Starting phenix.real_space_refine on Wed Apr 8 09:52:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dbw_27311/04_2026/8dbw_27311.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dbw_27311/04_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 { model { file = "/net/cci-nas-00/data/ceres_data/8dbw_27311/04_2026/8dbw_27311.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dbw_27311/04_2026/8dbw_27311.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dbw_27311/04_2026/8dbw_27311.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dbw_27311/04_2026/8dbw_27311.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/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: 8.37, per 1000 atoms: 0.23 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: 3.10 Conformation dependent library (CDL) restraints added in 1.6 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: 1.13 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: 7.44 Time building geometry restraints manager: 4.13 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: 21914 29.26 - 58.51: 713 58.51 - 87.77: 87 87.77 - 117.02: 7 117.02 - 146.28: 3 Dihedral angle restraints: 22724 sinusoidal: 8981 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 22721 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.690 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 33.220 Find NCS groups from input model: 0.890 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: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 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 : 14.491 146.278 13934 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 covalent geometry : bond 0.00422 (37392) covalent geometry : angle 0.80872 (50637) hydrogen bonds : bond 0.13178 ( 2208) hydrogen bonds : angle 5.92447 ( 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 : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2380 time to fit residues: 255.2301 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 : 1.256 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 R 52 GLN S 52 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3643 r_free = 0.3643 target = 0.063828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.046773 restraints weight = 244947.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047203 restraints weight = 141523.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.047820 restraints weight = 88813.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.047955 restraints weight = 69182.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.047961 restraints weight = 61798.305| |-----------------------------------------------------------------------------| r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37392 Z= 0.176 Angle : 0.681 16.828 50637 Z= 0.356 Chirality : 0.045 0.296 5901 Planarity : 0.005 0.073 6546 Dihedral : 8.185 136.574 5367 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.15 % Favored : 97.83 % Rotamer: Outliers : 0.10 % Allowed : 2.96 % Favored : 96.93 % 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: 0.45 (0.12), residues: 4793 helix: 1.20 (0.10), residues: 2623 sheet: 0.00 (0.22), residues: 521 loop : -1.01 (0.14), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.039 0.001 ARG R 41 TYR 0.031 0.002 TYR C 474 PHE 0.032 0.002 PHE G 95 TRP 0.040 0.003 TRP G 203 HIS 0.009 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00374 (37392) covalent geometry : angle 0.68128 (50637) hydrogen bonds : bond 0.06058 ( 2208) hydrogen bonds : angle 4.82937 ( 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: 4 poor density : 414 time to evaluate : 1.208 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: 0.8166 (mpp) cc_final: 0.7591 (mpp) REVERT: A 52 MET cc_start: 0.8241 (mtp) cc_final: 0.7943 (ttm) REVERT: A 69 ASP cc_start: 0.7326 (m-30) cc_final: 0.6869 (t0) REVERT: A 156 MET cc_start: 0.8846 (mtm) cc_final: 0.8610 (mtp) REVERT: A 386 MET cc_start: 0.9004 (tpp) cc_final: 0.8725 (tpp) REVERT: A 448 LEU cc_start: 0.9528 (mt) cc_final: 0.9259 (mt) REVERT: A 468 GLU cc_start: 0.9266 (tt0) cc_final: 0.8738 (tm-30) REVERT: B 156 MET cc_start: 0.9184 (mmm) cc_final: 0.8656 (mmm) REVERT: B 468 GLU cc_start: 0.8941 (tt0) cc_final: 0.8247 (tm-30) REVERT: C 76 MET cc_start: 0.8380 (mpp) cc_final: 0.7978 (mtm) REVERT: D 209 MET cc_start: 0.8329 (mtp) cc_final: 0.8128 (mpp) REVERT: D 263 SER cc_start: 0.9370 (t) cc_final: 0.9072 (m) REVERT: D 368 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8555 (tp40) REVERT: E 193 MET cc_start: 0.8258 (mtm) cc_final: 0.7942 (mpp) REVERT: E 209 MET cc_start: 0.8542 (mtm) cc_final: 0.8336 (mtm) REVERT: E 431 MET cc_start: 0.9503 (ttm) cc_final: 0.9294 (tpp) REVERT: F 56 MET cc_start: 0.9200 (mmm) cc_final: 0.8960 (mmm) REVERT: F 209 MET cc_start: 0.8671 (ptp) cc_final: 0.8282 (ptp) REVERT: F 274 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8283 (mt-10) REVERT: F 445 MET cc_start: 0.8117 (mmt) cc_final: 0.7753 (tmm) REVERT: G 54 HIS cc_start: 0.8177 (OUTLIER) cc_final: 0.7943 (p-80) REVERT: G 79 VAL cc_start: 0.9136 (t) cc_final: 0.8774 (t) REVERT: G 86 LEU cc_start: 0.8909 (mt) cc_final: 0.8582 (mm) REVERT: G 187 LEU cc_start: 0.8956 (tp) cc_final: 0.8705 (tp) REVERT: G 194 ASP cc_start: 0.8276 (p0) cc_final: 0.7991 (m-30) REVERT: H 15 MET cc_start: 0.5852 (tpp) cc_final: 0.5449 (tpp) REVERT: H 23 ILE cc_start: 0.7402 (pt) cc_final: 0.6652 (mm) REVERT: H 25 VAL cc_start: 0.8429 (t) cc_final: 0.7818 (t) REVERT: H 49 MET cc_start: 0.2015 (ppp) cc_final: 0.1265 (ppp) REVERT: H 127 GLN cc_start: 0.7296 (mp10) cc_final: 0.6681 (tt0) REVERT: L 75 MET cc_start: 0.5936 (ttt) cc_final: 0.5675 (ttt) REVERT: M 11 MET cc_start: 0.8179 (tpt) cc_final: 0.6817 (mmm) REVERT: N 75 MET cc_start: 0.3994 (ttt) cc_final: 0.3793 (mmm) REVERT: O 11 MET cc_start: 0.8167 (tpt) cc_final: 0.7449 (mtt) REVERT: O 54 PHE cc_start: 0.8973 (m-10) cc_final: 0.8764 (m-80) REVERT: P 30 ILE cc_start: 0.7156 (tt) cc_final: 0.6847 (pt) REVERT: Q 65 MET cc_start: 0.4161 (mtt) cc_final: 0.3336 (tpt) REVERT: S 17 MET cc_start: 0.4493 (ttt) cc_final: 0.4050 (tpt) REVERT: S 49 LEU cc_start: 0.8795 (mt) cc_final: 0.8363 (tp) REVERT: S 57 MET cc_start: 0.8207 (ppp) cc_final: 0.7984 (ppp) REVERT: W 43 MET cc_start: 0.9191 (tpp) cc_final: 0.8760 (tpp) REVERT: W 119 GLN cc_start: 0.9321 (tm-30) cc_final: 0.8965 (mp10) REVERT: X 22 MET cc_start: 0.4522 (ptp) cc_final: 0.4256 (ptp) REVERT: X 141 ASP cc_start: 0.8491 (m-30) cc_final: 0.7797 (t0) REVERT: Y 22 MET cc_start: 0.5125 (mmp) cc_final: 0.4186 (ttt) REVERT: Y 30 MET cc_start: 0.7105 (pmm) cc_final: 0.6320 (mmt) REVERT: Y 150 ASP cc_start: 0.9086 (m-30) cc_final: 0.8802 (m-30) REVERT: a 6 MET cc_start: -0.0319 (ttt) cc_final: -0.1129 (ttt) REVERT: a 47 MET cc_start: 0.7133 (tmm) cc_final: 0.6744 (ptt) REVERT: a 93 MET cc_start: 0.7040 (ttt) cc_final: 0.6678 (ptt) REVERT: a 97 LYS cc_start: 0.7738 (mttt) cc_final: 0.7235 (pttt) REVERT: a 252 GLN cc_start: 0.8706 (mm-40) cc_final: 0.8434 (mm-40) outliers start: 4 outliers final: 0 residues processed: 417 average time/residue: 0.2149 time to fit residues: 147.0635 Evaluate side-chains 309 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 308 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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: 6.9990 chunk 363 optimal weight: 6.9990 chunk 340 optimal weight: 10.0000 chunk 325 optimal weight: 30.0000 chunk 345 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 419 optimal weight: 10.0000 chunk 398 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN P 52 GLN Q 52 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 2 ASN 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 = 0.3576 r_free = 0.3576 target = 0.061294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.044895 restraints weight = 249243.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.045112 restraints weight = 141953.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.045538 restraints weight = 94985.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.045647 restraints weight = 78566.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.045671 restraints weight = 66015.639| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 37392 Z= 0.208 Angle : 0.671 10.726 50637 Z= 0.348 Chirality : 0.044 0.217 5901 Planarity : 0.005 0.058 6546 Dihedral : 7.725 134.278 5367 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.59 % Favored : 97.39 % Rotamer: Outliers : 0.10 % Allowed : 3.41 % Favored : 96.48 % 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: 0.69 (0.12), residues: 4793 helix: 1.44 (0.10), residues: 2609 sheet: -0.18 (0.22), residues: 536 loop : -0.85 (0.15), residues: 1648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 220 TYR 0.019 0.002 TYR C 236 PHE 0.034 0.002 PHE D 312 TRP 0.018 0.002 TRP Y 26 HIS 0.013 0.002 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00451 (37392) covalent geometry : angle 0.67056 (50637) hydrogen bonds : bond 0.05576 ( 2208) hydrogen bonds : angle 4.70354 ( 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 378 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 374 time to evaluate : 1.479 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: 0.8544 (mpp) cc_final: 0.8323 (mpp) REVERT: A 156 MET cc_start: 0.8984 (mtm) cc_final: 0.8745 (mtp) REVERT: A 386 MET cc_start: 0.9135 (tpp) cc_final: 0.8533 (tpp) REVERT: A 448 LEU cc_start: 0.9543 (mt) cc_final: 0.9254 (mt) REVERT: A 468 GLU cc_start: 0.9207 (tt0) cc_final: 0.8807 (tm-30) REVERT: B 156 MET cc_start: 0.9253 (mmm) cc_final: 0.8713 (mmm) REVERT: B 412 ASP cc_start: 0.7716 (m-30) cc_final: 0.7267 (t70) REVERT: B 468 GLU cc_start: 0.8932 (tt0) cc_final: 0.8399 (tm-30) REVERT: B 472 LEU cc_start: 0.9348 (mt) cc_final: 0.8876 (pp) REVERT: C 76 MET cc_start: 0.8414 (mpp) cc_final: 0.8073 (mtm) REVERT: D 263 SER cc_start: 0.9354 (t) cc_final: 0.9014 (p) REVERT: D 368 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8706 (tp40) REVERT: E 209 MET cc_start: 0.8580 (mtm) cc_final: 0.8362 (mtm) REVERT: F 56 MET cc_start: 0.9194 (mmm) cc_final: 0.8893 (mmm) REVERT: F 209 MET cc_start: 0.8607 (ptp) cc_final: 0.8312 (ptp) REVERT: F 445 MET cc_start: 0.8197 (mmt) cc_final: 0.7780 (tmm) REVERT: G 79 VAL cc_start: 0.9260 (t) cc_final: 0.8992 (t) REVERT: G 102 MET cc_start: 0.8687 (tmm) cc_final: 0.8444 (tmm) REVERT: G 187 LEU cc_start: 0.9059 (tp) cc_final: 0.8855 (tp) REVERT: G 194 ASP cc_start: 0.8288 (p0) cc_final: 0.8000 (m-30) REVERT: G 218 LEU cc_start: 0.9546 (tp) cc_final: 0.9332 (tt) REVERT: H 15 MET cc_start: 0.6195 (tpp) cc_final: 0.5878 (tpp) REVERT: H 49 MET cc_start: 0.3263 (ppp) cc_final: 0.2818 (ppp) REVERT: H 127 GLN cc_start: 0.7159 (mp10) cc_final: 0.6640 (tt0) REVERT: N 75 MET cc_start: 0.4035 (ttt) cc_final: 0.3730 (mmm) REVERT: O 11 MET cc_start: 0.7923 (tpt) cc_final: 0.7353 (mtt) REVERT: O 16 MET cc_start: 0.7414 (tmm) cc_final: 0.6532 (tmm) REVERT: O 17 MET cc_start: 0.7001 (mmp) cc_final: 0.6780 (mmm) REVERT: O 35 PHE cc_start: 0.7468 (t80) cc_final: 0.7213 (t80) REVERT: P 17 MET cc_start: 0.6616 (ttp) cc_final: 0.6291 (tpt) REVERT: P 30 ILE cc_start: 0.6992 (tt) cc_final: 0.6672 (pt) REVERT: Q 65 MET cc_start: 0.4075 (mtt) cc_final: 0.3265 (tpt) REVERT: R 11 MET cc_start: 0.6277 (mtm) cc_final: 0.5582 (mpp) REVERT: R 17 MET cc_start: 0.7865 (mtt) cc_final: 0.7221 (ptm) REVERT: S 17 MET cc_start: 0.4790 (ttt) cc_final: 0.4151 (tpt) REVERT: S 57 MET cc_start: 0.7895 (ppp) cc_final: 0.7657 (ppp) REVERT: W 43 MET cc_start: 0.9236 (tpp) cc_final: 0.8810 (tpp) REVERT: X 22 MET cc_start: 0.4619 (ptp) cc_final: 0.4184 (ptp) REVERT: X 141 ASP cc_start: 0.8475 (m-30) cc_final: 0.7826 (t0) REVERT: Y 22 MET cc_start: 0.5308 (mmp) cc_final: 0.4355 (ttt) REVERT: Y 30 MET cc_start: 0.7134 (pmm) cc_final: 0.6451 (mmt) REVERT: Y 150 ASP cc_start: 0.9189 (m-30) cc_final: 0.8905 (m-30) REVERT: a 6 MET cc_start: -0.0544 (ttt) cc_final: -0.0858 (ttt) REVERT: a 47 MET cc_start: 0.7010 (tmm) cc_final: 0.6683 (ptt) REVERT: a 93 MET cc_start: 0.6711 (ttt) cc_final: 0.6399 (mmp) REVERT: a 97 LYS cc_start: 0.7580 (mttt) cc_final: 0.7055 (pttt) outliers start: 4 outliers final: 1 residues processed: 376 average time/residue: 0.2055 time to fit residues: 130.0521 Evaluate side-chains 286 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 285 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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: 0.9990 chunk 431 optimal weight: 40.0000 chunk 6 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 273 optimal weight: 9.9990 chunk 322 optimal weight: 0.0070 chunk 305 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 467 optimal weight: 9.9990 chunk 180 optimal weight: 0.0060 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 7 GLN G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 HIS W 71 ASN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS a 33 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.062789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.046066 restraints weight = 250268.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.046127 restraints weight = 147494.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.046852 restraints weight = 95847.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047097 restraints weight = 67645.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.047110 restraints weight = 65379.042| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 37392 Z= 0.131 Angle : 0.594 11.220 50637 Z= 0.306 Chirality : 0.042 0.220 5901 Planarity : 0.004 0.045 6546 Dihedral : 7.281 135.662 5367 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.19 % Favored : 97.79 % Rotamer: Outliers : 0.03 % Allowed : 2.07 % Favored : 97.90 % 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: 0.99 (0.12), residues: 4793 helix: 1.71 (0.10), residues: 2616 sheet: -0.14 (0.22), residues: 532 loop : -0.73 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 83 TYR 0.022 0.001 TYR a 216 PHE 0.031 0.001 PHE W 95 TRP 0.013 0.001 TRP a 111 HIS 0.010 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00271 (37392) covalent geometry : angle 0.59418 (50637) hydrogen bonds : bond 0.04998 ( 2208) hydrogen bonds : angle 4.39074 ( 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 379 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 378 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8374 (mpp) cc_final: 0.8173 (mpp) REVERT: A 95 LEU cc_start: 0.8874 (pt) cc_final: 0.8661 (tt) REVERT: A 156 MET cc_start: 0.9005 (mtm) cc_final: 0.8759 (mtp) REVERT: A 386 MET cc_start: 0.9056 (tpp) cc_final: 0.8487 (tpp) REVERT: A 448 LEU cc_start: 0.9523 (mt) cc_final: 0.9240 (mt) REVERT: A 468 GLU cc_start: 0.9065 (tt0) cc_final: 0.8798 (tm-30) REVERT: B 48 MET cc_start: 0.7674 (ptp) cc_final: 0.6891 (ptp) REVERT: B 52 MET cc_start: 0.7387 (mtm) cc_final: 0.6884 (mpp) REVERT: B 156 MET cc_start: 0.9217 (mmm) cc_final: 0.7545 (mmm) REVERT: B 208 VAL cc_start: 0.9723 (t) cc_final: 0.9488 (p) REVERT: B 412 ASP cc_start: 0.7425 (m-30) cc_final: 0.7007 (t70) REVERT: B 468 GLU cc_start: 0.8857 (tt0) cc_final: 0.8349 (tm-30) REVERT: B 472 LEU cc_start: 0.9377 (mt) cc_final: 0.8895 (pp) REVERT: B 483 MET cc_start: 0.9211 (mmm) cc_final: 0.8968 (mmm) REVERT: C 76 MET cc_start: 0.8436 (mpp) cc_final: 0.8113 (mtm) REVERT: D 263 SER cc_start: 0.9266 (t) cc_final: 0.8865 (p) REVERT: D 342 ARG cc_start: 0.8635 (mtt-85) cc_final: 0.8370 (tmm-80) REVERT: D 368 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8776 (tp40) REVERT: F 56 MET cc_start: 0.9219 (mmm) cc_final: 0.9005 (mmm) REVERT: F 136 MET cc_start: 0.9300 (mmm) cc_final: 0.8756 (mmp) REVERT: F 209 MET cc_start: 0.8360 (ptp) cc_final: 0.8126 (ptp) REVERT: F 274 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8339 (mt-10) REVERT: F 445 MET cc_start: 0.8203 (mmt) cc_final: 0.7781 (tmm) REVERT: G 23 MET cc_start: 0.8487 (ttm) cc_final: 0.8251 (ttm) REVERT: G 79 VAL cc_start: 0.9265 (t) cc_final: 0.8932 (t) REVERT: G 102 MET cc_start: 0.8732 (tmm) cc_final: 0.8412 (tmm) REVERT: G 194 ASP cc_start: 0.8202 (p0) cc_final: 0.7985 (m-30) REVERT: H 15 MET cc_start: 0.6163 (tpp) cc_final: 0.5758 (tpp) REVERT: H 49 MET cc_start: 0.2498 (ppp) cc_final: 0.2176 (ppp) REVERT: H 54 LYS cc_start: 0.6908 (mmtm) cc_final: 0.6498 (mmmt) REVERT: M 11 MET cc_start: 0.6891 (tmm) cc_final: 0.6225 (tpt) REVERT: M 54 PHE cc_start: 0.6447 (m-80) cc_final: 0.5977 (t80) REVERT: N 75 MET cc_start: 0.4002 (ttt) cc_final: 0.3701 (mmm) REVERT: O 11 MET cc_start: 0.7848 (tpt) cc_final: 0.7220 (mtp) REVERT: O 16 MET cc_start: 0.7387 (tmm) cc_final: 0.6447 (tmm) REVERT: O 17 MET cc_start: 0.7062 (mmp) cc_final: 0.6726 (mmm) REVERT: O 35 PHE cc_start: 0.7341 (t80) cc_final: 0.7020 (t80) REVERT: P 17 MET cc_start: 0.6734 (ttp) cc_final: 0.6281 (tpt) REVERT: P 30 ILE cc_start: 0.7100 (tt) cc_final: 0.6809 (pt) REVERT: Q 11 MET cc_start: 0.8149 (ppp) cc_final: 0.7848 (ppp) REVERT: Q 65 MET cc_start: 0.4164 (mtt) cc_final: 0.3376 (tpt) REVERT: R 35 PHE cc_start: 0.5326 (t80) cc_final: 0.5085 (t80) REVERT: R 53 PHE cc_start: 0.8697 (t80) cc_final: 0.8135 (t80) REVERT: S 17 MET cc_start: 0.5070 (ttt) cc_final: 0.4400 (tpt) REVERT: S 57 MET cc_start: 0.8003 (ppp) cc_final: 0.7783 (ppp) REVERT: W 119 GLN cc_start: 0.9312 (tm-30) cc_final: 0.8910 (mp10) REVERT: W 147 MET cc_start: 0.8466 (mmp) cc_final: 0.8263 (mmm) REVERT: X 22 MET cc_start: 0.4961 (ptp) cc_final: 0.4683 (ptp) REVERT: X 141 ASP cc_start: 0.8416 (m-30) cc_final: 0.7848 (t0) REVERT: Y 22 MET cc_start: 0.5259 (mmp) cc_final: 0.4292 (ttt) REVERT: Y 30 MET cc_start: 0.6569 (pmm) cc_final: 0.6131 (mmp) REVERT: Y 150 ASP cc_start: 0.9205 (m-30) cc_final: 0.8899 (m-30) REVERT: a 6 MET cc_start: -0.0756 (ttt) cc_final: -0.1097 (ttt) REVERT: a 47 MET cc_start: 0.6804 (tmm) cc_final: 0.6431 (ptt) REVERT: a 97 LYS cc_start: 0.7545 (mttt) cc_final: 0.6992 (pttt) REVERT: a 248 ILE cc_start: 0.7854 (mt) cc_final: 0.7572 (mt) outliers start: 1 outliers final: 0 residues processed: 379 average time/residue: 0.2057 time to fit residues: 130.6491 Evaluate side-chains 289 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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: 10.0000 chunk 200 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 204 optimal weight: 0.8980 chunk 173 optimal weight: 0.0570 chunk 53 optimal weight: 20.0000 chunk 334 optimal weight: 0.6980 chunk 412 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 388 optimal weight: 5.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 D 294 GLN G 35 GLN G 226 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 42 GLN X 85 GLN ** X 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.062829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.046341 restraints weight = 248202.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.046594 restraints weight = 146914.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.046902 restraints weight = 98291.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.047117 restraints weight = 74062.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.047116 restraints weight = 65592.756| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 37392 Z= 0.121 Angle : 0.570 9.970 50637 Z= 0.292 Chirality : 0.042 0.243 5901 Planarity : 0.004 0.046 6546 Dihedral : 6.875 130.035 5367 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.34 % Favored : 97.64 % Rotamer: Outliers : 0.03 % Allowed : 1.94 % Favored : 98.03 % 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: 1.86 (0.10), residues: 2619 sheet: -0.04 (0.22), residues: 532 loop : -0.68 (0.15), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 15 TYR 0.020 0.001 TYR a 216 PHE 0.022 0.001 PHE a 60 TRP 0.007 0.001 TRP a 111 HIS 0.008 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00245 (37392) covalent geometry : angle 0.56953 (50637) hydrogen bonds : bond 0.04652 ( 2208) hydrogen bonds : angle 4.25702 ( 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 361 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.354 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 156 MET cc_start: 0.9051 (mtm) cc_final: 0.8792 (mtp) REVERT: A 386 MET cc_start: 0.9040 (tpp) cc_final: 0.8551 (tpp) REVERT: A 448 LEU cc_start: 0.9483 (mt) cc_final: 0.9205 (mt) REVERT: A 468 GLU cc_start: 0.9056 (tt0) cc_final: 0.8819 (tm-30) REVERT: B 48 MET cc_start: 0.7747 (ptp) cc_final: 0.7014 (ptp) REVERT: B 52 MET cc_start: 0.7289 (mtm) cc_final: 0.6951 (mtm) REVERT: B 156 MET cc_start: 0.9110 (mmm) cc_final: 0.8825 (mmm) REVERT: B 208 VAL cc_start: 0.9726 (t) cc_final: 0.9515 (p) REVERT: B 412 ASP cc_start: 0.7500 (m-30) cc_final: 0.7105 (t70) REVERT: B 468 GLU cc_start: 0.8903 (tt0) cc_final: 0.8405 (tm-30) REVERT: B 472 LEU cc_start: 0.9328 (mt) cc_final: 0.8854 (pp) REVERT: B 483 MET cc_start: 0.9226 (mmm) cc_final: 0.9013 (mtt) REVERT: C 76 MET cc_start: 0.8449 (mpp) cc_final: 0.8103 (mtm) REVERT: D 368 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8817 (tp40) REVERT: F 56 MET cc_start: 0.9205 (mmm) cc_final: 0.8896 (mmm) REVERT: F 136 MET cc_start: 0.9289 (mmm) cc_final: 0.8764 (mmp) REVERT: F 274 GLU cc_start: 0.8696 (mt-10) cc_final: 0.8373 (mt-10) REVERT: F 445 MET cc_start: 0.8202 (mmt) cc_final: 0.7726 (tmm) REVERT: G 23 MET cc_start: 0.8477 (ttm) cc_final: 0.8215 (ttm) REVERT: G 48 MET cc_start: 0.9166 (ttm) cc_final: 0.8670 (mtp) REVERT: G 79 VAL cc_start: 0.9204 (t) cc_final: 0.8844 (t) REVERT: G 102 MET cc_start: 0.8699 (tmm) cc_final: 0.8403 (tmm) REVERT: G 187 LEU cc_start: 0.8913 (tp) cc_final: 0.8684 (tp) REVERT: G 194 ASP cc_start: 0.8310 (p0) cc_final: 0.8072 (m-30) REVERT: H 15 MET cc_start: 0.6190 (tpp) cc_final: 0.5694 (tpp) REVERT: H 49 MET cc_start: 0.2661 (ppp) cc_final: 0.2301 (ppp) REVERT: H 54 LYS cc_start: 0.7320 (mmtm) cc_final: 0.6996 (mmmt) REVERT: M 11 MET cc_start: 0.6789 (tmm) cc_final: 0.6213 (tpt) REVERT: M 54 PHE cc_start: 0.6588 (m-80) cc_final: 0.6089 (t80) REVERT: N 75 MET cc_start: 0.3966 (ttt) cc_final: 0.3735 (mmm) REVERT: O 11 MET cc_start: 0.7812 (tpt) cc_final: 0.7167 (mtp) REVERT: O 16 MET cc_start: 0.7210 (tmm) cc_final: 0.6517 (tmm) REVERT: O 17 MET cc_start: 0.6971 (mmp) cc_final: 0.6706 (mmm) REVERT: O 35 PHE cc_start: 0.7300 (t80) cc_final: 0.7057 (t80) REVERT: P 30 ILE cc_start: 0.7217 (tt) cc_final: 0.6906 (pt) REVERT: Q 11 MET cc_start: 0.8149 (ppp) cc_final: 0.7776 (ppp) REVERT: Q 53 PHE cc_start: 0.8281 (t80) cc_final: 0.7553 (t80) REVERT: Q 65 MET cc_start: 0.4308 (mtt) cc_final: 0.3583 (tpt) REVERT: R 11 MET cc_start: 0.6125 (mtm) cc_final: 0.5862 (mpp) REVERT: R 17 MET cc_start: 0.7701 (mtt) cc_final: 0.7173 (tpt) REVERT: R 35 PHE cc_start: 0.5593 (t80) cc_final: 0.5268 (t80) REVERT: R 53 PHE cc_start: 0.8843 (t80) cc_final: 0.8299 (t80) REVERT: S 17 MET cc_start: 0.5168 (ttt) cc_final: 0.4465 (tpt) REVERT: S 57 MET cc_start: 0.7996 (ppp) cc_final: 0.7764 (ppp) REVERT: W 43 MET cc_start: 0.9154 (tpt) cc_final: 0.8782 (tpt) REVERT: W 119 GLN cc_start: 0.9341 (tm-30) cc_final: 0.8936 (mp10) REVERT: W 147 MET cc_start: 0.8528 (mmp) cc_final: 0.8308 (mmm) REVERT: X 22 MET cc_start: 0.4976 (ptp) cc_final: 0.4756 (ptp) REVERT: X 141 ASP cc_start: 0.8487 (m-30) cc_final: 0.8033 (t0) REVERT: Y 22 MET cc_start: 0.5174 (mmp) cc_final: 0.4198 (ttt) REVERT: Y 30 MET cc_start: 0.6828 (pmm) cc_final: 0.6307 (mmp) REVERT: Y 150 ASP cc_start: 0.9194 (m-30) cc_final: 0.8901 (m-30) REVERT: a 6 MET cc_start: -0.0318 (ttt) cc_final: -0.0655 (ttt) REVERT: a 47 MET cc_start: 0.6765 (tmm) cc_final: 0.6403 (ptt) REVERT: a 97 LYS cc_start: 0.7515 (mttt) cc_final: 0.6965 (pttt) REVERT: a 216 TYR cc_start: 0.8397 (t80) cc_final: 0.8192 (t80) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.1994 time to fit residues: 121.4778 Evaluate side-chains 285 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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: 5.9990 chunk 155 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 365 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 274 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 262 optimal weight: 20.0000 chunk 186 optimal weight: 8.9990 chunk 242 optimal weight: 0.1980 chunk 220 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 GLN A 185 ASN ** 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 F 7 GLN G 35 GLN G 200 HIS H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 GLN O 52 GLN Q 42 GLN R 5 ASN X 106 GLN a 33 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.060191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.043222 restraints weight = 253015.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.044100 restraints weight = 156197.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044627 restraints weight = 94372.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.044922 restraints weight = 64332.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.045042 restraints weight = 54177.521| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 37392 Z= 0.190 Angle : 0.641 12.627 50637 Z= 0.329 Chirality : 0.043 0.267 5901 Planarity : 0.004 0.048 6546 Dihedral : 6.803 114.944 5367 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.96 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: 1.13 (0.12), residues: 4793 helix: 1.80 (0.10), residues: 2610 sheet: -0.16 (0.22), residues: 559 loop : -0.60 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 358 TYR 0.018 0.002 TYR a 216 PHE 0.031 0.002 PHE a 56 TRP 0.012 0.001 TRP Y 26 HIS 0.006 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00413 (37392) covalent geometry : angle 0.64111 (50637) hydrogen bonds : bond 0.04833 ( 2208) hydrogen bonds : angle 4.39676 ( 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 335 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.260 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: 0.9090 (mtm) cc_final: 0.8850 (mtp) REVERT: A 386 MET cc_start: 0.9167 (tpp) cc_final: 0.8888 (tpp) REVERT: A 448 LEU cc_start: 0.9536 (mt) cc_final: 0.9218 (mt) REVERT: A 468 GLU cc_start: 0.9013 (tt0) cc_final: 0.8764 (tm-30) REVERT: B 52 MET cc_start: 0.7211 (mtm) cc_final: 0.6926 (mtm) REVERT: B 412 ASP cc_start: 0.7448 (m-30) cc_final: 0.7161 (t70) REVERT: B 468 GLU cc_start: 0.8938 (tt0) cc_final: 0.8621 (tm-30) REVERT: B 472 LEU cc_start: 0.9387 (mt) cc_final: 0.9007 (pp) REVERT: C 76 MET cc_start: 0.8386 (mpp) cc_final: 0.7930 (mpp) REVERT: C 245 MET cc_start: 0.8414 (mtm) cc_final: 0.8180 (mtm) REVERT: D 209 MET cc_start: 0.8390 (mpp) cc_final: 0.8124 (mpp) REVERT: D 263 SER cc_start: 0.9149 (t) cc_final: 0.8736 (p) REVERT: D 368 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8844 (tp40) REVERT: D 397 GLN cc_start: 0.9070 (tt0) cc_final: 0.8468 (tm-30) REVERT: D 445 MET cc_start: 0.8894 (mmm) cc_final: 0.7952 (mmm) REVERT: F 56 MET cc_start: 0.9147 (mmm) cc_final: 0.8766 (mmm) REVERT: F 136 MET cc_start: 0.9328 (mmm) cc_final: 0.8850 (mmp) REVERT: F 209 MET cc_start: 0.8082 (ptp) cc_final: 0.7882 (ptp) REVERT: F 445 MET cc_start: 0.8272 (mmt) cc_final: 0.7753 (tmm) REVERT: G 79 VAL cc_start: 0.9237 (t) cc_final: 0.8896 (t) REVERT: G 102 MET cc_start: 0.8629 (tmm) cc_final: 0.8379 (tmm) REVERT: G 194 ASP cc_start: 0.8310 (p0) cc_final: 0.8087 (m-30) REVERT: G 246 MET cc_start: 0.8857 (mmp) cc_final: 0.8464 (mmp) REVERT: H 15 MET cc_start: 0.6333 (tpp) cc_final: 0.5765 (tpp) REVERT: H 49 MET cc_start: 0.3803 (ppp) cc_final: 0.3349 (ppp) REVERT: H 54 LYS cc_start: 0.7178 (mmtm) cc_final: 0.6933 (mmmt) REVERT: M 54 PHE cc_start: 0.6615 (m-80) cc_final: 0.6055 (t80) REVERT: O 11 MET cc_start: 0.7844 (tpt) cc_final: 0.7067 (mtp) REVERT: O 35 PHE cc_start: 0.7015 (t80) cc_final: 0.6704 (t80) REVERT: P 30 ILE cc_start: 0.6835 (tt) cc_final: 0.6542 (pt) REVERT: Q 11 MET cc_start: 0.8141 (ppp) cc_final: 0.7878 (ppp) REVERT: Q 65 MET cc_start: 0.4240 (mtt) cc_final: 0.3391 (tpt) REVERT: R 35 PHE cc_start: 0.5643 (t80) cc_final: 0.5057 (t80) REVERT: R 53 PHE cc_start: 0.8868 (t80) cc_final: 0.8459 (t80) REVERT: S 17 MET cc_start: 0.5013 (ttt) cc_final: 0.4538 (tpt) REVERT: S 57 MET cc_start: 0.7946 (ppp) cc_final: 0.7684 (ppp) REVERT: X 22 MET cc_start: 0.4752 (ptp) cc_final: 0.4547 (ptp) REVERT: X 69 LYS cc_start: 0.4962 (tptt) cc_final: 0.4112 (tptt) REVERT: X 141 ASP cc_start: 0.8447 (m-30) cc_final: 0.8046 (t0) REVERT: Y 22 MET cc_start: 0.5168 (mmp) cc_final: 0.4230 (ttt) REVERT: Y 30 MET cc_start: 0.6866 (pmm) cc_final: 0.6364 (mmp) REVERT: Y 150 ASP cc_start: 0.9221 (m-30) cc_final: 0.8962 (m-30) REVERT: a 6 MET cc_start: -0.0552 (ttt) cc_final: -0.0968 (ttt) REVERT: a 47 MET cc_start: 0.6828 (tmm) cc_final: 0.6441 (ptt) REVERT: a 97 LYS cc_start: 0.7435 (mttt) cc_final: 0.6838 (pttt) REVERT: a 216 TYR cc_start: 0.8422 (t80) cc_final: 0.8179 (t80) REVERT: a 219 GLU cc_start: 0.8044 (tp30) cc_final: 0.7707 (tp30) outliers start: 0 outliers final: 0 residues processed: 335 average time/residue: 0.1987 time to fit residues: 113.9282 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 : 1.619 ------------------------------------------------------------------------------- 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: 0.2980 chunk 373 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 36 optimal weight: 0.0670 chunk 66 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 398 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 420 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 399 optimal weight: 20.0000 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN B 361 ASN C 185 ASN C 186 GLN C 352 GLN D 343 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** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.061477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.045488 restraints weight = 250182.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.045613 restraints weight = 142958.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.045979 restraints weight = 100073.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.046174 restraints weight = 72432.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.046167 restraints weight = 63440.045| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 37392 Z= 0.121 Angle : 0.586 11.992 50637 Z= 0.298 Chirality : 0.042 0.231 5901 Planarity : 0.004 0.050 6546 Dihedral : 6.565 118.145 5367 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 1.26 (0.12), residues: 4793 helix: 1.89 (0.10), residues: 2645 sheet: -0.02 (0.22), residues: 552 loop : -0.59 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 83 TYR 0.020 0.001 TYR B 236 PHE 0.044 0.001 PHE a 60 TRP 0.012 0.001 TRP W 27 HIS 0.006 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00248 (37392) covalent geometry : angle 0.58636 (50637) hydrogen bonds : bond 0.04464 ( 2208) hydrogen bonds : angle 4.20781 ( 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 336 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 1.361 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 156 MET cc_start: 0.9085 (mtm) cc_final: 0.8832 (mtp) REVERT: A 448 LEU cc_start: 0.9495 (mt) cc_final: 0.9231 (mt) REVERT: B 52 MET cc_start: 0.7171 (mtm) cc_final: 0.6861 (mtm) REVERT: B 156 MET cc_start: 0.9320 (mmm) cc_final: 0.8980 (mmm) REVERT: B 412 ASP cc_start: 0.7401 (m-30) cc_final: 0.7017 (t70) REVERT: B 468 GLU cc_start: 0.8933 (tt0) cc_final: 0.8601 (tm-30) REVERT: B 472 LEU cc_start: 0.9318 (mt) cc_final: 0.8924 (pp) REVERT: C 76 MET cc_start: 0.8384 (mpp) cc_final: 0.8130 (mtm) REVERT: D 56 MET cc_start: 0.9227 (mmm) cc_final: 0.8937 (mmp) REVERT: D 397 GLN cc_start: 0.9030 (tt0) cc_final: 0.8466 (tm-30) REVERT: F 56 MET cc_start: 0.9231 (mmm) cc_final: 0.8914 (mmm) REVERT: F 136 MET cc_start: 0.9328 (mmm) cc_final: 0.8743 (mmp) REVERT: F 274 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8330 (mt-10) REVERT: F 445 MET cc_start: 0.8267 (mmt) cc_final: 0.7708 (tmm) REVERT: G 23 MET cc_start: 0.8558 (ttm) cc_final: 0.8246 (ttm) REVERT: G 48 MET cc_start: 0.9112 (ttm) cc_final: 0.8620 (mtp) REVERT: G 79 VAL cc_start: 0.9233 (t) cc_final: 0.8877 (t) REVERT: G 102 MET cc_start: 0.8662 (tmm) cc_final: 0.8361 (tmm) REVERT: G 187 LEU cc_start: 0.9017 (tp) cc_final: 0.8804 (tp) REVERT: G 194 ASP cc_start: 0.8414 (p0) cc_final: 0.8133 (m-30) REVERT: H 15 MET cc_start: 0.6063 (tpp) cc_final: 0.5617 (tpp) REVERT: H 49 MET cc_start: 0.3331 (ppp) cc_final: 0.2947 (ppp) REVERT: M 11 MET cc_start: 0.6902 (tmm) cc_final: 0.6140 (tpt) REVERT: M 54 PHE cc_start: 0.6841 (m-80) cc_final: 0.6302 (t80) REVERT: O 11 MET cc_start: 0.7600 (tpt) cc_final: 0.6905 (mtp) REVERT: O 35 PHE cc_start: 0.7158 (t80) cc_final: 0.6477 (t80) REVERT: O 53 PHE cc_start: 0.8235 (t80) cc_final: 0.7504 (t80) REVERT: P 16 MET cc_start: 0.5585 (tmm) cc_final: 0.5161 (tmm) REVERT: P 30 ILE cc_start: 0.6747 (tt) cc_final: 0.6460 (pt) REVERT: Q 11 MET cc_start: 0.8035 (ppp) cc_final: 0.7823 (ppp) REVERT: Q 65 MET cc_start: 0.4190 (mtt) cc_final: 0.3491 (tpt) REVERT: R 35 PHE cc_start: 0.5723 (t80) cc_final: 0.5491 (t80) REVERT: R 53 PHE cc_start: 0.8833 (t80) cc_final: 0.8580 (t80) REVERT: R 57 MET cc_start: 0.6959 (ppp) cc_final: 0.5961 (mmm) REVERT: R 61 ASP cc_start: 0.8603 (m-30) cc_final: 0.8240 (p0) REVERT: S 17 MET cc_start: 0.5000 (ttt) cc_final: 0.4439 (tpt) REVERT: X 69 LYS cc_start: 0.4823 (tptt) cc_final: 0.4073 (tptt) REVERT: X 141 ASP cc_start: 0.8497 (m-30) cc_final: 0.8051 (t0) REVERT: Y 22 MET cc_start: 0.5157 (mmp) cc_final: 0.4281 (ttt) REVERT: Y 30 MET cc_start: 0.6792 (pmm) cc_final: 0.6319 (mmp) REVERT: Y 150 ASP cc_start: 0.9251 (m-30) cc_final: 0.9003 (m-30) REVERT: a 6 MET cc_start: -0.0412 (ttt) cc_final: -0.0758 (ttt) REVERT: a 47 MET cc_start: 0.6715 (tmm) cc_final: 0.6352 (ptt) REVERT: a 97 LYS cc_start: 0.7471 (mttt) cc_final: 0.6925 (pttt) REVERT: a 216 TYR cc_start: 0.8430 (t80) cc_final: 0.8145 (t80) REVERT: a 219 GLU cc_start: 0.8145 (tp30) cc_final: 0.7822 (tp30) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1997 time to fit residues: 115.4899 Evaluate side-chains 279 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.417 ------------------------------------------------------------------------------- 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: 8.9990 chunk 394 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 284 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 6.9990 chunk 104 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 365 GLN E 208 GLN F 7 GLN F 19 GLN 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.058255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.042168 restraints weight = 254163.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.042671 restraints weight = 137956.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.043077 restraints weight = 88681.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.043329 restraints weight = 70082.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.043339 restraints weight = 62497.750| |-----------------------------------------------------------------------------| r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 37392 Z= 0.244 Angle : 0.720 10.403 50637 Z= 0.366 Chirality : 0.045 0.236 5901 Planarity : 0.005 0.049 6546 Dihedral : 6.832 110.784 5367 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % 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: 0.96 (0.12), residues: 4793 helix: 1.62 (0.10), residues: 2640 sheet: -0.15 (0.22), residues: 547 loop : -0.67 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 281 TYR 0.021 0.002 TYR B 236 PHE 0.033 0.002 PHE a 60 TRP 0.016 0.002 TRP Y 26 HIS 0.008 0.002 HIS B 123 Details of bonding type rmsd covalent geometry : bond 0.00530 (37392) covalent geometry : angle 0.72031 (50637) hydrogen bonds : bond 0.05074 ( 2208) hydrogen bonds : angle 4.56918 ( 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 321 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.480 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 156 MET cc_start: 0.9145 (mtm) cc_final: 0.8924 (mtp) REVERT: A 386 MET cc_start: 0.9126 (tpp) cc_final: 0.8763 (tpp) REVERT: A 448 LEU cc_start: 0.9595 (mt) cc_final: 0.9282 (mt) REVERT: B 48 MET cc_start: 0.8017 (ptp) cc_final: 0.7350 (ptp) REVERT: B 156 MET cc_start: 0.9390 (mmm) cc_final: 0.9028 (mmm) REVERT: B 412 ASP cc_start: 0.7641 (m-30) cc_final: 0.7298 (t70) REVERT: B 472 LEU cc_start: 0.9393 (mt) cc_final: 0.9057 (pp) REVERT: C 76 MET cc_start: 0.8398 (mpp) cc_final: 0.7954 (mpp) REVERT: D 263 SER cc_start: 0.9153 (t) cc_final: 0.8790 (p) REVERT: D 397 GLN cc_start: 0.9155 (tt0) cc_final: 0.8633 (tm-30) REVERT: E 56 MET cc_start: 0.8855 (mmp) cc_final: 0.8606 (mmp) REVERT: F 56 MET cc_start: 0.9126 (mmm) cc_final: 0.8726 (mmm) REVERT: F 136 MET cc_start: 0.9358 (mmm) cc_final: 0.8871 (mmp) REVERT: F 431 MET cc_start: 0.9071 (ttm) cc_final: 0.8867 (ttm) REVERT: F 445 MET cc_start: 0.8370 (mmt) cc_final: 0.7764 (tmm) REVERT: G 23 MET cc_start: 0.8690 (ttm) cc_final: 0.8428 (ttm) REVERT: G 48 MET cc_start: 0.9071 (ttm) cc_final: 0.8649 (mtp) REVERT: G 79 VAL cc_start: 0.9341 (t) cc_final: 0.9010 (t) REVERT: G 102 MET cc_start: 0.8702 (tmm) cc_final: 0.8466 (tmm) REVERT: G 187 LEU cc_start: 0.9122 (tp) cc_final: 0.8911 (tp) REVERT: G 194 ASP cc_start: 0.8395 (p0) cc_final: 0.8138 (m-30) REVERT: G 243 MET cc_start: 0.8963 (mmm) cc_final: 0.8749 (mmm) REVERT: H 15 MET cc_start: 0.6402 (tpp) cc_final: 0.5840 (tpp) REVERT: H 49 MET cc_start: 0.4621 (ppp) cc_final: 0.4161 (ppp) REVERT: H 54 LYS cc_start: 0.7286 (mmpt) cc_final: 0.6880 (mmmt) REVERT: I 17 MET cc_start: 0.2442 (ppp) cc_final: 0.2071 (ppp) REVERT: M 54 PHE cc_start: 0.6869 (m-80) cc_final: 0.6211 (t80) REVERT: O 11 MET cc_start: 0.7650 (tpt) cc_final: 0.6967 (mtp) REVERT: O 16 MET cc_start: 0.6388 (ppp) cc_final: 0.5541 (ppp) REVERT: O 35 PHE cc_start: 0.7090 (t80) cc_final: 0.6707 (t80) REVERT: P 17 MET cc_start: 0.5866 (ttp) cc_final: 0.5359 (tmm) REVERT: Q 35 PHE cc_start: 0.6452 (t80) cc_final: 0.5713 (t80) REVERT: Q 65 MET cc_start: 0.4195 (mtt) cc_final: 0.3336 (tpt) REVERT: R 53 PHE cc_start: 0.9043 (t80) cc_final: 0.8651 (t80) REVERT: S 17 MET cc_start: 0.5389 (ttt) cc_final: 0.4713 (tpt) REVERT: S 34 LYS cc_start: 0.7738 (tppp) cc_final: 0.7322 (mtmt) REVERT: X 44 LEU cc_start: 0.7326 (mt) cc_final: 0.7110 (pp) REVERT: X 69 LYS cc_start: 0.5284 (tptt) cc_final: 0.4497 (tptt) REVERT: X 141 ASP cc_start: 0.8529 (m-30) cc_final: 0.8109 (t0) REVERT: Y 22 MET cc_start: 0.4892 (mmp) cc_final: 0.4033 (ttt) REVERT: Y 30 MET cc_start: 0.6849 (pmm) cc_final: 0.6416 (mmp) REVERT: Y 150 ASP cc_start: 0.9331 (m-30) cc_final: 0.9109 (m-30) REVERT: a 6 MET cc_start: -0.0921 (ttt) cc_final: -0.1262 (ttt) REVERT: a 47 MET cc_start: 0.6798 (tmm) cc_final: 0.6393 (ptt) REVERT: a 97 LYS cc_start: 0.7356 (mttt) cc_final: 0.6665 (pttt) REVERT: a 216 TYR cc_start: 0.8529 (t80) cc_final: 0.8309 (t80) outliers start: 0 outliers final: 0 residues processed: 321 average time/residue: 0.1949 time to fit residues: 106.8037 Evaluate side-chains 261 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.401 ------------------------------------------------------------------------------- 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: 6.9990 chunk 194 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 chunk 173 optimal weight: 0.0570 chunk 417 optimal weight: 20.0000 chunk 414 optimal weight: 20.0000 chunk 304 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 457 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN C 186 GLN D 7 GLN D 123 GLN F 7 GLN F 121 ASN G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 78 GLN a 33 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.059772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043005 restraints weight = 250952.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.044097 restraints weight = 148909.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044585 restraints weight = 88658.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.044897 restraints weight = 60413.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044978 restraints weight = 51454.019| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5590 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= 0.134 Angle : 0.621 10.826 50637 Z= 0.316 Chirality : 0.043 0.214 5901 Planarity : 0.004 0.049 6546 Dihedral : 6.597 120.426 5367 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.40 % Favored : 97.58 % Rotamer: Outliers : 0.05 % Allowed : 0.58 % Favored : 99.37 % 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: 1.18 (0.12), residues: 4793 helix: 1.81 (0.10), residues: 2635 sheet: -0.17 (0.22), residues: 560 loop : -0.55 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 83 TYR 0.028 0.001 TYR M 10 PHE 0.026 0.001 PHE W 95 TRP 0.013 0.001 TRP W 27 HIS 0.005 0.001 HIS A 423 Details of bonding type rmsd covalent geometry : bond 0.00285 (37392) covalent geometry : angle 0.62146 (50637) hydrogen bonds : bond 0.04654 ( 2208) hydrogen bonds : angle 4.31799 ( 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 323 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8679 (mpp) cc_final: 0.8359 (mmt) REVERT: A 156 MET cc_start: 0.9110 (mtm) cc_final: 0.8889 (mtp) REVERT: A 245 MET cc_start: 0.8504 (mpp) cc_final: 0.8276 (mpp) REVERT: A 386 MET cc_start: 0.8966 (tpp) cc_final: 0.8605 (tpp) REVERT: A 448 LEU cc_start: 0.9554 (mt) cc_final: 0.9239 (mt) REVERT: B 48 MET cc_start: 0.8066 (ptp) cc_final: 0.7341 (ptp) REVERT: B 412 ASP cc_start: 0.7576 (m-30) cc_final: 0.7165 (t70) REVERT: C 76 MET cc_start: 0.8399 (mpp) cc_final: 0.8164 (mtm) REVERT: D 263 SER cc_start: 0.9094 (t) cc_final: 0.8689 (p) REVERT: D 397 GLN cc_start: 0.9141 (tt0) cc_final: 0.8672 (tm-30) REVERT: D 445 MET cc_start: 0.9015 (mmm) cc_final: 0.8020 (mmm) REVERT: E 275 MET cc_start: 0.9395 (tpp) cc_final: 0.8949 (tpp) REVERT: F 56 MET cc_start: 0.9210 (mmm) cc_final: 0.8857 (mmm) REVERT: F 136 MET cc_start: 0.9313 (mmm) cc_final: 0.8766 (mmp) REVERT: F 431 MET cc_start: 0.9032 (ttm) cc_final: 0.8784 (ttm) REVERT: F 445 MET cc_start: 0.8327 (mmt) cc_final: 0.7630 (tmm) REVERT: G 48 MET cc_start: 0.9091 (ttm) cc_final: 0.8662 (mtp) REVERT: G 79 VAL cc_start: 0.9264 (t) cc_final: 0.8926 (t) REVERT: G 102 MET cc_start: 0.8568 (tmm) cc_final: 0.8350 (tmm) REVERT: G 178 MET cc_start: 0.8537 (pmm) cc_final: 0.8226 (pmm) REVERT: G 187 LEU cc_start: 0.8999 (tp) cc_final: 0.8764 (tp) REVERT: G 194 ASP cc_start: 0.8363 (p0) cc_final: 0.8121 (m-30) REVERT: G 246 MET cc_start: 0.8820 (mmp) cc_final: 0.8270 (mmp) REVERT: H 15 MET cc_start: 0.6397 (tpp) cc_final: 0.5813 (tpp) REVERT: H 49 MET cc_start: 0.4111 (ppp) cc_final: 0.3764 (ppp) REVERT: H 54 LYS cc_start: 0.7058 (mmpt) cc_final: 0.6689 (mmmt) REVERT: I 17 MET cc_start: 0.2227 (ppp) cc_final: 0.1858 (ppp) REVERT: M 11 MET cc_start: 0.7379 (tmm) cc_final: 0.6341 (tpt) REVERT: M 54 PHE cc_start: 0.6947 (m-80) cc_final: 0.6274 (t80) REVERT: N 53 PHE cc_start: 0.8760 (t80) cc_final: 0.8465 (t80) REVERT: O 11 MET cc_start: 0.7665 (tpt) cc_final: 0.6915 (mtp) REVERT: O 16 MET cc_start: 0.6083 (ppp) cc_final: 0.5106 (ppp) REVERT: O 35 PHE cc_start: 0.6848 (t80) cc_final: 0.6220 (t80) REVERT: O 53 PHE cc_start: 0.8103 (t80) cc_final: 0.7449 (t80) REVERT: P 30 ILE cc_start: 0.7024 (tt) cc_final: 0.6789 (pt) REVERT: Q 35 PHE cc_start: 0.6553 (t80) cc_final: 0.5863 (t80) REVERT: Q 65 MET cc_start: 0.4427 (mtt) cc_final: 0.3568 (tpt) REVERT: R 16 MET cc_start: 0.5236 (ttt) cc_final: 0.4865 (ttm) REVERT: R 35 PHE cc_start: 0.5775 (t80) cc_final: 0.5011 (t80) REVERT: R 53 PHE cc_start: 0.8978 (t80) cc_final: 0.8649 (t80) REVERT: R 57 MET cc_start: 0.6982 (ppp) cc_final: 0.5827 (mmm) REVERT: R 61 ASP cc_start: 0.8479 (m-30) cc_final: 0.8144 (p0) REVERT: S 17 MET cc_start: 0.5462 (ttt) cc_final: 0.4629 (tpt) REVERT: X 44 LEU cc_start: 0.7345 (mt) cc_final: 0.7140 (pp) REVERT: X 141 ASP cc_start: 0.8399 (m-30) cc_final: 0.8011 (t0) REVERT: Y 22 MET cc_start: 0.4904 (mmp) cc_final: 0.4006 (ttt) REVERT: Y 30 MET cc_start: 0.6831 (pmm) cc_final: 0.6459 (mmt) REVERT: Y 150 ASP cc_start: 0.9301 (m-30) cc_final: 0.9067 (m-30) REVERT: a 6 MET cc_start: -0.1237 (ttt) cc_final: -0.1737 (ttt) REVERT: a 47 MET cc_start: 0.6829 (tmm) cc_final: 0.6426 (ptt) REVERT: a 97 LYS cc_start: 0.7300 (mttt) cc_final: 0.6583 (pttt) REVERT: a 216 TYR cc_start: 0.8479 (t80) cc_final: 0.8011 (t80) outliers start: 2 outliers final: 0 residues processed: 323 average time/residue: 0.1924 time to fit residues: 107.0286 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 : 1.339 ------------------------------------------------------------------------------- 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: 9.9990 chunk 415 optimal weight: 7.9990 chunk 390 optimal weight: 0.9990 chunk 418 optimal weight: 40.0000 chunk 335 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 463 optimal weight: 6.9990 chunk 468 optimal weight: 6.9990 chunk 325 optimal weight: 7.9990 chunk 341 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 123 GLN 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.059753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.043026 restraints weight = 253049.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043954 restraints weight = 146392.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.044430 restraints weight = 91999.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.044776 restraints weight = 62384.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.044826 restraints weight = 53860.184| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37392 Z= 0.135 Angle : 0.616 10.870 50637 Z= 0.312 Chirality : 0.042 0.221 5901 Planarity : 0.004 0.045 6546 Dihedral : 6.465 122.100 5367 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 0.05 % Allowed : 0.31 % Favored : 99.63 % 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: 1.19 (0.12), residues: 4793 helix: 1.80 (0.10), residues: 2646 sheet: -0.07 (0.22), residues: 541 loop : -0.58 (0.16), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG a 210 TYR 0.019 0.001 TYR R 10 PHE 0.030 0.002 PHE M 53 TRP 0.009 0.001 TRP W 27 HIS 0.006 0.001 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00293 (37392) covalent geometry : angle 0.61594 (50637) hydrogen bonds : bond 0.04500 ( 2208) hydrogen bonds : angle 4.28870 ( 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 316 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 1.201 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 48 MET cc_start: 0.8682 (mpp) cc_final: 0.8366 (mmt) REVERT: A 156 MET cc_start: 0.9092 (mtm) cc_final: 0.8880 (mtp) REVERT: A 245 MET cc_start: 0.8543 (mpp) cc_final: 0.8321 (mpp) REVERT: A 386 MET cc_start: 0.8979 (tpp) cc_final: 0.8637 (tpp) REVERT: A 448 LEU cc_start: 0.9550 (mt) cc_final: 0.9246 (mt) REVERT: B 48 MET cc_start: 0.8069 (ptp) cc_final: 0.7287 (ptp) REVERT: B 76 MET cc_start: 0.8830 (mtp) cc_final: 0.8507 (mtp) REVERT: B 412 ASP cc_start: 0.7573 (m-30) cc_final: 0.7183 (t70) REVERT: B 468 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8333 (tm-30) REVERT: C 76 MET cc_start: 0.8378 (mpp) cc_final: 0.8152 (mtm) REVERT: D 159 MET cc_start: 0.8922 (tpp) cc_final: 0.8651 (tpp) REVERT: D 160 MET cc_start: 0.8272 (tpt) cc_final: 0.8009 (tpt) REVERT: D 397 GLN cc_start: 0.9143 (tt0) cc_final: 0.8697 (tm-30) REVERT: D 445 MET cc_start: 0.9026 (mmm) cc_final: 0.8064 (mmm) REVERT: E 275 MET cc_start: 0.9389 (tpp) cc_final: 0.8954 (tpp) REVERT: F 56 MET cc_start: 0.9221 (mmm) cc_final: 0.8829 (mmm) REVERT: F 136 MET cc_start: 0.9339 (mmm) cc_final: 0.8786 (mmp) REVERT: F 431 MET cc_start: 0.9022 (ttm) cc_final: 0.8786 (ttm) REVERT: F 445 MET cc_start: 0.8287 (mmt) cc_final: 0.7623 (tmm) REVERT: G 23 MET cc_start: 0.8630 (ttm) cc_final: 0.8420 (ttm) REVERT: G 79 VAL cc_start: 0.9278 (t) cc_final: 0.8956 (t) REVERT: G 178 MET cc_start: 0.8518 (pmm) cc_final: 0.8260 (pmm) REVERT: G 194 ASP cc_start: 0.8423 (p0) cc_final: 0.8143 (m-30) REVERT: G 243 MET cc_start: 0.8937 (mmm) cc_final: 0.8589 (mmm) REVERT: H 15 MET cc_start: 0.6812 (tpp) cc_final: 0.6305 (tpp) REVERT: H 49 MET cc_start: 0.4140 (ppp) cc_final: 0.3836 (ppp) REVERT: H 54 LYS cc_start: 0.7222 (mmpt) cc_final: 0.6832 (mmmt) REVERT: I 17 MET cc_start: 0.2249 (ppp) cc_final: 0.1925 (ppp) REVERT: I 57 MET cc_start: 0.4271 (tpt) cc_final: 0.4044 (tpt) REVERT: M 11 MET cc_start: 0.6954 (tmm) cc_final: 0.5951 (tpt) REVERT: M 54 PHE cc_start: 0.6870 (m-80) cc_final: 0.6240 (t80) REVERT: O 11 MET cc_start: 0.7629 (tpt) cc_final: 0.7299 (tpt) REVERT: O 16 MET cc_start: 0.5864 (ppp) cc_final: 0.5361 (tmm) REVERT: O 35 PHE cc_start: 0.6867 (t80) cc_final: 0.6227 (t80) REVERT: O 53 PHE cc_start: 0.8197 (t80) cc_final: 0.7536 (t80) REVERT: P 30 ILE cc_start: 0.7108 (tt) cc_final: 0.6842 (pt) REVERT: Q 35 PHE cc_start: 0.6589 (t80) cc_final: 0.5906 (t80) REVERT: Q 65 MET cc_start: 0.4310 (mtt) cc_final: 0.3512 (tpt) REVERT: R 16 MET cc_start: 0.5002 (ttt) cc_final: 0.4734 (ttm) REVERT: R 35 PHE cc_start: 0.5747 (t80) cc_final: 0.4944 (t80) REVERT: R 53 PHE cc_start: 0.9022 (t80) cc_final: 0.8676 (t80) REVERT: R 57 MET cc_start: 0.7032 (ppp) cc_final: 0.5963 (mmm) REVERT: R 61 ASP cc_start: 0.8511 (m-30) cc_final: 0.8187 (p0) REVERT: S 17 MET cc_start: 0.5550 (ttt) cc_final: 0.4875 (tpt) REVERT: X 69 LYS cc_start: 0.5299 (tptt) cc_final: 0.4544 (tptt) REVERT: X 141 ASP cc_start: 0.8363 (m-30) cc_final: 0.7954 (t0) REVERT: Y 22 MET cc_start: 0.4648 (mmp) cc_final: 0.3840 (ttt) REVERT: Y 30 MET cc_start: 0.6877 (pmm) cc_final: 0.6500 (mmt) REVERT: Y 150 ASP cc_start: 0.9330 (m-30) cc_final: 0.9104 (m-30) REVERT: a 6 MET cc_start: -0.1273 (ttt) cc_final: -0.1509 (ttt) REVERT: a 47 MET cc_start: 0.6807 (tmm) cc_final: 0.6407 (ptt) REVERT: a 97 LYS cc_start: 0.7397 (mttt) cc_final: 0.6557 (ttpt) REVERT: a 216 TYR cc_start: 0.8630 (t80) cc_final: 0.8188 (t80) outliers start: 2 outliers final: 0 residues processed: 316 average time/residue: 0.1975 time to fit residues: 107.5554 Evaluate side-chains 268 residues out of total 3824 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 1.230 ------------------------------------------------------------------------------- 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: 8.9990 chunk 426 optimal weight: 5.9990 chunk 465 optimal weight: 20.0000 chunk 327 optimal weight: 1.9990 chunk 317 optimal weight: 6.9990 chunk 213 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 F 121 ASN G 35 GLN H 14 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.058857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.042732 restraints weight = 253168.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.043316 restraints weight = 137632.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.043984 restraints weight = 85000.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.043992 restraints weight = 65794.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.044063 restraints weight = 54876.051| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.5987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 37392 Z= 0.169 Angle : 0.642 10.361 50637 Z= 0.324 Chirality : 0.043 0.218 5901 Planarity : 0.004 0.043 6546 Dihedral : 6.504 124.043 5367 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.98 % Favored : 97.00 % Rotamer: Outliers : 0.03 % Allowed : 0.39 % Favored : 99.58 % 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: 1.15 (0.12), residues: 4793 helix: 1.78 (0.10), residues: 2642 sheet: -0.12 (0.22), residues: 546 loop : -0.59 (0.16), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 83 TYR 0.026 0.001 TYR G 205 PHE 0.028 0.002 PHE E 189 TRP 0.012 0.001 TRP G 203 HIS 0.007 0.001 HIS D 170 Details of bonding type rmsd covalent geometry : bond 0.00373 (37392) covalent geometry : angle 0.64158 (50637) hydrogen bonds : bond 0.04510 ( 2208) hydrogen bonds : angle 4.35205 ( 6471) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5576.18 seconds wall clock time: 97 minutes 20.74 seconds (5840.74 seconds total)