Starting phenix.real_space_refine on Mon Jul 6 16:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.map" model { file = "/net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8dbw_27311/07_2026/8dbw_27311.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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 16 5.49 5 Mg 5 5.21 5 S 178 5.16 5 C 23389 2.51 5 N 6292 2.21 5 O 6955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 36835 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3852 Classifications: {'peptide': 510} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Chain: "B" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3810 Classifications: {'peptide': 505} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 486} Chain: "C" Number of atoms: 3845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3845 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3534 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "E" Number of atoms: 3534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3534 Classifications: {'peptide': 460} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "F" Number of atoms: 3521 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3521 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "G" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2187 Classifications: {'peptide': 284} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 274} Chain: "H" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1022 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "I" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "P" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "R" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 552 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "S" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 558 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "W" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1318 Classifications: {'peptide': 173} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 169} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "X" Number of atoms: 1179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1179 Classifications: {'peptide': 153} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 150} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "Y" Number of atoms: 1172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1172 Classifications: {'peptide': 155} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 152} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "a" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2104 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 7.15, per 1000 atoms: 0.19 Number of scatterers: 36835 At special positions: 0 Unit cell: (178.035, 220.116, 135.954, 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 178 16.00 P 16 15.00 Mg 5 11.99 O 6955 8.00 N 6292 7.00 C 23389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8790 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 21 sheets defined 61.0% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 4 through 20 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.721A pdb=" N LEU A 103 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.610A pdb=" N ILE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N HIS A 215 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 219 Processing helix chain 'A' and resid 231 through 253 Proline residue: A 239 - end of helix removed outlier: 3.570A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.602A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 288 No H-bonds generated for 'chain 'A' and resid 287 through 288' Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 356 through 363 Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.541A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN A 382 " --> pdb=" O GLY A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 407 removed outlier: 4.556A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N THR A 395 " --> pdb=" O GLY A 391 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 459 removed outlier: 4.367A pdb=" N ASP A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 478 removed outlier: 4.144A pdb=" N GLY A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N SER A 466 " --> pdb=" O SER A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 489 removed outlier: 3.542A pdb=" N MET A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'B' and resid 10 through 18 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.823A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.625A pdb=" N ARG B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 313 Processing helix chain 'B' and resid 339 through 349 Processing helix chain 'B' and resid 356 through 362 removed outlier: 3.555A pdb=" N PHE B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 4.098A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 390 through 408 removed outlier: 3.798A pdb=" N ARG B 394 " --> pdb=" O SER B 390 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 431 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 479 Processing helix chain 'B' and resid 479 through 490 removed outlier: 3.878A pdb=" N MET B 483 " --> pdb=" O HIS B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 510 removed outlier: 3.905A pdb=" N ALA B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 20 through 24 removed outlier: 4.068A pdb=" N SER C 23 " --> pdb=" O ASN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.600A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU C 104 " --> pdb=" O ARG C 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 100 through 104' Processing helix chain 'C' and resid 150 through 157 Processing helix chain 'C' and resid 174 through 190 removed outlier: 4.457A pdb=" N ASP C 188 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N SER C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 216 through 219 removed outlier: 4.468A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 252 Proline residue: C 239 - end of helix removed outlier: 3.883A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 289 through 299 Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.889A pdb=" N ASP C 336 " --> pdb=" O GLN C 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 339 through 347 Processing helix chain 'C' and resid 356 through 361 Processing helix chain 'C' and resid 377 through 381 removed outlier: 3.681A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 Processing helix chain 'C' and resid 392 through 407 Processing helix chain 'C' and resid 415 through 431 Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 463 through 478 removed outlier: 4.026A pdb=" N PHE C 467 " --> pdb=" O LYS C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 488 removed outlier: 3.883A pdb=" N GLU C 485 " --> pdb=" O PRO C 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 510 removed outlier: 3.729A pdb=" N THR C 510 " --> pdb=" O SER C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 115 through 119 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 170 removed outlier: 3.841A pdb=" N ILE D 168 " --> pdb=" O ARG D 164 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLU D 169 " --> pdb=" O ASN D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.671A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 256 removed outlier: 3.940A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL D 254 " --> pdb=" O ALA D 250 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA D 256 " --> pdb=" O THR D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 259 No H-bonds generated for 'chain 'D' and resid 257 through 259' Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.638A pdb=" N LEU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 313 removed outlier: 4.036A pdb=" N ALA D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 350 through 378 removed outlier: 3.603A pdb=" N GLU D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU D 370 " --> pdb=" O ARG D 366 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.926A pdb=" N THR D 411 " --> pdb=" O ALA D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 419 through 432 Processing helix chain 'D' and resid 439 through 443 Processing helix chain 'D' and resid 448 through 459 Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.716A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 Processing helix chain 'E' and resid 182 through 196 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 233 removed outlier: 3.538A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.733A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 298 through 302 removed outlier: 3.524A pdb=" N ASP E 301 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 313 removed outlier: 3.666A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 377 removed outlier: 3.862A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 378 through 382 Processing helix chain 'E' and resid 383 through 400 Processing helix chain 'E' and resid 406 through 412 removed outlier: 4.036A pdb=" N PHE E 410 " --> pdb=" O VAL E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 432 Processing helix chain 'E' and resid 439 through 444 Processing helix chain 'E' and resid 448 through 459 removed outlier: 3.695A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 removed outlier: 3.671A pdb=" N ASP F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 167 Processing helix chain 'F' and resid 182 through 196 Processing helix chain 'F' and resid 212 through 232 removed outlier: 4.223A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 4.253A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 Processing helix chain 'F' and resid 298 through 302 removed outlier: 3.962A pdb=" N ASP F 301 " --> pdb=" O VAL F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 Processing helix chain 'F' and resid 311 through 315 removed outlier: 3.797A pdb=" N LEU F 315 " --> pdb=" O PHE F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 322 through 328 Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 4.078A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 400 Processing helix chain 'F' and resid 419 through 432 Processing helix chain 'F' and resid 439 through 444 Processing helix chain 'F' and resid 448 through 459 removed outlier: 3.539A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 56 Proline residue: G 43 - end of helix Processing helix chain 'G' and resid 89 through 108 Processing helix chain 'G' and resid 118 through 129 Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.739A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N GLY G 150 " --> pdb=" O SER G 146 " (cutoff:3.500A) Proline residue: G 151 - end of helix Processing helix chain 'G' and resid 204 through 208 removed outlier: 3.633A pdb=" N TYR G 207 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 284 removed outlier: 3.512A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ALA G 284 " --> pdb=" O VAL G 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 108 removed outlier: 3.659A pdb=" N SER H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 135 removed outlier: 4.221A pdb=" N GLN H 116 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ALA H 119 " --> pdb=" O ALA H 115 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLU H 132 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS H 135 " --> pdb=" O ILE H 131 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 42 removed outlier: 3.764A pdb=" N LEU I 9 " --> pdb=" O ASN I 5 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N MET I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.875A pdb=" N THR I 51 " --> pdb=" O PRO I 47 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Proline residue: I 64 - end of helix Processing helix chain 'J' and resid 4 through 42 removed outlier: 4.098A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 3.716A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.145A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS L 34 " --> pdb=" O ILE L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.876A pdb=" N THR L 51 " --> pdb=" O PRO L 47 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY L 58 " --> pdb=" O PHE L 54 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.762A pdb=" N MET L 65 " --> pdb=" O ASP L 61 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE L 76 " --> pdb=" O LEU L 72 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.654A pdb=" N MET M 11 " --> pdb=" O ASP M 7 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 77 removed outlier: 4.179A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.166A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 77 removed outlier: 3.683A pdb=" N THR N 51 " --> pdb=" O PRO N 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE N 63 " --> pdb=" O LEU N 59 " (cutoff:3.500A) Proline residue: N 64 - end of helix Processing helix chain 'O' and resid 4 through 42 removed outlier: 3.623A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.820A pdb=" N THR O 51 " --> pdb=" O PRO O 47 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.649A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS P 34 " --> pdb=" O ILE P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.849A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.841A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 3.779A pdb=" N LEU Q 8 " --> pdb=" O LEU Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 3.922A pdb=" N THR Q 51 " --> pdb=" O PRO Q 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE Q 55 " --> pdb=" O THR Q 51 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix removed outlier: 3.611A pdb=" N ALA Q 67 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 42 removed outlier: 3.736A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 77 removed outlier: 4.428A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'S' and resid 5 through 7 No H-bonds generated for 'chain 'S' and resid 5 through 7' Processing helix chain 'S' and resid 8 through 42 removed outlier: 3.711A pdb=" N ARG S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN S 42 " --> pdb=" O GLY S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 Processing helix chain 'S' and resid 61 through 78 Processing helix chain 'W' and resid 3 through 21 Proline residue: W 9 - end of helix removed outlier: 3.652A pdb=" N GLU W 20 " --> pdb=" O ASP W 16 " (cutoff:3.500A) Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.753A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 Processing helix chain 'W' and resid 52 through 63 removed outlier: 3.966A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 82 removed outlier: 3.793A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN W 82 " --> pdb=" O VAL W 78 " (cutoff:3.500A) Processing helix chain 'W' and resid 84 through 86 No H-bonds generated for 'chain 'W' and resid 84 through 86' Processing helix chain 'W' and resid 87 through 103 removed outlier: 3.666A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 132 Processing helix chain 'W' and resid 144 through 147 Processing helix chain 'W' and resid 162 through 174 Processing helix chain 'X' and resid 5 through 24 Processing helix chain 'X' and resid 26 through 29 Processing helix chain 'X' and resid 30 through 137 removed outlier: 3.945A pdb=" N GLU X 34 " --> pdb=" O MET X 30 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 146 No H-bonds generated for 'chain 'X' and resid 144 through 146' Processing helix chain 'X' and resid 147 through 153 removed outlier: 3.616A pdb=" N LYS X 151 " --> pdb=" O ASP X 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.503A pdb=" N THR Y 6 " --> pdb=" O ASN Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 140 Processing helix chain 'Y' and resid 141 through 153 Processing helix chain 'a' and resid 7 through 16 Processing helix chain 'a' and resid 43 through 65 Processing helix chain 'a' and resid 73 through 93 removed outlier: 4.090A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 166 removed outlier: 3.532A pdb=" N TYR a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 167 through 172 Processing helix chain 'a' and resid 172 through 180 Processing helix chain 'a' and resid 187 through 229 removed outlier: 3.832A pdb=" N VAL a 191 " --> pdb=" O ALA a 187 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.715A pdb=" N LEU a 207 " --> pdb=" O LYS a 203 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.396A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 3.942A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 35 removed outlier: 6.351A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 38 through 43 current: chain 'A' and resid 60 through 67 removed outlier: 5.625A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 70 " --> pdb=" O GLU A 67 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 75 current: chain 'C' and resid 38 through 43 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 38 through 43 current: chain 'C' and resid 59 through 66 removed outlier: 4.628A pdb=" N TYR C 60 " --> pdb=" O MET C 76 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 71 through 76 current: chain 'D' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 12 through 16 current: chain 'D' and resid 36 through 46 removed outlier: 6.729A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 50 through 55 current: chain 'F' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 12 through 16 current: chain 'F' and resid 36 through 45 removed outlier: 6.656A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.426A pdb=" N VAL A 108 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 8.346A pdb=" N THR A 227 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA A 193 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL A 224 " --> pdb=" O ALA A 193 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR A 195 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ALA A 226 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA A 197 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LYS A 192 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ILE A 259 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE A 194 " --> pdb=" O ILE A 259 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 25 through 35 removed outlier: 6.434A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 38 through 42 current: chain 'B' and resid 59 through 66 removed outlier: 4.562A pdb=" N TYR B 60 " --> pdb=" O MET B 76 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 71 through 76 current: chain 'E' and resid 12 through 16 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 12 through 16 current: chain 'E' and resid 36 through 45 removed outlier: 6.690A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 50 through 55 current: chain 'W' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 139 through 142 current: chain 'W' and resid 157 through 160 Processing sheet with id=AA5, first strand: chain 'B' and resid 96 through 99 Processing sheet with id=AA6, first strand: chain 'B' and resid 107 through 108 removed outlier: 6.390A pdb=" N VAL B 108 " --> pdb=" O VAL B 225 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LYS B 192 " --> pdb=" O LEU B 257 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N ILE B 259 " --> pdb=" O LYS B 192 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE B 194 " --> pdb=" O ILE B 259 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP B 261 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 196 " --> pdb=" O ASP B 261 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR B 260 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.366A pdb=" N ILE B 159 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AA9, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.327A pdb=" N LYS C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ILE C 259 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE C 194 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N TYR C 260 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.512A pdb=" N ILE C 159 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.245A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.065A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.950A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N TYR D 297 " --> pdb=" O VAL D 241 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 79 removed outlier: 4.502A pdb=" N GLU E 105 " --> pdb=" O VAL E 79 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.922A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N GLN E 208 " --> pdb=" O MET E 88 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.264A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 78 Processing sheet with id=AB8, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.087A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 132 through 135 removed outlier: 7.226A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.310A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 4 through 9 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 14 through 20 current: chain 'H' and resid 32 through 33 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 32 through 33 current: chain 'H' and resid 61 through 69 removed outlier: 7.018A pdb=" N LEU H 64 " --> pdb=" O ALA H 83 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA H 83 " --> pdb=" O LEU H 64 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLY H 66 " --> pdb=" O ASP H 81 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 105 through 106 Processing sheet with id=AC3, first strand: chain 'a' and resid 21 through 22 2208 hydrogen bonds defined for protein. 6471 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: 7.37 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8630 1.33 - 1.45: 6796 1.45 - 1.57: 21583 1.57 - 1.69: 27 1.69 - 1.81: 356 Bond restraints: 37392 Sorted by residual: bond pdb=" N ALA H 39 " pdb=" CA ALA H 39 " ideal model delta sigma weight residual 1.455 1.495 -0.040 9.60e-03 1.09e+04 1.78e+01 bond pdb=" N GLN H 72 " pdb=" CA GLN H 72 " ideal model delta sigma weight residual 1.461 1.494 -0.033 9.20e-03 1.18e+04 1.27e+01 bond pdb=" N LEU H 42 " pdb=" CA LEU H 42 " ideal model delta sigma weight residual 1.455 1.497 -0.042 1.25e-02 6.40e+03 1.15e+01 bond pdb=" N TRP G 203 " pdb=" CA TRP G 203 " ideal model delta sigma weight residual 1.455 1.497 -0.041 1.23e-02 6.61e+03 1.14e+01 bond pdb=" N TYR H 35 " pdb=" CA TYR H 35 " ideal model delta sigma weight residual 1.455 1.485 -0.030 9.60e-03 1.09e+04 9.79e+00 ... (remaining 37387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 49553 2.47 - 4.94: 964 4.94 - 7.42: 93 7.42 - 9.89: 23 9.89 - 12.36: 4 Bond angle restraints: 50637 Sorted by residual: angle pdb=" N ALA H 39 " pdb=" CA ALA H 39 " pdb=" C ALA H 39 " ideal model delta sigma weight residual 108.25 116.59 -8.34 1.16e+00 7.43e-01 5.17e+01 angle pdb=" N PRO H 73 " pdb=" CA PRO H 73 " pdb=" C PRO H 73 " ideal model delta sigma weight residual 111.41 120.14 -8.73 1.50e+00 4.44e-01 3.39e+01 angle pdb=" N LEU H 42 " pdb=" CA LEU H 42 " pdb=" C LEU H 42 " ideal model delta sigma weight residual 108.99 117.67 -8.68 1.57e+00 4.06e-01 3.06e+01 angle pdb=" C LEU Q 45 " pdb=" N ILE Q 46 " pdb=" CA ILE Q 46 " ideal model delta sigma weight residual 120.24 123.66 -3.42 6.30e-01 2.52e+00 2.95e+01 angle pdb=" C PRO H 40 " pdb=" CA PRO H 40 " pdb=" CB PRO H 40 " ideal model delta sigma weight residual 111.56 102.80 8.76 1.65e+00 3.67e-01 2.82e+01 ... (remaining 50632 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 21840 29.26 - 58.51: 671 58.51 - 87.77: 81 87.77 - 117.02: 5 117.02 - 146.28: 3 Dihedral angle restraints: 22600 sinusoidal: 8857 harmonic: 13743 Sorted by residual: dihedral pdb=" O1B ADP D 501 " pdb=" O3A ADP D 501 " pdb=" PB ADP D 501 " pdb=" PA ADP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 86.28 -146.28 1 2.00e+01 2.50e-03 4.40e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 70.25 -130.26 1 2.00e+01 2.50e-03 3.95e+01 dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 63.42 -123.42 1 2.00e+01 2.50e-03 3.72e+01 ... (remaining 22597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 5373 0.087 - 0.173: 508 0.173 - 0.260: 14 0.260 - 0.347: 4 0.347 - 0.433: 2 Chirality restraints: 5901 Sorted by residual: chirality pdb=" CA HIS H 38 " pdb=" N HIS H 38 " pdb=" C HIS H 38 " pdb=" CB HIS H 38 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CB THR H 43 " pdb=" CA THR H 43 " pdb=" OG1 THR H 43 " pdb=" CG2 THR H 43 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CA PRO H 73 " pdb=" N PRO H 73 " pdb=" C PRO H 73 " pdb=" CB PRO H 73 " both_signs ideal model delta sigma weight residual False 2.72 2.38 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 5898 not shown) Planarity restraints: 6546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 474 " -0.005 2.00e-02 2.50e+03 3.46e-02 2.39e+01 pdb=" CG TYR B 474 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 TYR B 474 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 TYR B 474 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 474 " 0.049 2.00e-02 2.50e+03 pdb=" CE2 TYR B 474 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 474 " 0.049 2.00e-02 2.50e+03 pdb=" OH TYR B 474 " -0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP G 203 " 0.023 2.00e-02 2.50e+03 4.71e-02 2.22e+01 pdb=" C TRP G 203 " -0.081 2.00e-02 2.50e+03 pdb=" O TRP G 203 " 0.030 2.00e-02 2.50e+03 pdb=" N ASP G 204 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS a 167 " 0.023 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" C LYS a 167 " -0.079 2.00e-02 2.50e+03 pdb=" O LYS a 167 " 0.030 2.00e-02 2.50e+03 pdb=" N MET a 168 " 0.026 2.00e-02 2.50e+03 ... (remaining 6543 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 167 2.60 - 3.18: 32660 3.18 - 3.75: 57077 3.75 - 4.33: 79215 4.33 - 4.90: 129959 Nonbonded interactions: 299078 Sorted by model distance: nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 2.029 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 2.081 2.170 nonbonded pdb=" O2A ATP A 600 " pdb="MG MG A 601 " model vdw 2.107 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 2.111 2.170 nonbonded pdb=" OG1 THR F 156 " pdb="MG MG F 501 " model vdw 2.125 2.170 ... (remaining 299073 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB )) or resid 420 through 511 or resid 600 through 601)) selection = (chain 'B' and (resid 7 through 418 or (resid 419 and (name N or name CA or name \ C or name O or name CB )) or resid 420 through 601)) selection = (chain 'C' and resid 7 through 601) } ncs_group { reference = (chain 'D' and resid 2 through 459) selection = (chain 'E' and resid 2 through 459) selection = (chain 'F' and resid 2 through 459) } ncs_group { reference = (chain 'I' and resid 3 through 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = (chain 'X' and (resid 1 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 57 or (resid 58 through 59 and (nam \ e N or name CA or name C or name O or name CB )) or resid 60 through 62 or (resi \ d 63 and (name N or name CA or name C or name O or name CB )) or resid 64 throug \ h 65 or (resid 66 through 70 and (name N or name CA or name C or name O or name \ CB )) or resid 71 through 72 or (resid 73 and (name N or name CA or name C or na \ me O or name CB )) or resid 74 through 76 or (resid 77 and (name N or name CA or \ name C or name O or name CB )) or resid 78 through 153)) selection = (chain 'Y' and (resid 1 through 90 or (resid 91 through 92 and (name N or name C \ A or name C or name O or name CB )) or resid 93 through 153)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.780 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 31.210 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 0.089 37392 Z= 0.222 Angle : 0.809 12.359 50637 Z= 0.441 Chirality : 0.050 0.433 5901 Planarity : 0.010 0.120 6546 Dihedral : 14.230 146.278 13810 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.23 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 6.87 % Favored : 92.03 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.11), residues: 4793 helix: 0.69 (0.10), residues: 2631 sheet: -0.05 (0.23), residues: 497 loop : -1.18 (0.14), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.004 ARG A 283 TYR 0.053 0.006 TYR B 474 PHE 0.028 0.002 PHE O 54 TRP 0.040 0.004 TRP G 203 HIS 0.018 0.002 HIS G 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.22 (37392) covalent geometry : angle 0.80872 / 0.44 (50637) hydrogen bonds : bond 0.13178 / 8.86 ( 2208) hydrogen bonds : angle 5.92447 / 4.16 ( 6471) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 633 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 MET cc_start: 0.8280 (mtp) cc_final: 0.7759 (mtp) REVERT: A 69 ASP cc_start: 0.7133 (m-30) cc_final: 0.6609 (t0) REVERT: A 148 THR cc_start: 0.8912 (m) cc_final: 0.8677 (p) REVERT: A 156 MET cc_start: 0.8985 (mtm) cc_final: 0.8655 (mtp) REVERT: A 448 LEU cc_start: 0.9441 (mt) cc_final: 0.9033 (tp) REVERT: A 468 GLU cc_start: 0.9135 (tt0) cc_final: 0.8866 (tm-30) REVERT: B 468 GLU cc_start: 0.8799 (tt0) cc_final: 0.8103 (tm-30) REVERT: C 430 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9350 (tp) REVERT: D 205 VAL cc_start: 0.8740 (t) cc_final: 0.8400 (p) REVERT: D 263 SER cc_start: 0.9376 (t) cc_final: 0.9156 (m) REVERT: D 445 MET cc_start: 0.8274 (mmt) cc_final: 0.7897 (tpp) REVERT: E 160 MET cc_start: 0.9217 (mtm) cc_final: 0.8978 (mtp) REVERT: F 209 MET cc_start: 0.8747 (ptp) cc_final: 0.8288 (ptp) REVERT: F 318 THR cc_start: 0.9189 (p) cc_final: 0.8895 (t) REVERT: F 381 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7193 (tm-30) REVERT: F 445 MET cc_start: 0.7979 (mmt) cc_final: 0.7705 (tmm) REVERT: G 79 VAL cc_start: 0.8954 (t) cc_final: 0.8617 (t) REVERT: G 86 LEU cc_start: 0.8873 (mt) cc_final: 0.8421 (mm) REVERT: G 139 MET cc_start: 0.8274 (mmm) cc_final: 0.7282 (tpt) REVERT: G 194 ASP cc_start: 0.8083 (p0) cc_final: 0.7813 (m-30) REVERT: G 224 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8600 (pt0) REVERT: H 15 MET cc_start: 0.6065 (tpp) cc_final: 0.4837 (tpp) REVERT: H 76 VAL cc_start: -0.1406 (OUTLIER) cc_final: -0.1846 (p) REVERT: J 11 MET cc_start: 0.8223 (tpp) cc_final: 0.7952 (mtp) REVERT: L 75 MET cc_start: 0.6204 (ttt) cc_final: 0.5939 (ttt) REVERT: L 78 VAL cc_start: 0.4000 (t) cc_final: 0.3696 (t) REVERT: M 11 MET cc_start: 0.7893 (tpt) cc_final: 0.6578 (mmm) REVERT: M 60 VAL cc_start: 0.5298 (t) cc_final: 0.5019 (t) REVERT: M 68 VAL cc_start: 0.8825 (t) cc_final: 0.8371 (t) REVERT: O 9 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6451 (mm) REVERT: O 11 MET cc_start: 0.8086 (tpt) cc_final: 0.7542 (mtt) REVERT: P 6 MET cc_start: 0.6847 (mmt) cc_final: 0.6610 (mmt) REVERT: Q 57 MET cc_start: 0.5430 (tmm) cc_final: 0.5210 (tmm) REVERT: Q 65 MET cc_start: 0.4304 (mtt) cc_final: 0.3289 (tpt) REVERT: R 11 MET cc_start: 0.5855 (tpt) cc_final: 0.5399 (mtm) REVERT: S 49 LEU cc_start: 0.8677 (mt) cc_final: 0.8233 (tp) REVERT: S 75 MET cc_start: 0.4214 (ttt) cc_final: 0.3804 (ttt) REVERT: W 119 GLN cc_start: 0.9300 (tm-30) cc_final: 0.9025 (mp10) REVERT: X 141 ASP cc_start: 0.8264 (m-30) cc_final: 0.7831 (p0) REVERT: Y 22 MET cc_start: 0.5065 (mmp) cc_final: 0.4454 (mmm) REVERT: Y 150 ASP cc_start: 0.9158 (m-30) cc_final: 0.8407 (p0) REVERT: Y 151 LYS cc_start: 0.8963 (tttt) cc_final: 0.8691 (ptpp) REVERT: a 47 MET cc_start: 0.6970 (tmt) cc_final: 0.6496 (ptt) REVERT: a 97 LYS cc_start: 0.7710 (mttt) cc_final: 0.7344 (pttt) REVERT: a 252 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8061 (mm-40) outliers start: 42 outliers final: 11 residues processed: 668 average time/residue: 0.2305 time to fit residues: 246.6477 Evaluate side-chains 351 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 337 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 0.0770 chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 7.9990 chunk 455 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.0980 chunk 470 optimal weight: 4.9990 overall best weight: 2.8344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 HIS B 361 ASN C 185 ASN D 73 HIS D 353 HIS E 170 HIS G 91 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS Q 42 GLN S 52 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN Y 64 GLN ** a 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 17 ASN a 33 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.063959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.046890 restraints weight = 245383.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047344 restraints weight = 142061.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.047927 restraints weight = 89162.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.048104 restraints weight = 70908.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.048131 restraints weight = 63485.588| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 37392 Z= 0.173 Angle : 0.674 16.708 50637 Z= 0.352 Chirality : 0.045 0.299 5901 Planarity : 0.005 0.066 6546 Dihedral : 7.261 136.133 5243 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 0.08 % Allowed : 2.96 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.12), residues: 4793 helix: 1.19 (0.10), residues: 2623 sheet: -0.01 (0.22), residues: 521 loop : -1.01 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 41 TYR 0.036 0.002 TYR C 474 PHE 0.031 0.002 PHE a 163 TRP 0.038 0.003 TRP G 203 HIS 0.009 0.001 HIS W 21 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (37392) covalent geometry : angle 0.67391 / 0.35 (50637) hydrogen bonds : bond 0.06117 / 4.07 ( 2208) hydrogen bonds : angle 4.84758 / 3.42 ( 6471) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 415 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8124 (mpp) cc_final: 0.7553 (mpp) REVERT: A 52 MET cc_start: 0.8179 (mtp) cc_final: 0.7906 (ttm) REVERT: A 69 ASP cc_start: 0.7299 (m-30) cc_final: 0.6854 (t0) REVERT: A 156 MET cc_start: 0.8868 (mtm) cc_final: 0.8637 (mtp) REVERT: A 386 MET cc_start: 0.8973 (tpp) cc_final: 0.8670 (tpp) REVERT: A 448 LEU cc_start: 0.9525 (mt) cc_final: 0.9256 (mt) REVERT: A 468 GLU cc_start: 0.9264 (tt0) cc_final: 0.8732 (tm-30) REVERT: B 156 MET cc_start: 0.9187 (mmm) cc_final: 0.8700 (mmm) REVERT: B 468 GLU cc_start: 0.8945 (tt0) cc_final: 0.8249 (tm-30) REVERT: C 76 MET cc_start: 0.8377 (mpp) cc_final: 0.8001 (mtm) REVERT: D 209 MET cc_start: 0.8340 (mtp) cc_final: 0.8134 (mpp) REVERT: D 263 SER cc_start: 0.9369 (t) cc_final: 0.9065 (m) REVERT: D 368 GLN cc_start: 0.9053 (mm-40) cc_final: 0.8553 (tp40) REVERT: E 193 MET cc_start: 0.8246 (mtm) cc_final: 0.7934 (mpp) REVERT: E 209 MET cc_start: 0.8555 (mtm) cc_final: 0.8346 (mtm) REVERT: E 431 MET cc_start: 0.9506 (ttm) cc_final: 0.9296 (tpp) REVERT: E 445 MET cc_start: 0.8713 (mmm) cc_final: 0.7850 (mmm) REVERT: F 56 MET cc_start: 0.9184 (mmm) cc_final: 0.8968 (mmm) REVERT: F 209 MET cc_start: 0.8669 (ptp) cc_final: 0.8286 (ptp) REVERT: F 274 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8266 (mt-10) REVERT: F 445 MET cc_start: 0.8140 (mmt) cc_final: 0.7765 (tmm) REVERT: G 54 HIS cc_start: 0.8197 (OUTLIER) cc_final: 0.7961 (p-80) REVERT: G 79 VAL cc_start: 0.9128 (t) cc_final: 0.8815 (t) REVERT: G 86 LEU cc_start: 0.8901 (mt) cc_final: 0.8568 (mm) REVERT: G 187 LEU cc_start: 0.8940 (tp) cc_final: 0.8694 (tp) REVERT: G 194 ASP cc_start: 0.8274 (p0) cc_final: 0.7988 (m-30) REVERT: H 15 MET cc_start: 0.5833 (tpp) cc_final: 0.5430 (tpp) REVERT: H 49 MET cc_start: 0.2055 (ppp) cc_final: 0.1523 (ppp) REVERT: H 127 GLN cc_start: 0.7224 (mp10) cc_final: 0.6593 (tt0) REVERT: L 75 MET cc_start: 0.6057 (ttt) cc_final: 0.5793 (ttt) REVERT: M 11 MET cc_start: 0.8174 (tpt) cc_final: 0.6816 (mmm) REVERT: O 11 MET cc_start: 0.8172 (tpt) cc_final: 0.7453 (mtt) REVERT: O 35 PHE cc_start: 0.7139 (t80) cc_final: 0.6809 (t80) REVERT: P 15 VAL cc_start: 0.7336 (t) cc_final: 0.7118 (p) REVERT: Q 65 MET cc_start: 0.4179 (mtt) cc_final: 0.3345 (tpt) REVERT: R 17 MET cc_start: 0.7793 (mtt) cc_final: 0.7215 (ptm) REVERT: S 17 MET cc_start: 0.4563 (ttt) cc_final: 0.4179 (tpt) REVERT: S 49 LEU cc_start: 0.8798 (mt) cc_final: 0.8355 (tp) REVERT: W 43 MET cc_start: 0.9191 (tpp) cc_final: 0.8763 (tpp) REVERT: W 119 GLN cc_start: 0.9314 (tm-30) cc_final: 0.8962 (mp10) REVERT: X 22 MET cc_start: 0.4808 (ptp) cc_final: 0.4552 (ptp) REVERT: X 141 ASP cc_start: 0.8428 (m-30) cc_final: 0.7715 (t0) REVERT: Y 22 MET cc_start: 0.5123 (mmp) cc_final: 0.4191 (ttt) REVERT: Y 30 MET cc_start: 0.7102 (pmm) cc_final: 0.6320 (mmt) REVERT: Y 150 ASP cc_start: 0.9074 (m-30) cc_final: 0.8790 (m-30) REVERT: a 6 MET cc_start: -0.0244 (ttt) cc_final: -0.1060 (ttt) REVERT: a 47 MET cc_start: 0.7139 (tmm) cc_final: 0.6749 (ptt) REVERT: a 93 MET cc_start: 0.6836 (ttt) cc_final: 0.6229 (ptt) REVERT: a 97 LYS cc_start: 0.7742 (mttt) cc_final: 0.7237 (pttt) outliers start: 3 outliers final: 0 residues processed: 418 average time/residue: 0.2293 time to fit residues: 157.6410 Evaluate side-chains 308 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 307 time to evaluate : 1.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 133 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 363 optimal weight: 3.9990 chunk 340 optimal weight: 5.9990 chunk 325 optimal weight: 20.0000 chunk 345 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 3.9990 chunk 419 optimal weight: 9.9990 chunk 398 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 GLN B 361 ASN B 511 GLN C 185 ASN C 186 GLN D 215 ASN E 191 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN Q 52 GLN R 52 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 33 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.061928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.045336 restraints weight = 247676.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.045430 restraints weight = 146803.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.046395 restraints weight = 98646.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046403 restraints weight = 68828.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.046474 restraints weight = 51436.721| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 37392 Z= 0.184 Angle : 0.649 10.820 50637 Z= 0.336 Chirality : 0.044 0.219 5901 Planarity : 0.005 0.045 6546 Dihedral : 6.849 135.020 5243 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.44 % Favored : 97.54 % Rotamer: Outliers : 0.10 % Allowed : 3.15 % Favored : 96.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.12), residues: 4793 helix: 1.50 (0.10), residues: 2609 sheet: -0.16 (0.22), residues: 536 loop : -0.84 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 41 TYR 0.020 0.002 TYR N 10 PHE 0.036 0.002 PHE Q 53 TRP 0.033 0.002 TRP a 111 HIS 0.016 0.002 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 (37392) covalent geometry : angle 0.64887 / 0.34 (50637) hydrogen bonds : bond 0.05469 / 3.64 ( 2208) hydrogen bonds : angle 4.64720 / 3.29 ( 6471) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 378 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8439 (mpp) cc_final: 0.7849 (mpp) REVERT: A 156 MET cc_start: 0.9018 (mtm) cc_final: 0.8770 (mtp) REVERT: A 386 MET cc_start: 0.9122 (tpp) cc_final: 0.8883 (tpp) REVERT: A 448 LEU cc_start: 0.9532 (mt) cc_final: 0.9226 (mt) REVERT: A 468 GLU cc_start: 0.9174 (tt0) cc_final: 0.8808 (tm-30) REVERT: B 156 MET cc_start: 0.9270 (mmm) cc_final: 0.8809 (mmm) REVERT: B 412 ASP cc_start: 0.7572 (m-30) cc_final: 0.7161 (t70) REVERT: B 468 GLU cc_start: 0.8929 (tt0) cc_final: 0.8383 (tm-30) REVERT: B 472 LEU cc_start: 0.9351 (mt) cc_final: 0.8891 (pp) REVERT: B 504 LEU cc_start: 0.9349 (mm) cc_final: 0.9046 (mt) REVERT: C 76 MET cc_start: 0.8388 (mpp) cc_final: 0.8049 (mtm) REVERT: D 263 SER cc_start: 0.9341 (t) cc_final: 0.8991 (p) REVERT: D 368 GLN cc_start: 0.9139 (mm-40) cc_final: 0.8700 (tp40) REVERT: E 209 MET cc_start: 0.8531 (mtm) cc_final: 0.8301 (mtm) REVERT: F 56 MET cc_start: 0.9157 (mmm) cc_final: 0.8874 (mmm) REVERT: F 209 MET cc_start: 0.8574 (ptp) cc_final: 0.8281 (ptp) REVERT: F 445 MET cc_start: 0.8177 (mmt) cc_final: 0.7783 (tmm) REVERT: G 79 VAL cc_start: 0.9218 (t) cc_final: 0.8929 (t) REVERT: G 102 MET cc_start: 0.8576 (tmm) cc_final: 0.8343 (tmm) REVERT: G 194 ASP cc_start: 0.8332 (p0) cc_final: 0.8022 (m-30) REVERT: H 15 MET cc_start: 0.6148 (tpp) cc_final: 0.5852 (tpp) REVERT: H 49 MET cc_start: 0.3014 (ppp) cc_final: 0.2329 (ppp) REVERT: H 127 GLN cc_start: 0.7173 (mp10) cc_final: 0.6708 (tt0) REVERT: O 11 MET cc_start: 0.7933 (tpt) cc_final: 0.7338 (mtt) REVERT: O 16 MET cc_start: 0.7073 (tmm) cc_final: 0.6733 (tmm) REVERT: P 17 MET cc_start: 0.6655 (ttp) cc_final: 0.6299 (tpt) REVERT: P 30 ILE cc_start: 0.7161 (tt) cc_final: 0.6859 (pt) REVERT: Q 65 MET cc_start: 0.4218 (mtt) cc_final: 0.3375 (tpt) REVERT: R 11 MET cc_start: 0.6221 (mtm) cc_final: 0.5555 (mpp) REVERT: S 17 MET cc_start: 0.4807 (ttt) cc_final: 0.4157 (tpt) REVERT: X 22 MET cc_start: 0.4524 (ptp) cc_final: 0.4107 (ptp) REVERT: X 141 ASP cc_start: 0.8426 (m-30) cc_final: 0.7794 (t0) REVERT: Y 22 MET cc_start: 0.5316 (mmp) cc_final: 0.4351 (ttt) REVERT: Y 30 MET cc_start: 0.7151 (pmm) cc_final: 0.6428 (mmt) REVERT: Y 150 ASP cc_start: 0.9154 (m-30) cc_final: 0.8855 (m-30) REVERT: a 6 MET cc_start: -0.0891 (ttt) cc_final: -0.1206 (ttt) REVERT: a 47 MET cc_start: 0.7021 (tmm) cc_final: 0.6684 (ptt) REVERT: a 93 MET cc_start: 0.6987 (ttt) cc_final: 0.6550 (mmm) REVERT: a 97 LYS cc_start: 0.7567 (mttt) cc_final: 0.7035 (pttt) REVERT: a 216 TYR cc_start: 0.8358 (t80) cc_final: 0.7617 (t80) outliers start: 4 outliers final: 1 residues processed: 380 average time/residue: 0.2185 time to fit residues: 140.5413 Evaluate side-chains 283 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 282 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 10 optimal weight: 4.9990 chunk 431 optimal weight: 40.0000 chunk 6 optimal weight: 0.4980 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 273 optimal weight: 10.0000 chunk 322 optimal weight: 0.8980 chunk 305 optimal weight: 0.7980 chunk 113 optimal weight: 9.9990 chunk 467 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN C 185 ASN D 294 GLN G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.062483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.045170 restraints weight = 247539.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.046236 restraints weight = 144349.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.046703 restraints weight = 88602.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047242 restraints weight = 60217.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.047237 restraints weight = 52506.836| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37392 Z= 0.131 Angle : 0.593 11.410 50637 Z= 0.306 Chirality : 0.043 0.328 5901 Planarity : 0.004 0.065 6546 Dihedral : 6.491 134.639 5243 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.27 % Favored : 97.70 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.12), residues: 4793 helix: 1.72 (0.10), residues: 2614 sheet: -0.15 (0.22), residues: 535 loop : -0.72 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 41 TYR 0.019 0.001 TYR I 10 PHE 0.035 0.002 PHE a 256 TRP 0.025 0.001 TRP a 111 HIS 0.010 0.001 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (37392) covalent geometry : angle 0.59349 / 0.31 (50637) hydrogen bonds : bond 0.04975 / 3.31 ( 2208) hydrogen bonds : angle 4.41482 / 3.12 ( 6471) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8372 (mpp) cc_final: 0.8166 (mpp) REVERT: A 156 MET cc_start: 0.9001 (mtm) cc_final: 0.8756 (mtp) REVERT: A 386 MET cc_start: 0.9056 (tpp) cc_final: 0.8846 (tpp) REVERT: A 448 LEU cc_start: 0.9518 (mt) cc_final: 0.9242 (mt) REVERT: A 468 GLU cc_start: 0.9056 (tt0) cc_final: 0.8804 (tm-30) REVERT: B 52 MET cc_start: 0.7365 (mtm) cc_final: 0.6866 (mpp) REVERT: B 156 MET cc_start: 0.9221 (mmm) cc_final: 0.7590 (mmm) REVERT: B 412 ASP cc_start: 0.7412 (m-30) cc_final: 0.7027 (t70) REVERT: B 468 GLU cc_start: 0.8848 (tt0) cc_final: 0.8356 (tm-30) REVERT: B 472 LEU cc_start: 0.9386 (mt) cc_final: 0.8906 (pp) REVERT: B 483 MET cc_start: 0.9229 (mmm) cc_final: 0.8986 (mmm) REVERT: B 504 LEU cc_start: 0.9424 (mm) cc_final: 0.9075 (mt) REVERT: C 76 MET cc_start: 0.8451 (mpp) cc_final: 0.8149 (mtm) REVERT: D 263 SER cc_start: 0.9286 (t) cc_final: 0.8864 (p) REVERT: D 342 ARG cc_start: 0.8662 (mtt-85) cc_final: 0.8377 (tmm-80) REVERT: D 368 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8779 (tp40) REVERT: F 56 MET cc_start: 0.9205 (mmm) cc_final: 0.8927 (mmm) REVERT: F 136 MET cc_start: 0.9296 (mmm) cc_final: 0.8754 (mmp) REVERT: F 209 MET cc_start: 0.8350 (ptp) cc_final: 0.8142 (ptp) REVERT: F 274 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8301 (mt-10) REVERT: F 445 MET cc_start: 0.8213 (mmt) cc_final: 0.7782 (tmm) REVERT: G 79 VAL cc_start: 0.9201 (t) cc_final: 0.8890 (t) REVERT: G 102 MET cc_start: 0.8633 (tmm) cc_final: 0.8323 (tmm) REVERT: G 187 LEU cc_start: 0.8942 (tp) cc_final: 0.8724 (tp) REVERT: G 194 ASP cc_start: 0.8211 (p0) cc_final: 0.7851 (m-30) REVERT: H 15 MET cc_start: 0.6361 (tpp) cc_final: 0.5865 (tpp) REVERT: H 49 MET cc_start: 0.2763 (ppp) cc_final: 0.2411 (ppp) REVERT: H 127 GLN cc_start: 0.7084 (mp10) cc_final: 0.6609 (tt0) REVERT: M 11 MET cc_start: 0.7004 (tmm) cc_final: 0.6349 (tpt) REVERT: O 11 MET cc_start: 0.7833 (tpt) cc_final: 0.7194 (mtp) REVERT: O 35 PHE cc_start: 0.7286 (t80) cc_final: 0.6973 (t80) REVERT: P 17 MET cc_start: 0.6585 (ttp) cc_final: 0.6155 (tpt) REVERT: P 30 ILE cc_start: 0.7193 (tt) cc_final: 0.6895 (pt) REVERT: Q 11 MET cc_start: 0.7977 (tmm) cc_final: 0.7589 (ptt) REVERT: Q 53 PHE cc_start: 0.8220 (t80) cc_final: 0.7811 (t80) REVERT: Q 65 MET cc_start: 0.4194 (mtt) cc_final: 0.3356 (tpt) REVERT: S 17 MET cc_start: 0.4872 (ttt) cc_final: 0.4287 (tpt) REVERT: W 43 MET cc_start: 0.9117 (tpt) cc_final: 0.8704 (tpt) REVERT: W 119 GLN cc_start: 0.9249 (tm-30) cc_final: 0.8864 (mp10) REVERT: X 22 MET cc_start: 0.4813 (ptp) cc_final: 0.4477 (ptp) REVERT: X 141 ASP cc_start: 0.8354 (m-30) cc_final: 0.7807 (t0) REVERT: Y 22 MET cc_start: 0.5255 (mmp) cc_final: 0.4268 (ttt) REVERT: Y 30 MET cc_start: 0.6590 (pmm) cc_final: 0.6130 (mmp) REVERT: Y 150 ASP cc_start: 0.9165 (m-30) cc_final: 0.8863 (m-30) REVERT: a 6 MET cc_start: -0.0737 (ttt) cc_final: -0.1154 (ttt) REVERT: a 47 MET cc_start: 0.6889 (tmm) cc_final: 0.6554 (ptt) REVERT: a 97 LYS cc_start: 0.7525 (mttt) cc_final: 0.6968 (pttt) REVERT: a 216 TYR cc_start: 0.8441 (t80) cc_final: 0.7777 (t80) REVERT: a 248 ILE cc_start: 0.7870 (mt) cc_final: 0.7538 (mt) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.2147 time to fit residues: 136.5059 Evaluate side-chains 290 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 40 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 204 optimal weight: 20.0000 chunk 173 optimal weight: 0.0770 chunk 53 optimal weight: 20.0000 chunk 334 optimal weight: 5.9990 chunk 412 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 388 optimal weight: 7.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN B 361 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN ** D 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 208 GLN F 170 HIS G 35 GLN G 200 HIS G 226 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 52 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.060135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.042831 restraints weight = 250902.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.043980 restraints weight = 152067.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.044370 restraints weight = 95362.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.044940 restraints weight = 63181.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.044919 restraints weight = 54299.747| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.4547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 37392 Z= 0.201 Angle : 0.644 9.450 50637 Z= 0.330 Chirality : 0.043 0.223 5901 Planarity : 0.004 0.049 6546 Dihedral : 6.313 121.064 5243 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.12), residues: 4793 helix: 1.72 (0.10), residues: 2613 sheet: -0.25 (0.22), residues: 535 loop : -0.67 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG R 41 TYR 0.018 0.002 TYR B 236 PHE 0.040 0.002 PHE R 53 TRP 0.022 0.002 TRP a 111 HIS 0.006 0.001 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.20 (37392) covalent geometry : angle 0.64368 / 0.33 (50637) hydrogen bonds : bond 0.04980 / 3.32 ( 2208) hydrogen bonds : angle 4.47588 / 3.17 ( 6471) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 1.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9104 (mtm) cc_final: 0.8846 (mtp) REVERT: A 386 MET cc_start: 0.9236 (tpp) cc_final: 0.8725 (tpp) REVERT: A 448 LEU cc_start: 0.9530 (mt) cc_final: 0.9224 (mt) REVERT: A 468 GLU cc_start: 0.9042 (tt0) cc_final: 0.8779 (tm-30) REVERT: B 52 MET cc_start: 0.7372 (mtm) cc_final: 0.7092 (mtm) REVERT: B 412 ASP cc_start: 0.7505 (m-30) cc_final: 0.7145 (t70) REVERT: B 468 GLU cc_start: 0.8943 (tt0) cc_final: 0.8600 (tm-30) REVERT: B 472 LEU cc_start: 0.9392 (mt) cc_final: 0.9009 (pp) REVERT: B 483 MET cc_start: 0.9246 (mmm) cc_final: 0.9026 (mtt) REVERT: B 504 LEU cc_start: 0.9487 (mm) cc_final: 0.9149 (mt) REVERT: C 76 MET cc_start: 0.8465 (mpp) cc_final: 0.8146 (mtm) REVERT: D 263 SER cc_start: 0.9275 (t) cc_final: 0.8895 (p) REVERT: D 342 ARG cc_start: 0.8729 (mtt-85) cc_final: 0.8509 (tmm-80) REVERT: D 368 GLN cc_start: 0.9161 (mm-40) cc_final: 0.8804 (tp40) REVERT: D 397 GLN cc_start: 0.9105 (tt0) cc_final: 0.8507 (tm-30) REVERT: F 56 MET cc_start: 0.9143 (mmm) cc_final: 0.8749 (mmm) REVERT: F 136 MET cc_start: 0.9317 (mmm) cc_final: 0.8806 (mmp) REVERT: F 445 MET cc_start: 0.8259 (mmt) cc_final: 0.7783 (tmm) REVERT: G 23 MET cc_start: 0.8698 (ttm) cc_final: 0.8490 (ttm) REVERT: G 79 VAL cc_start: 0.9262 (t) cc_final: 0.8984 (t) REVERT: G 102 MET cc_start: 0.8623 (tmm) cc_final: 0.8342 (tmm) REVERT: G 194 ASP cc_start: 0.8194 (p0) cc_final: 0.7992 (m-30) REVERT: G 243 MET cc_start: 0.8910 (mmm) cc_final: 0.8598 (mmm) REVERT: H 15 MET cc_start: 0.6385 (tpp) cc_final: 0.5851 (tpp) REVERT: H 49 MET cc_start: 0.3865 (ppp) cc_final: 0.3402 (ppp) REVERT: M 11 MET cc_start: 0.6950 (tmm) cc_final: 0.6317 (tpt) REVERT: M 54 PHE cc_start: 0.6491 (m-80) cc_final: 0.5940 (t80) REVERT: O 11 MET cc_start: 0.7715 (tpt) cc_final: 0.7090 (mtp) REVERT: O 16 MET cc_start: 0.6973 (tmm) cc_final: 0.5767 (ppp) REVERT: O 35 PHE cc_start: 0.7094 (t80) cc_final: 0.6835 (t80) REVERT: P 30 ILE cc_start: 0.7091 (tt) cc_final: 0.6790 (pt) REVERT: Q 53 PHE cc_start: 0.8171 (t80) cc_final: 0.7650 (t80) REVERT: Q 54 PHE cc_start: 0.7540 (m-80) cc_final: 0.6073 (t80) REVERT: Q 65 MET cc_start: 0.4252 (mtt) cc_final: 0.3371 (tpt) REVERT: R 11 MET cc_start: 0.6071 (mtm) cc_final: 0.5778 (mpp) REVERT: R 17 MET cc_start: 0.7908 (mtt) cc_final: 0.7219 (ptp) REVERT: R 61 ASP cc_start: 0.8502 (m-30) cc_final: 0.8110 (p0) REVERT: S 17 MET cc_start: 0.5049 (ttt) cc_final: 0.4404 (tpt) REVERT: X 22 MET cc_start: 0.4696 (ptp) cc_final: 0.4457 (ptp) REVERT: X 141 ASP cc_start: 0.8492 (m-30) cc_final: 0.8074 (t0) REVERT: Y 22 MET cc_start: 0.5168 (mmp) cc_final: 0.4221 (ttt) REVERT: Y 30 MET cc_start: 0.6901 (pmm) cc_final: 0.6373 (mmp) REVERT: Y 150 ASP cc_start: 0.9200 (m-30) cc_final: 0.8925 (m-30) REVERT: a 6 MET cc_start: -0.0712 (ttt) cc_final: -0.1181 (ttt) REVERT: a 47 MET cc_start: 0.6833 (tmm) cc_final: 0.6447 (ptt) REVERT: a 97 LYS cc_start: 0.7419 (mttt) cc_final: 0.6825 (pttt) REVERT: a 216 TYR cc_start: 0.8387 (t80) cc_final: 0.7733 (t80) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.2133 time to fit residues: 124.1710 Evaluate side-chains 275 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 318 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 365 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 57 optimal weight: 0.0010 chunk 262 optimal weight: 0.0980 chunk 186 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 220 optimal weight: 7.9990 overall best weight: 2.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 186 GLN C 352 GLN D 353 HIS F 7 GLN G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.060629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.043578 restraints weight = 249926.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.044519 restraints weight = 147341.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.045061 restraints weight = 92031.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045432 restraints weight = 60614.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045507 restraints weight = 54246.403| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 37392 Z= 0.141 Angle : 0.586 9.255 50637 Z= 0.301 Chirality : 0.042 0.251 5901 Planarity : 0.004 0.043 6546 Dihedral : 6.119 120.361 5243 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.52 % Favored : 97.45 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.12), residues: 4793 helix: 1.83 (0.10), residues: 2628 sheet: -0.12 (0.22), residues: 548 loop : -0.63 (0.16), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG R 41 TYR 0.018 0.001 TYR B 236 PHE 0.029 0.001 PHE R 53 TRP 0.010 0.001 TRP a 111 HIS 0.006 0.001 HIS A 423 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.14 (37392) covalent geometry : angle 0.58644 / 0.30 (50637) hydrogen bonds : bond 0.04687 / 3.13 ( 2208) hydrogen bonds : angle 4.30876 / 3.05 ( 6471) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9096 (mtm) cc_final: 0.8846 (mtp) REVERT: A 386 MET cc_start: 0.9132 (tpp) cc_final: 0.8857 (tpp) REVERT: A 448 LEU cc_start: 0.9550 (mt) cc_final: 0.9230 (mt) REVERT: A 468 GLU cc_start: 0.8998 (tt0) cc_final: 0.8784 (tm-30) REVERT: B 48 MET cc_start: 0.7974 (ptp) cc_final: 0.7173 (ptp) REVERT: B 52 MET cc_start: 0.7276 (mtm) cc_final: 0.6974 (mtm) REVERT: B 412 ASP cc_start: 0.7428 (m-30) cc_final: 0.7157 (t70) REVERT: B 468 GLU cc_start: 0.8890 (tt0) cc_final: 0.8581 (tm-30) REVERT: B 472 LEU cc_start: 0.9350 (mt) cc_final: 0.8934 (pp) REVERT: C 76 MET cc_start: 0.8445 (mpp) cc_final: 0.8145 (mtm) REVERT: D 263 SER cc_start: 0.9077 (t) cc_final: 0.8677 (p) REVERT: D 368 GLN cc_start: 0.9135 (mm-40) cc_final: 0.8849 (tp40) REVERT: D 397 GLN cc_start: 0.9086 (tt0) cc_final: 0.8492 (tm-30) REVERT: D 445 MET cc_start: 0.8866 (mmm) cc_final: 0.7898 (mmm) REVERT: E 193 MET cc_start: 0.8302 (mpp) cc_final: 0.8098 (mpp) REVERT: F 56 MET cc_start: 0.9215 (mmm) cc_final: 0.8903 (mmm) REVERT: F 136 MET cc_start: 0.9300 (mmm) cc_final: 0.8760 (mmp) REVERT: F 445 MET cc_start: 0.8299 (mmt) cc_final: 0.7785 (tmm) REVERT: G 23 MET cc_start: 0.8677 (ttm) cc_final: 0.8448 (ttm) REVERT: G 79 VAL cc_start: 0.9225 (t) cc_final: 0.9024 (t) REVERT: G 102 MET cc_start: 0.8612 (tmm) cc_final: 0.8341 (tmm) REVERT: G 187 LEU cc_start: 0.9010 (tp) cc_final: 0.8778 (tp) REVERT: G 194 ASP cc_start: 0.8289 (p0) cc_final: 0.8065 (m-30) REVERT: G 224 GLU cc_start: 0.9290 (tt0) cc_final: 0.8962 (tp30) REVERT: H 15 MET cc_start: 0.6473 (tpp) cc_final: 0.5943 (tpp) REVERT: H 49 MET cc_start: 0.3932 (ppp) cc_final: 0.3458 (ppp) REVERT: H 127 GLN cc_start: 0.7110 (mp10) cc_final: 0.6693 (tt0) REVERT: M 54 PHE cc_start: 0.6609 (m-80) cc_final: 0.6028 (t80) REVERT: O 11 MET cc_start: 0.7756 (tpt) cc_final: 0.7086 (mtp) REVERT: O 35 PHE cc_start: 0.7037 (t80) cc_final: 0.6668 (t80) REVERT: P 30 ILE cc_start: 0.6878 (tt) cc_final: 0.6587 (pt) REVERT: Q 53 PHE cc_start: 0.8313 (t80) cc_final: 0.7393 (t80) REVERT: Q 54 PHE cc_start: 0.7450 (m-80) cc_final: 0.6050 (t80) REVERT: Q 60 VAL cc_start: 0.3363 (t) cc_final: 0.3135 (t) REVERT: Q 65 MET cc_start: 0.4274 (mtt) cc_final: 0.3400 (tpt) REVERT: S 17 MET cc_start: 0.5070 (ttt) cc_final: 0.4608 (tpt) REVERT: X 69 LYS cc_start: 0.4859 (tptt) cc_final: 0.4012 (tptt) REVERT: X 141 ASP cc_start: 0.8471 (m-30) cc_final: 0.8064 (t0) REVERT: Y 22 MET cc_start: 0.5091 (mmp) cc_final: 0.4156 (ttt) REVERT: Y 30 MET cc_start: 0.6863 (pmm) cc_final: 0.6360 (mmp) REVERT: Y 150 ASP cc_start: 0.9219 (m-30) cc_final: 0.8962 (m-30) REVERT: a 6 MET cc_start: -0.0848 (ttt) cc_final: -0.1207 (ttt) REVERT: a 47 MET cc_start: 0.6783 (tmm) cc_final: 0.6404 (ptt) REVERT: a 97 LYS cc_start: 0.7446 (mttt) cc_final: 0.6864 (pttt) REVERT: a 216 TYR cc_start: 0.8387 (t80) cc_final: 0.7986 (t80) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.2159 time to fit residues: 123.2486 Evaluate side-chains 278 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 161 optimal weight: 1.9990 chunk 373 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 398 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 420 optimal weight: 7.9990 chunk 35 optimal weight: 0.7980 chunk 399 optimal weight: 7.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 GLN A 185 ASN ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN A 488 GLN B 361 ASN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 186 GLN D 343 GLN G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 5 ASN X 106 GLN a 33 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.059556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.043351 restraints weight = 252948.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.043704 restraints weight = 144072.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.044260 restraints weight = 96052.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.044377 restraints weight = 68512.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044420 restraints weight = 60849.621| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 37392 Z= 0.174 Angle : 0.628 11.731 50637 Z= 0.320 Chirality : 0.043 0.235 5901 Planarity : 0.004 0.043 6546 Dihedral : 6.044 113.470 5243 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.82 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.12), residues: 4793 helix: 1.76 (0.10), residues: 2637 sheet: -0.11 (0.22), residues: 548 loop : -0.63 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG R 41 TYR 0.027 0.001 TYR X 24 PHE 0.031 0.002 PHE R 53 TRP 0.021 0.002 TRP a 111 HIS 0.006 0.001 HIS H 38 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.17 (37392) covalent geometry : angle 0.62795 / 0.32 (50637) hydrogen bonds : bond 0.04741 / 3.17 ( 2208) hydrogen bonds : angle 4.38496 / 3.13 ( 6471) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.9116 (mtm) cc_final: 0.8858 (mtp) REVERT: A 386 MET cc_start: 0.9209 (tpp) cc_final: 0.8655 (tpp) REVERT: A 448 LEU cc_start: 0.9588 (mt) cc_final: 0.9292 (mt) REVERT: A 468 GLU cc_start: 0.8999 (tt0) cc_final: 0.8775 (tm-30) REVERT: B 48 MET cc_start: 0.8056 (ptp) cc_final: 0.7232 (ptp) REVERT: B 52 MET cc_start: 0.7250 (mtm) cc_final: 0.6991 (mtm) REVERT: B 412 ASP cc_start: 0.7468 (m-30) cc_final: 0.7167 (t70) REVERT: B 472 LEU cc_start: 0.9358 (mt) cc_final: 0.9122 (pp) REVERT: C 76 MET cc_start: 0.8441 (mpp) cc_final: 0.8139 (mtm) REVERT: D 160 MET cc_start: 0.8418 (tpt) cc_final: 0.8200 (tpp) REVERT: D 263 SER cc_start: 0.9112 (t) cc_final: 0.8731 (p) REVERT: D 368 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8857 (tp40) REVERT: D 397 GLN cc_start: 0.9144 (tt0) cc_final: 0.8614 (tm-30) REVERT: F 56 MET cc_start: 0.9171 (mmm) cc_final: 0.8781 (mmm) REVERT: F 136 MET cc_start: 0.9340 (mmm) cc_final: 0.8805 (mmp) REVERT: F 209 MET cc_start: 0.8030 (ptp) cc_final: 0.7819 (ptp) REVERT: F 445 MET cc_start: 0.8334 (mmt) cc_final: 0.7788 (tmm) REVERT: G 23 MET cc_start: 0.8747 (ttm) cc_final: 0.8493 (ttm) REVERT: G 79 VAL cc_start: 0.9264 (t) cc_final: 0.9050 (t) REVERT: G 102 MET cc_start: 0.8666 (tmm) cc_final: 0.8422 (tmm) REVERT: G 187 LEU cc_start: 0.9117 (tp) cc_final: 0.8909 (tp) REVERT: G 194 ASP cc_start: 0.8342 (p0) cc_final: 0.8087 (m-30) REVERT: G 224 GLU cc_start: 0.9338 (tt0) cc_final: 0.9006 (tp30) REVERT: G 243 MET cc_start: 0.8970 (mmm) cc_final: 0.8581 (mmm) REVERT: H 15 MET cc_start: 0.6308 (tpp) cc_final: 0.5814 (tpp) REVERT: H 49 MET cc_start: 0.4040 (ppp) cc_final: 0.3495 (ppp) REVERT: L 31 LEU cc_start: 0.7389 (tp) cc_final: 0.6865 (mt) REVERT: M 54 PHE cc_start: 0.6628 (m-80) cc_final: 0.6050 (t80) REVERT: O 11 MET cc_start: 0.7632 (tpt) cc_final: 0.6974 (mtp) REVERT: O 17 MET cc_start: 0.7110 (mmm) cc_final: 0.6758 (mmm) REVERT: O 35 PHE cc_start: 0.7102 (t80) cc_final: 0.6711 (t80) REVERT: P 17 MET cc_start: 0.6524 (tmm) cc_final: 0.5857 (tpt) REVERT: P 30 ILE cc_start: 0.6841 (tt) cc_final: 0.6537 (pt) REVERT: Q 35 PHE cc_start: 0.6687 (t80) cc_final: 0.6380 (t80) REVERT: Q 60 VAL cc_start: 0.3442 (t) cc_final: 0.3080 (t) REVERT: Q 65 MET cc_start: 0.4106 (mtt) cc_final: 0.3321 (tpt) REVERT: R 17 MET cc_start: 0.7704 (mtt) cc_final: 0.7302 (tpt) REVERT: S 17 MET cc_start: 0.5332 (ttt) cc_final: 0.4761 (tpt) REVERT: X 141 ASP cc_start: 0.8545 (m-30) cc_final: 0.8121 (t0) REVERT: Y 22 MET cc_start: 0.5055 (mmp) cc_final: 0.4143 (ttt) REVERT: Y 30 MET cc_start: 0.6862 (pmm) cc_final: 0.6382 (mmp) REVERT: Y 150 ASP cc_start: 0.9298 (m-30) cc_final: 0.9059 (m-30) REVERT: a 6 MET cc_start: -0.0884 (ttt) cc_final: -0.1259 (ttt) REVERT: a 47 MET cc_start: 0.6815 (tmm) cc_final: 0.6439 (ptt) REVERT: a 97 LYS cc_start: 0.7379 (mttt) cc_final: 0.6774 (pttt) REVERT: a 157 VAL cc_start: 0.8738 (t) cc_final: 0.8442 (p) REVERT: a 216 TYR cc_start: 0.8550 (t80) cc_final: 0.8209 (t80) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.2177 time to fit residues: 123.8418 Evaluate side-chains 274 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 274 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 271 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 394 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 284 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 0.0010 chunk 104 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN A 511 GLN B 361 ASN B 425 GLN C 185 ASN C 186 GLN ** D 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN ** a 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.060423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.043757 restraints weight = 248522.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.044433 restraints weight = 141038.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.045020 restraints weight = 89203.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045425 restraints weight = 59989.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.045437 restraints weight = 51436.821| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.5321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 37392 Z= 0.128 Angle : 0.603 11.399 50637 Z= 0.304 Chirality : 0.042 0.213 5901 Planarity : 0.004 0.042 6546 Dihedral : 5.891 117.424 5243 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.36 % Favored : 97.62 % Rotamer: Outliers : 0.05 % Allowed : 0.66 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.23 (0.12), residues: 4793 helix: 1.84 (0.10), residues: 2644 sheet: -0.01 (0.22), residues: 553 loop : -0.59 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG R 41 TYR 0.019 0.001 TYR R 10 PHE 0.027 0.001 PHE R 53 TRP 0.007 0.001 TRP Y 26 HIS 0.006 0.001 HIS D 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (37392) covalent geometry : angle 0.60258 / 0.30 (50637) hydrogen bonds : bond 0.04522 / 3.02 ( 2208) hydrogen bonds : angle 4.25776 / 3.03 ( 6471) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 1.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 MET cc_start: 0.9079 (tpp) cc_final: 0.8554 (tpp) REVERT: A 448 LEU cc_start: 0.9549 (mt) cc_final: 0.9255 (mt) REVERT: B 48 MET cc_start: 0.8016 (ptp) cc_final: 0.7180 (ptp) REVERT: B 52 MET cc_start: 0.7141 (mtm) cc_final: 0.6936 (mtm) REVERT: B 412 ASP cc_start: 0.7433 (m-30) cc_final: 0.7116 (t70) REVERT: B 468 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8512 (tm-30) REVERT: C 76 MET cc_start: 0.8425 (mpp) cc_final: 0.8157 (mtm) REVERT: C 393 ILE cc_start: 0.8962 (pt) cc_final: 0.8712 (tp) REVERT: D 368 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8913 (tp40) REVERT: D 397 GLN cc_start: 0.9076 (tt0) cc_final: 0.8588 (tm-30) REVERT: D 445 MET cc_start: 0.8904 (mmm) cc_final: 0.7926 (mmm) REVERT: F 56 MET cc_start: 0.9231 (mmm) cc_final: 0.8900 (mmm) REVERT: F 136 MET cc_start: 0.9293 (mmm) cc_final: 0.8739 (mmp) REVERT: F 445 MET cc_start: 0.8310 (mmt) cc_final: 0.7684 (tmm) REVERT: G 23 MET cc_start: 0.8753 (ttm) cc_final: 0.8470 (ttm) REVERT: G 79 VAL cc_start: 0.9165 (t) cc_final: 0.8954 (t) REVERT: G 102 MET cc_start: 0.8558 (tmm) cc_final: 0.8315 (tmm) REVERT: G 116 MET cc_start: 0.7525 (mmp) cc_final: 0.7272 (mmp) REVERT: G 187 LEU cc_start: 0.9039 (tp) cc_final: 0.8817 (tp) REVERT: G 194 ASP cc_start: 0.8335 (p0) cc_final: 0.8093 (m-30) REVERT: G 224 GLU cc_start: 0.9259 (tt0) cc_final: 0.8945 (tp30) REVERT: G 243 MET cc_start: 0.8981 (mmm) cc_final: 0.8586 (mmm) REVERT: H 15 MET cc_start: 0.6405 (tpp) cc_final: 0.5807 (tpp) REVERT: H 49 MET cc_start: 0.4193 (ppp) cc_final: 0.3666 (ppp) REVERT: H 54 LYS cc_start: 0.6421 (mmmt) cc_final: 0.5897 (mmmt) REVERT: M 54 PHE cc_start: 0.6728 (m-80) cc_final: 0.6126 (t80) REVERT: N 53 PHE cc_start: 0.8723 (t80) cc_final: 0.8437 (t80) REVERT: O 11 MET cc_start: 0.7662 (tpt) cc_final: 0.6949 (mtp) REVERT: O 16 MET cc_start: 0.6570 (tmm) cc_final: 0.5193 (ppp) REVERT: O 35 PHE cc_start: 0.6897 (t80) cc_final: 0.6563 (t80) REVERT: P 30 ILE cc_start: 0.6716 (tt) cc_final: 0.6426 (pt) REVERT: Q 60 VAL cc_start: 0.3981 (t) cc_final: 0.3766 (p) REVERT: Q 65 MET cc_start: 0.4217 (mtt) cc_final: 0.3451 (tpt) REVERT: R 16 MET cc_start: 0.5470 (ttt) cc_final: 0.4937 (ttm) REVERT: R 57 MET cc_start: 0.7175 (ppp) cc_final: 0.6058 (mmm) REVERT: S 17 MET cc_start: 0.5278 (ttt) cc_final: 0.4638 (tpt) REVERT: X 141 ASP cc_start: 0.8442 (m-30) cc_final: 0.8042 (t0) REVERT: Y 22 MET cc_start: 0.5072 (mmp) cc_final: 0.4179 (ttt) REVERT: Y 30 MET cc_start: 0.6855 (pmm) cc_final: 0.6454 (mmt) REVERT: Y 150 ASP cc_start: 0.9272 (m-30) cc_final: 0.9021 (m-30) REVERT: a 6 MET cc_start: -0.1264 (ttt) cc_final: -0.1755 (ttt) REVERT: a 47 MET cc_start: 0.6679 (tmm) cc_final: 0.6271 (ptt) REVERT: a 97 LYS cc_start: 0.7326 (mttt) cc_final: 0.6654 (pttt) REVERT: a 216 TYR cc_start: 0.8503 (t80) cc_final: 0.8104 (t80) outliers start: 2 outliers final: 0 residues processed: 327 average time/residue: 0.2192 time to fit residues: 122.3785 Evaluate side-chains 272 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 1.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 348 optimal weight: 0.1980 chunk 194 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 286 optimal weight: 1.9990 chunk 173 optimal weight: 6.9990 chunk 417 optimal weight: 10.0000 chunk 414 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 457 optimal weight: 30.0000 chunk 5 optimal weight: 6.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN B 425 GLN C 185 ASN C 186 GLN D 7 GLN F 19 GLN F 121 ASN G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.060096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043894 restraints weight = 250432.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.044318 restraints weight = 139884.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.044898 restraints weight = 87504.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.045003 restraints weight = 69055.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.045014 restraints weight = 58975.198| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37392 Z= 0.132 Angle : 0.606 11.248 50637 Z= 0.305 Chirality : 0.042 0.220 5901 Planarity : 0.004 0.042 6546 Dihedral : 5.784 120.034 5243 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.69 % Favored : 97.29 % Rotamer: Outliers : 0.05 % Allowed : 0.68 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.12), residues: 4793 helix: 1.82 (0.10), residues: 2648 sheet: -0.02 (0.22), residues: 554 loop : -0.58 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG a 210 TYR 0.022 0.001 TYR R 10 PHE 0.031 0.002 PHE a 163 TRP 0.007 0.001 TRP Y 26 HIS 0.006 0.001 HIS D 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (37392) covalent geometry : angle 0.60571 / 0.31 (50637) hydrogen bonds : bond 0.04409 / 2.95 ( 2208) hydrogen bonds : angle 4.23703 / 3.01 ( 6471) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 323 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8643 (mpp) cc_final: 0.8357 (mmt) REVERT: A 386 MET cc_start: 0.9090 (tpp) cc_final: 0.8561 (tpp) REVERT: A 448 LEU cc_start: 0.9560 (mt) cc_final: 0.9254 (mt) REVERT: B 48 MET cc_start: 0.8032 (ptp) cc_final: 0.7217 (ptp) REVERT: B 412 ASP cc_start: 0.7581 (m-30) cc_final: 0.7244 (t70) REVERT: B 425 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8299 (pp30) REVERT: B 468 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8352 (tm-30) REVERT: C 76 MET cc_start: 0.8425 (mpp) cc_final: 0.8126 (mtm) REVERT: C 393 ILE cc_start: 0.8978 (pt) cc_final: 0.8744 (tp) REVERT: D 160 MET cc_start: 0.8259 (tpt) cc_final: 0.8006 (tpt) REVERT: D 368 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8945 (tp40) REVERT: D 397 GLN cc_start: 0.9077 (tt0) cc_final: 0.8624 (tm-30) REVERT: D 445 MET cc_start: 0.8931 (mmm) cc_final: 0.7965 (mmm) REVERT: F 56 MET cc_start: 0.9239 (mmm) cc_final: 0.8903 (mmm) REVERT: F 136 MET cc_start: 0.9284 (mmm) cc_final: 0.8748 (mmp) REVERT: F 445 MET cc_start: 0.8323 (mmt) cc_final: 0.7674 (tmm) REVERT: G 23 MET cc_start: 0.8710 (ttm) cc_final: 0.8418 (ttm) REVERT: G 31 MET cc_start: 0.9016 (tmm) cc_final: 0.8717 (tmm) REVERT: G 48 MET cc_start: 0.8461 (ppp) cc_final: 0.8153 (ppp) REVERT: G 79 VAL cc_start: 0.9179 (t) cc_final: 0.8978 (t) REVERT: G 102 MET cc_start: 0.8628 (tmm) cc_final: 0.8399 (tmm) REVERT: G 116 MET cc_start: 0.7710 (mmp) cc_final: 0.7472 (mmp) REVERT: G 194 ASP cc_start: 0.8433 (p0) cc_final: 0.8151 (m-30) REVERT: G 224 GLU cc_start: 0.9218 (tt0) cc_final: 0.8888 (tp30) REVERT: G 243 MET cc_start: 0.9002 (mmm) cc_final: 0.8603 (mmm) REVERT: H 15 MET cc_start: 0.6838 (tpp) cc_final: 0.6267 (tpp) REVERT: H 49 MET cc_start: 0.4459 (ppp) cc_final: 0.3970 (ppp) REVERT: H 54 LYS cc_start: 0.6694 (mmmt) cc_final: 0.6215 (mmmt) REVERT: M 11 MET cc_start: 0.7248 (tmm) cc_final: 0.6012 (tpt) REVERT: M 54 PHE cc_start: 0.6733 (m-80) cc_final: 0.6130 (t80) REVERT: O 11 MET cc_start: 0.7604 (tpt) cc_final: 0.6842 (mtp) REVERT: O 35 PHE cc_start: 0.6946 (t80) cc_final: 0.6609 (t80) REVERT: P 30 ILE cc_start: 0.6674 (tt) cc_final: 0.6369 (pt) REVERT: Q 65 MET cc_start: 0.4172 (mtt) cc_final: 0.3450 (tpt) REVERT: R 17 MET cc_start: 0.7551 (mmt) cc_final: 0.7003 (ttm) REVERT: R 57 MET cc_start: 0.7136 (ppp) cc_final: 0.6060 (mmm) REVERT: S 17 MET cc_start: 0.5515 (ttt) cc_final: 0.4780 (tpt) REVERT: X 141 ASP cc_start: 0.8431 (m-30) cc_final: 0.8017 (t0) REVERT: Y 22 MET cc_start: 0.4768 (mmp) cc_final: 0.3947 (ttt) REVERT: Y 30 MET cc_start: 0.6841 (pmm) cc_final: 0.6448 (mmt) REVERT: Y 150 ASP cc_start: 0.9298 (m-30) cc_final: 0.9067 (m-30) REVERT: a 6 MET cc_start: -0.1139 (ttt) cc_final: -0.1518 (ttt) REVERT: a 47 MET cc_start: 0.6607 (tmm) cc_final: 0.6210 (ptt) REVERT: a 97 LYS cc_start: 0.7302 (mttt) cc_final: 0.6459 (ttpt) REVERT: a 216 TYR cc_start: 0.8569 (t80) cc_final: 0.8200 (t80) outliers start: 2 outliers final: 0 residues processed: 325 average time/residue: 0.2223 time to fit residues: 122.8649 Evaluate side-chains 269 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 268 time to evaluate : 1.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 250 optimal weight: 8.9990 chunk 415 optimal weight: 6.9990 chunk 390 optimal weight: 0.0270 chunk 418 optimal weight: 30.0000 chunk 335 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 463 optimal weight: 9.9990 chunk 468 optimal weight: 6.9990 chunk 325 optimal weight: 9.9990 chunk 341 optimal weight: 8.9990 chunk 33 optimal weight: 0.2980 overall best weight: 4.0644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN C 185 ASN C 186 GLN F 121 ASN G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.058973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.042856 restraints weight = 253096.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043342 restraints weight = 139310.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.044123 restraints weight = 86830.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.044106 restraints weight = 64637.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.044189 restraints weight = 53041.542| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 37392 Z= 0.182 Angle : 0.653 17.437 50637 Z= 0.328 Chirality : 0.043 0.215 5901 Planarity : 0.004 0.042 6546 Dihedral : 5.870 122.337 5243 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 0.03 % Allowed : 0.21 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4793 helix: 1.76 (0.10), residues: 2645 sheet: -0.06 (0.22), residues: 543 loop : -0.60 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 358 TYR 0.020 0.001 TYR R 10 PHE 0.038 0.002 PHE R 53 TRP 0.011 0.001 TRP Y 26 HIS 0.006 0.001 HIS D 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.18 (37392) covalent geometry : angle 0.65273 / 0.33 (50637) hydrogen bonds : bond 0.04584 / 3.06 ( 2208) hydrogen bonds : angle 4.39234 / 3.12 ( 6471) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9586 Ramachandran restraints generated. 4793 Oldfield, 0 Emsley, 4793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 318 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8696 (mpp) cc_final: 0.8416 (mmt) REVERT: A 245 MET cc_start: 0.8541 (mpp) cc_final: 0.8295 (mpp) REVERT: A 386 MET cc_start: 0.9171 (tpp) cc_final: 0.8755 (tpp) REVERT: A 448 LEU cc_start: 0.9587 (mt) cc_final: 0.9365 (mt) REVERT: B 48 MET cc_start: 0.8081 (ptp) cc_final: 0.7191 (ptp) REVERT: B 52 MET cc_start: 0.7537 (mtm) cc_final: 0.7328 (mpp) REVERT: B 412 ASP cc_start: 0.7490 (m-30) cc_final: 0.7228 (t70) REVERT: B 468 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8371 (tm-30) REVERT: C 76 MET cc_start: 0.8454 (mpp) cc_final: 0.8147 (mtm) REVERT: C 393 ILE cc_start: 0.9007 (pt) cc_final: 0.8791 (tp) REVERT: D 193 MET cc_start: 0.8579 (mpp) cc_final: 0.8315 (mpp) REVERT: D 368 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8889 (tp40) REVERT: D 397 GLN cc_start: 0.9170 (tt0) cc_final: 0.8700 (tm-30) REVERT: D 445 MET cc_start: 0.8969 (mmm) cc_final: 0.8087 (mmm) REVERT: E 275 MET cc_start: 0.9369 (tpp) cc_final: 0.8951 (tpp) REVERT: F 56 MET cc_start: 0.9210 (mmm) cc_final: 0.8855 (mmm) REVERT: F 136 MET cc_start: 0.9305 (mmm) cc_final: 0.8773 (mmp) REVERT: F 445 MET cc_start: 0.8345 (mmt) cc_final: 0.7693 (tmm) REVERT: G 23 MET cc_start: 0.8829 (ttm) cc_final: 0.8524 (ttm) REVERT: G 48 MET cc_start: 0.8542 (ppp) cc_final: 0.8223 (ppp) REVERT: G 102 MET cc_start: 0.8575 (tmm) cc_final: 0.8365 (tmm) REVERT: G 116 MET cc_start: 0.7740 (mmp) cc_final: 0.7503 (mmp) REVERT: G 178 MET cc_start: 0.8561 (pmm) cc_final: 0.8266 (pmm) REVERT: G 194 ASP cc_start: 0.8403 (p0) cc_final: 0.8161 (m-30) REVERT: G 224 GLU cc_start: 0.9239 (tt0) cc_final: 0.8930 (tp30) REVERT: G 243 MET cc_start: 0.8992 (mmm) cc_final: 0.8591 (mmm) REVERT: H 15 MET cc_start: 0.6914 (tpp) cc_final: 0.6336 (tpp) REVERT: H 49 MET cc_start: 0.4427 (ppp) cc_final: 0.3660 (ppp) REVERT: H 54 LYS cc_start: 0.6751 (mmmt) cc_final: 0.6270 (mmmt) REVERT: H 64 LEU cc_start: 0.8389 (mt) cc_final: 0.7600 (pp) REVERT: L 31 LEU cc_start: 0.7504 (tp) cc_final: 0.6974 (mt) REVERT: M 54 PHE cc_start: 0.6637 (m-80) cc_final: 0.6088 (t80) REVERT: O 11 MET cc_start: 0.7647 (tpt) cc_final: 0.6867 (mtp) REVERT: O 17 MET cc_start: 0.6275 (mmp) cc_final: 0.6038 (mmm) REVERT: O 35 PHE cc_start: 0.6973 (t80) cc_final: 0.6543 (t80) REVERT: P 30 ILE cc_start: 0.6551 (tt) cc_final: 0.6260 (pt) REVERT: Q 11 MET cc_start: 0.7611 (tmm) cc_final: 0.7291 (ppp) REVERT: Q 65 MET cc_start: 0.4238 (mtt) cc_final: 0.3478 (tpt) REVERT: R 6 MET cc_start: 0.3799 (ptp) cc_final: 0.2368 (tpp) REVERT: S 17 MET cc_start: 0.5654 (ttt) cc_final: 0.5029 (tpt) REVERT: X 141 ASP cc_start: 0.8426 (m-30) cc_final: 0.8017 (t0) REVERT: Y 22 MET cc_start: 0.4638 (mmp) cc_final: 0.3851 (ttt) REVERT: Y 30 MET cc_start: 0.6844 (pmm) cc_final: 0.6461 (mmt) REVERT: Y 150 ASP cc_start: 0.9331 (m-30) cc_final: 0.9109 (m-30) REVERT: a 6 MET cc_start: -0.1248 (ttt) cc_final: -0.1538 (ttt) REVERT: a 47 MET cc_start: 0.6697 (tmm) cc_final: 0.6278 (ptt) REVERT: a 97 LYS cc_start: 0.7366 (mttt) cc_final: 0.6495 (ttpt) REVERT: a 216 TYR cc_start: 0.8587 (t80) cc_final: 0.8215 (t80) outliers start: 1 outliers final: 0 residues processed: 319 average time/residue: 0.2209 time to fit residues: 120.3274 Evaluate side-chains 264 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 19 optimal weight: 9.9990 chunk 426 optimal weight: 7.9990 chunk 465 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 213 optimal weight: 5.9990 chunk 40 optimal weight: 0.1980 chunk 26 optimal weight: 6.9990 chunk 308 optimal weight: 8.9990 chunk 316 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 ASN C 185 ASN F 121 ASN G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 33 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.058265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.042176 restraints weight = 254060.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.042739 restraints weight = 138708.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.043338 restraints weight = 85217.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.043337 restraints weight = 69235.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.043347 restraints weight = 59745.061| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.6058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 37392 Z= 0.190 Angle : 0.659 11.158 50637 Z= 0.333 Chirality : 0.043 0.239 5901 Planarity : 0.004 0.080 6546 Dihedral : 5.922 123.611 5243 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.90 % Favored : 97.08 % Rotamer: Outliers : 0.03 % Allowed : 0.31 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.91 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.12), residues: 4793 helix: 1.69 (0.10), residues: 2656 sheet: -0.14 (0.22), residues: 546 loop : -0.65 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 358 TYR 0.020 0.001 TYR G 205 PHE 0.037 0.002 PHE R 53 TRP 0.013 0.001 TRP Y 26 HIS 0.006 0.001 HIS D 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (37392) covalent geometry : angle 0.65908 / 0.33 (50637) hydrogen bonds : bond 0.04705 / 3.14 ( 2208) hydrogen bonds : angle 4.43961 / 3.15 ( 6471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5986.20 seconds wall clock time: 104 minutes 45.42 seconds (6285.42 seconds total)