 352 ARG cc_start: 0.5967 (OUTLIER) cc_final: 0.5560 (ptt180) outliers start: 170 outliers final: 59 residues processed: 463 average time/residue: 1.2879 time to fit residues: 689.1596 Evaluate side-chains 356 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 286 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 271 ARG Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 400 VAL Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 220 GLU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 347 LEU Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 5 ARG Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 283 THR Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 142 optimal weight: 7.9990 chunk 79 optimal weight: 10.0000 chunk 213 optimal weight: 2.9990 chunk 174 optimal weight: 9.9990 chunk 70 optimal weight: 4.9990 chunk 256 optimal weight: 0.9990 chunk 277 optimal weight: 3.9990 chunk 228 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 205 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 467 ASN B 143 HIS B 322 GLN B 483 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 474 HIS D 259 GLN D 330 ASN D 401 HIS E 38 ASN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 412 GLN F 34 HIS F 38 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 22371 Z= 0.263 Angle : 0.640 9.359 30345 Z= 0.335 Chirality : 0.047 0.173 3485 Planarity : 0.006 0.054 3962 Dihedral : 8.785 83.283 3276 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 6.64 % Allowed : 20.22 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.15), residues: 2824 helix: 0.08 (0.15), residues: 1074 sheet: 0.26 (0.24), residues: 476 loop : -1.05 (0.17), residues: 1274 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS F 363 PHE 0.020 0.002 PHE C 236 TYR 0.017 0.002 TYR F 199 ARG 0.013 0.001 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 317 time to evaluate : 2.398 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: A 93 ARG cc_start: 0.7132 (OUTLIER) cc_final: 0.6494 (mtp180) REVERT: B 409 LYS cc_start: 0.6195 (OUTLIER) cc_final: 0.4629 (ttpp) REVERT: C 190 ASN cc_start: 0.6309 (OUTLIER) cc_final: 0.5502 (p0) REVERT: C 375 MET cc_start: 0.6437 (ttp) cc_final: 0.5843 (tpp) REVERT: C 409 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6785 (ttpp) REVERT: D 115 ARG cc_start: 0.6187 (ptp-110) cc_final: 0.5845 (ptp-170) REVERT: D 271 MET cc_start: 0.6841 (mtp) cc_final: 0.6638 (mtm) REVERT: D 322 PHE cc_start: 0.7627 (OUTLIER) cc_final: 0.6877 (m-80) REVERT: D 337 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: D 351 SER cc_start: 0.5515 (m) cc_final: 0.4907 (t) REVERT: E 285 MET cc_start: 0.6418 (ttm) cc_final: 0.6180 (ttm) REVERT: E 413 ASN cc_start: 0.7135 (OUTLIER) cc_final: 0.6688 (p0) REVERT: F 213 MET cc_start: 0.6615 (mtt) cc_final: 0.6264 (mtt) REVERT: F 240 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5880 (ptt90) REVERT: F 326 ASP cc_start: 0.7223 (OUTLIER) cc_final: 0.6949 (m-30) outliers start: 154 outliers final: 70 residues processed: 415 average time/residue: 1.1396 time to fit residues: 546.6502 Evaluate side-chains 351 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 272 time to evaluate : 2.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 435 LEU Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 409 LYS Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 326 ASP Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 451 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 253 optimal weight: 10.0000 chunk 192 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 122 optimal weight: 0.0970 chunk 172 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 134 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 467 ASN B 483 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 330 ASN D 407 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 363 HIS F 401 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6671 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22371 Z= 0.258 Angle : 0.626 9.466 30345 Z= 0.328 Chirality : 0.046 0.189 3485 Planarity : 0.005 0.056 3962 Dihedral : 8.606 86.040 3276 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 6.94 % Allowed : 21.81 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 2824 helix: 0.06 (0.15), residues: 1083 sheet: 0.25 (0.24), residues: 478 loop : -1.13 (0.17), residues: 1263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.001 HIS C 470 PHE 0.019 0.002 PHE E 250 TYR 0.016 0.002 TYR B 286 ARG 0.011 0.001 ARG D 405 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 298 time to evaluate : 2.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.6477 (mtp180) REVERT: A 278 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.5537 (mtm-85) REVERT: B 409 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.4721 (ttpp) REVERT: C 190 ASN cc_start: 0.6279 (OUTLIER) cc_final: 0.5535 (p0) REVERT: C 375 MET cc_start: 0.6395 (ttp) cc_final: 0.5856 (tpp) REVERT: C 454 ARG cc_start: 0.4531 (OUTLIER) cc_final: 0.2723 (mmt180) REVERT: D 115 ARG cc_start: 0.6300 (ptp-110) cc_final: 0.5834 (ptp-170) REVERT: D 271 MET cc_start: 0.6844 (mtp) cc_final: 0.6631 (mtm) REVERT: D 313 TYR cc_start: 0.6619 (m-80) cc_final: 0.6270 (m-80) REVERT: D 337 GLU cc_start: 0.7299 (OUTLIER) cc_final: 0.6070 (mp0) REVERT: D 351 SER cc_start: 0.5667 (m) cc_final: 0.4981 (t) REVERT: E 413 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.6869 (p0) REVERT: F 213 MET cc_start: 0.6543 (OUTLIER) cc_final: 0.6250 (mtt) REVERT: F 240 ARG cc_start: 0.6093 (OUTLIER) cc_final: 0.5859 (ptt90) outliers start: 161 outliers final: 79 residues processed: 406 average time/residue: 1.1384 time to fit residues: 543.6866 Evaluate side-chains 360 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 272 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 213 MET Chi-restraints excluded: chain F residue 214 VAL Chi-restraints excluded: chain F residue 240 ARG Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 451 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 227 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 202 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 232 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 ASN A 65 ASN A 341 GLN A 467 ASN B 483 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 426 GLN C 474 HIS D 8 GLN E 33 GLN ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 174 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 22371 Z= 0.344 Angle : 0.693 11.995 30345 Z= 0.363 Chirality : 0.049 0.219 3485 Planarity : 0.006 0.063 3962 Dihedral : 8.799 87.848 3275 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 7.80 % Allowed : 22.28 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.15), residues: 2824 helix: -0.21 (0.15), residues: 1083 sheet: -0.01 (0.23), residues: 486 loop : -1.29 (0.17), residues: 1255 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS C 470 PHE 0.030 0.002 PHE F 409 TYR 0.022 0.002 TYR F 238 ARG 0.008 0.001 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 286 time to evaluate : 2.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6548 (mtp180) REVERT: A 278 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.5405 (mtm-85) REVERT: B 345 GLN cc_start: 0.6697 (OUTLIER) cc_final: 0.6264 (mt0) REVERT: B 409 LYS cc_start: 0.6464 (OUTLIER) cc_final: 0.4885 (ttpp) REVERT: C 171 ARG cc_start: 0.7656 (mtm110) cc_final: 0.7432 (mtm-85) REVERT: C 190 ASN cc_start: 0.6271 (OUTLIER) cc_final: 0.5550 (p0) REVERT: C 236 PHE cc_start: 0.7423 (OUTLIER) cc_final: 0.7220 (p90) REVERT: C 299 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5675 (mt-10) REVERT: C 317 PRO cc_start: 0.7078 (Cg_endo) cc_final: 0.6803 (Cg_exo) REVERT: C 357 ILE cc_start: 0.6173 (OUTLIER) cc_final: 0.5763 (pp) REVERT: C 454 ARG cc_start: 0.4405 (OUTLIER) cc_final: 0.2347 (mmt180) REVERT: D 115 ARG cc_start: 0.6517 (ptp-110) cc_final: 0.6181 (ptp-170) REVERT: D 271 MET cc_start: 0.6818 (mtp) cc_final: 0.6611 (mtm) REVERT: D 313 TYR cc_start: 0.6708 (m-80) cc_final: 0.6337 (m-80) REVERT: D 337 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6434 (mp0) REVERT: D 382 ASP cc_start: 0.6598 (OUTLIER) cc_final: 0.6395 (m-30) REVERT: F 35 LYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6158 (mtpp) REVERT: F 226 MET cc_start: 0.7004 (OUTLIER) cc_final: 0.6667 (mtm) REVERT: F 333 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6618 (tpp-160) REVERT: F 352 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5800 (ptt180) outliers start: 181 outliers final: 94 residues processed: 413 average time/residue: 1.1620 time to fit residues: 555.0343 Evaluate side-chains 378 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 269 time to evaluate : 2.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 491 ILE Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 319 VAL Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 395 PHE Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 236 PHE Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 382 ASP Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 384 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 439 GLU Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain E residue 433 THR Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 226 MET Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 333 ARG Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 442 GLU Chi-restraints excluded: chain F residue 451 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 91 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 160 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 272 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN A 467 ASN B 322 GLN B 483 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 8 GLN D 304 GLN E 33 GLN E 179 HIS ** E 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.4811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22371 Z= 0.253 Angle : 0.625 10.030 30345 Z= 0.327 Chirality : 0.046 0.204 3485 Planarity : 0.005 0.058 3962 Dihedral : 8.326 89.704 3270 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 7.11 % Allowed : 23.84 % Favored : 69.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 2824 helix: -0.03 (0.15), residues: 1093 sheet: 0.01 (0.23), residues: 487 loop : -1.25 (0.17), residues: 1244 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.001 HIS C 474 PHE 0.020 0.002 PHE F 409 TYR 0.018 0.002 TYR A 260 ARG 0.006 0.000 ARG F 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 287 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6538 (mtp180) REVERT: A 278 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.5303 (mtm-85) REVERT: B 45 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7383 (p0) REVERT: B 345 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6182 (mt0) REVERT: B 403 ASP cc_start: 0.6626 (t70) cc_final: 0.6182 (t0) REVERT: B 409 LYS cc_start: 0.6380 (OUTLIER) cc_final: 0.4852 (ttpp) REVERT: B 492 GLU cc_start: 0.6219 (mm-30) cc_final: 0.5858 (pt0) REVERT: C 190 ASN cc_start: 0.6175 (OUTLIER) cc_final: 0.5475 (p0) REVERT: C 299 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5560 (mt-10) REVERT: C 317 PRO cc_start: 0.7057 (Cg_endo) cc_final: 0.6815 (Cg_exo) REVERT: C 357 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5970 (pp) REVERT: C 375 MET cc_start: 0.6549 (OUTLIER) cc_final: 0.6160 (tpp) REVERT: D 3 ARG cc_start: 0.6011 (mpp-170) cc_final: 0.5734 (pmm150) REVERT: D 115 ARG cc_start: 0.6496 (ptp-110) cc_final: 0.6260 (ptp-170) REVERT: D 313 TYR cc_start: 0.6648 (m-80) cc_final: 0.6250 (m-80) REVERT: D 337 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6448 (mp0) REVERT: D 459 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6527 (tt) REVERT: E 335 LEU cc_start: 0.6309 (OUTLIER) cc_final: 0.5998 (mm) REVERT: E 413 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.6929 (p0) REVERT: F 352 ARG cc_start: 0.6169 (OUTLIER) cc_final: 0.5842 (ptt180) REVERT: F 431 LYS cc_start: 0.7592 (OUTLIER) cc_final: 0.7345 (mppt) outliers start: 165 outliers final: 91 residues processed: 406 average time/residue: 1.1356 time to fit residues: 535.6676 Evaluate side-chains 374 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 268 time to evaluate : 2.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 198 ILE Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 289 ASP Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 296 ARG Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 357 ILE Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 332 GLU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 90 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 118 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 326 ASP Chi-restraints excluded: chain E residue 335 LEU Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 416 VAL Chi-restraints excluded: chain E residue 419 GLN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain E residue 430 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 166 VAL Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 358 ILE Chi-restraints excluded: chain F residue 386 ILE Chi-restraints excluded: chain F residue 387 LEU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 431 LYS Chi-restraints excluded: chain F residue 442 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 263 optimal weight: 0.3980 chunk 30 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 chunk 199 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 229 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 chunk 271 optimal weight: 0.9990 chunk 170 optimal weight: 0.0670 chunk 165 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 341 GLN ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN B 483 ASN C 163 GLN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS E 304 GLN ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 375 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22371 Z= 0.158 Angle : 0.565 11.543 30345 Z= 0.292 Chirality : 0.044 0.175 3485 Planarity : 0.005 0.064 3962 Dihedral : 7.601 81.890 3270 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 4.05 % Allowed : 27.59 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.16), residues: 2824 helix: 0.40 (0.16), residues: 1087 sheet: 0.18 (0.23), residues: 488 loop : -1.09 (0.17), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.001 HIS C 474 PHE 0.033 0.001 PHE C 456 TYR 0.017 0.001 TYR E 148 ARG 0.012 0.000 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 285 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7043 (OUTLIER) cc_final: 0.6404 (mtp180) REVERT: A 278 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.5208 (mtm-85) REVERT: B 403 ASP cc_start: 0.6592 (t70) cc_final: 0.6258 (t0) REVERT: B 409 LYS cc_start: 0.6140 (OUTLIER) cc_final: 0.4718 (ttpp) REVERT: C 190 ASN cc_start: 0.6275 (OUTLIER) cc_final: 0.5688 (p0) REVERT: C 300 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.6679 (mtm110) REVERT: C 317 PRO cc_start: 0.7061 (Cg_endo) cc_final: 0.6793 (Cg_exo) REVERT: C 375 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5939 (tpp) REVERT: C 392 LEU cc_start: 0.6067 (pp) cc_final: 0.5819 (mp) REVERT: D 322 PHE cc_start: 0.7507 (OUTLIER) cc_final: 0.6911 (m-80) REVERT: D 337 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: D 459 ILE cc_start: 0.6701 (OUTLIER) cc_final: 0.6391 (tt) REVERT: E 256 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.7466 (mmt180) REVERT: E 413 ASN cc_start: 0.7239 (OUTLIER) cc_final: 0.6933 (p0) REVERT: F 352 ARG cc_start: 0.6037 (OUTLIER) cc_final: 0.5785 (ptt180) outliers start: 94 outliers final: 43 residues processed: 351 average time/residue: 1.2115 time to fit residues: 489.8188 Evaluate side-chains 313 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 258 time to evaluate : 2.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 384 LEU Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 389 MET Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 392 LEU Chi-restraints excluded: chain F residue 442 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 168 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 162 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 chunk 185 optimal weight: 20.0000 chunk 134 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 ASN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN A 470 HIS B 433 GLN B 483 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 259 GLN F 419 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 22371 Z= 0.244 Angle : 0.624 13.763 30345 Z= 0.323 Chirality : 0.046 0.230 3485 Planarity : 0.005 0.056 3962 Dihedral : 7.853 80.285 3270 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 5.22 % Allowed : 27.41 % Favored : 67.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.16), residues: 2824 helix: 0.20 (0.16), residues: 1088 sheet: 0.06 (0.23), residues: 489 loop : -1.03 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 470 PHE 0.026 0.002 PHE C 456 TYR 0.029 0.002 TYR D 148 ARG 0.015 0.000 ARG B 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 268 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ARG cc_start: 0.4819 (OUTLIER) cc_final: 0.4616 (mtm110) REVERT: A 93 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6505 (mtp180) REVERT: A 278 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.5236 (mtm-85) REVERT: B 45 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.7174 (p0) REVERT: B 345 GLN cc_start: 0.6632 (OUTLIER) cc_final: 0.6137 (mt0) REVERT: B 403 ASP cc_start: 0.6619 (t70) cc_final: 0.6267 (t0) REVERT: B 409 LYS cc_start: 0.6327 (OUTLIER) cc_final: 0.4817 (ttpp) REVERT: B 492 GLU cc_start: 0.6303 (mm-30) cc_final: 0.5918 (pt0) REVERT: C 62 MET cc_start: 0.6352 (ptm) cc_final: 0.6147 (ppp) REVERT: C 190 ASN cc_start: 0.6351 (OUTLIER) cc_final: 0.5740 (p0) REVERT: C 251 TYR cc_start: 0.5928 (m-10) cc_final: 0.5361 (m-80) REVERT: C 300 ARG cc_start: 0.6913 (OUTLIER) cc_final: 0.6682 (mtm110) REVERT: C 317 PRO cc_start: 0.7158 (Cg_endo) cc_final: 0.6882 (Cg_exo) REVERT: C 375 MET cc_start: 0.6380 (ttp) cc_final: 0.6032 (tpp) REVERT: C 454 ARG cc_start: 0.4528 (OUTLIER) cc_final: 0.2428 (mmt180) REVERT: D 271 MET cc_start: 0.6807 (mtp) cc_final: 0.6596 (mtm) REVERT: D 313 TYR cc_start: 0.6537 (m-80) cc_final: 0.6154 (m-80) REVERT: D 337 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: D 459 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.6529 (tt) REVERT: E 3 ARG cc_start: 0.5818 (OUTLIER) cc_final: 0.5551 (mmt180) REVERT: E 413 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6780 (p0) REVERT: F 35 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.6140 (mtpp) REVERT: F 352 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5759 (ptt180) outliers start: 121 outliers final: 65 residues processed: 355 average time/residue: 1.1800 time to fit residues: 483.1823 Evaluate side-chains 336 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 256 time to evaluate : 2.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 87 GLU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 300 ARG Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 454 ARG Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 145 LEU Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 326 ASP Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 459 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 379 GLU Chi-restraints excluded: chain F residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 247 optimal weight: 7.9990 chunk 260 optimal weight: 8.9990 chunk 237 optimal weight: 7.9990 chunk 253 optimal weight: 7.9990 chunk 152 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 198 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 chunk 252 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN A 470 HIS B 215 HIS B 426 GLN B 483 ASN C 70 ASN C 143 HIS ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 HIS D 8 GLN D 22 HIS E 33 GLN F 38 ASN ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN F 259 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6815 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 22371 Z= 0.424 Angle : 0.787 14.111 30345 Z= 0.411 Chirality : 0.051 0.277 3485 Planarity : 0.007 0.066 3962 Dihedral : 8.642 87.266 3270 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 6.21 % Allowed : 26.90 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 2824 helix: -0.48 (0.15), residues: 1087 sheet: -0.29 (0.24), residues: 468 loop : -1.45 (0.17), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS C 474 PHE 0.026 0.003 PHE F 255 TYR 0.025 0.003 TYR F 238 ARG 0.015 0.001 ARG C 171 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 271 time to evaluate : 2.450 Fit side-chains revert: symmetry clash REVERT: A 89 ARG cc_start: 0.4900 (OUTLIER) cc_final: 0.4690 (mtm110) REVERT: A 93 ARG cc_start: 0.7292 (OUTLIER) cc_final: 0.6618 (mtp180) REVERT: A 278 ARG cc_start: 0.6914 (OUTLIER) cc_final: 0.5419 (mtm-85) REVERT: B 345 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6343 (mt0) REVERT: B 409 LYS cc_start: 0.6493 (OUTLIER) cc_final: 0.4932 (ttpp) REVERT: B 492 GLU cc_start: 0.6360 (mm-30) cc_final: 0.5941 (pt0) REVERT: C 190 ASN cc_start: 0.6253 (OUTLIER) cc_final: 0.5555 (p0) REVERT: C 251 TYR cc_start: 0.6009 (m-10) cc_final: 0.5515 (m-80) REVERT: C 299 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5647 (mt-10) REVERT: C 375 MET cc_start: 0.6493 (OUTLIER) cc_final: 0.6134 (tpp) REVERT: C 392 LEU cc_start: 0.6059 (pp) cc_final: 0.5792 (mp) REVERT: D 3 ARG cc_start: 0.6341 (mpp-170) cc_final: 0.6010 (pmm150) REVERT: D 271 MET cc_start: 0.6850 (mtp) cc_final: 0.6625 (mtm) REVERT: D 313 TYR cc_start: 0.6686 (m-80) cc_final: 0.6368 (m-80) REVERT: D 337 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: D 351 SER cc_start: 0.5746 (m) cc_final: 0.5117 (t) REVERT: E 3 ARG cc_start: 0.6013 (OUTLIER) cc_final: 0.5479 (ptp-110) REVERT: F 3 ARG cc_start: 0.6805 (OUTLIER) cc_final: 0.6222 (pmt-80) REVERT: F 35 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.6156 (mtpp) REVERT: F 352 ARG cc_start: 0.6214 (OUTLIER) cc_final: 0.5799 (ptt180) outliers start: 144 outliers final: 84 residues processed: 374 average time/residue: 1.1562 time to fit residues: 501.0640 Evaluate side-chains 350 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 253 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 89 ARG Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 204 THR Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 345 GLN Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 406 THR Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 451 GLU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 46 ASN Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 129 ILE Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 202 GLU Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 299 GLU Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 115 ARG Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 188 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 366 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 389 MET Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 33 GLN Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 3 ARG Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 35 LYS Chi-restraints excluded: chain F residue 62 ILE Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 451 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 166 optimal weight: 0.1980 chunk 267 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 186 optimal weight: 0.6980 chunk 280 optimal weight: 3.9990 chunk 258 optimal weight: 0.9990 chunk 223 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 172 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN A 470 HIS B 294 HIS B 483 ASN ** C 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 407 GLN C 474 HIS D 8 GLN ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS ** E 324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 HIS ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 413 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 22371 Z= 0.174 Angle : 0.614 13.290 30345 Z= 0.317 Chirality : 0.045 0.227 3485 Planarity : 0.005 0.061 3962 Dihedral : 7.761 76.257 3270 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.10 % Allowed : 30.22 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2824 helix: 0.22 (0.16), residues: 1077 sheet: -0.10 (0.24), residues: 470 loop : -1.12 (0.17), residues: 1277 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.044 0.001 HIS C 474 PHE 0.029 0.001 PHE C 456 TYR 0.029 0.001 TYR D 148 ARG 0.014 0.001 ARG C 171 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5648 Ramachandran restraints generated. 2824 Oldfield, 0 Emsley, 2824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 268 time to evaluate : 2.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6404 (mtp180) REVERT: A 278 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.5316 (mtm-85) REVERT: B 322 GLN cc_start: 0.6844 (mp-120) cc_final: 0.6122 (mp-120) REVERT: B 403 ASP cc_start: 0.6598 (t70) cc_final: 0.6261 (t0) REVERT: B 409 LYS cc_start: 0.6233 (OUTLIER) cc_final: 0.4763 (ttpp) REVERT: B 492 GLU cc_start: 0.6435 (mm-30) cc_final: 0.6018 (pt0) REVERT: C 125 GLU cc_start: 0.5108 (pm20) cc_final: 0.4595 (pm20) REVERT: C 190 ASN cc_start: 0.6165 (OUTLIER) cc_final: 0.5551 (p0) REVERT: C 251 TYR cc_start: 0.6092 (m-10) cc_final: 0.5765 (m-80) REVERT: C 317 PRO cc_start: 0.7141 (Cg_endo) cc_final: 0.6909 (Cg_exo) REVERT: C 375 MET cc_start: 0.6446 (OUTLIER) cc_final: 0.6123 (tpp) REVERT: C 392 LEU cc_start: 0.6191 (pp) cc_final: 0.5910 (mp) REVERT: D 337 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.6091 (mp0) REVERT: E 256 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7441 (mmt180) REVERT: E 413 ASN cc_start: 0.7305 (OUTLIER) cc_final: 0.6975 (p0) REVERT: F 218 MET cc_start: 0.6711 (mtt) cc_final: 0.6203 (mtt) REVERT: F 352 ARG cc_start: 0.6073 (OUTLIER) cc_final: 0.5741 (ptt180) outliers start: 72 outliers final: 50 residues processed: 315 average time/residue: 1.1432 time to fit residues: 417.8937 Evaluate side-chains 312 residues out of total 2320 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 253 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 ARG Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 180 ILE Chi-restraints excluded: chain A residue 219 ASP Chi-restraints excluded: chain A residue 243 VAL Chi-restraints excluded: chain A residue 278 ARG Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 397 GLN Chi-restraints excluded: chain A residue 406 THR Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 200 GLN Chi-restraints excluded: chain B residue 203 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 264 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 409 LYS Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 121 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 190 ASN Chi-restraints excluded: chain C residue 366 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 474 HIS Chi-restraints excluded: chain C residue 483 ASN Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 32 ILE Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 162 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 322 PHE Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 349 SER Chi-restraints excluded: chain D residue 383 ILE Chi-restraints excluded: chain D residue 421 THR Chi-restraints excluded: chain E residue 9 VAL Chi-restraints excluded: chain E residue 67 THR Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 130 THR Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 396 ASP Chi-restraints excluded: chain E residue 413 ASN Chi-restraints excluded: chain E residue 428 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 219 ASN Chi-restraints excluded: chain F residue 322 PHE Chi-restraints excluded: chain F residue 352 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 177 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 206 optimal weight: 9.9990 chunk 33 optimal weight: 10.0000 chunk 62 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 93 optimal weight: 9.9990 chunk 230 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 ASN B 483 ASN ** C 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 173 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 407 GLN F 173 HIS ** F 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 253 ASN ** F 413 ASN ** 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 = 0.4519 r_free = 0.4519 target = 0.193251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.164118 restraints weight = 25282.654| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.18 r_work: 0.4117 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3982 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22371 Z= 0.364 Angle : 0.733 15.299 30345 Z= 0.380 Chirality : 0.049 0.207 3485 Planarity : 0.006 0.069 3962 Dihedral : 8.268 84.614 3270 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 4.35 % Allowed : 29.40 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 2824 helix: -0.24 (0.15), residues: 1081 sheet: -0.28 (0.23), residues: 473 loop : -1.32 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.028 0.002 HIS C 474 PHE 0.035 0.002 PHE F 414 TYR 0.028 0.002 TYR D 148 ARG 0.016 0.001 ARG C 171 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8718.21 seconds wall clock time: 154 minutes 41.91 seconds (9281.91 seconds total)