Starting phenix.real_space_refine on Sat Mar 7 02:23:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oqw_20172/03_2026/6oqw_20172_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oqw_20172/03_2026/6oqw_20172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6oqw_20172/03_2026/6oqw_20172_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oqw_20172/03_2026/6oqw_20172_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6oqw_20172/03_2026/6oqw_20172.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oqw_20172/03_2026/6oqw_20172.map" } resolution = 3.1 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 180 5.16 5 C 23445 2.51 5 N 6306 2.21 5 O 6949 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 279 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36901 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1317 Classifications: {'peptide': 173} 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: "C" Number of atoms: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 3852 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3852 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: "H" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1034 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "G" Number of atoms: 2186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2186 Classifications: {'peptide': 284} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 274} Chain: "F" Number of atoms: 3520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3520 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 437} Chain: "E" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "D" Number of atoms: 3533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 460, 3533 Classifications: {'peptide': 460} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 439} Chain: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 554 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 73} 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: "P" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Q" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} 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: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 1171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1171 Classifications: {'peptide': 155} 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} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 250} 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: "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: "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: "F" 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: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.41, per 1000 atoms: 0.23 Number of scatterers: 36901 At special positions: 0 Unit cell: (178.035, 214.721, 133.796, 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 180 16.00 P 16 15.00 Mg 5 11.99 O 6949 8.00 N 6306 7.00 C 23445 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8810 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 28 sheets defined 60.7% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'W' and resid 3 through 19 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 38 removed outlier: 3.719A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 49 removed outlier: 3.625A pdb=" N SER W 48 " --> pdb=" O ALA W 44 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY W 49 " --> pdb=" O GLU W 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 62 Processing helix chain 'W' and resid 71 through 82 removed outlier: 4.576A pdb=" N ARG W 77 " --> pdb=" O GLN W 73 " (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: 3.755A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 Processing helix chain 'W' and resid 144 through 147 Processing helix chain 'W' and resid 162 through 174 removed outlier: 3.596A pdb=" N ASP W 172 " --> pdb=" O GLU W 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 100 through 104 removed outlier: 3.625A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 174 through 186 removed outlier: 3.650A pdb=" N GLN C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 201 through 215 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 231 through 252 Proline residue: C 239 - end of helix removed outlier: 3.797A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.611A pdb=" N GLN C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 290 through 299 removed outlier: 3.855A pdb=" N ARG C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU C 297 " --> pdb=" O LEU C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 313 Processing helix chain 'C' and resid 333 through 336 removed outlier: 3.531A 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 362 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.802A 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 removed outlier: 3.695A pdb=" N GLU C 402 " --> pdb=" O ALA C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 432 removed outlier: 3.855A pdb=" N ASP C 422 " --> pdb=" O ARG C 418 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR C 428 " --> pdb=" O GLY C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 4.003A pdb=" N ARG C 453 " --> pdb=" O PHE C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 478 removed outlier: 3.512A pdb=" N ALA C 473 " --> pdb=" O ALA C 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 485 Processing helix chain 'C' and resid 493 through 509 removed outlier: 3.692A pdb=" N LYS C 499 " --> pdb=" O GLU C 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 18 Processing helix chain 'B' and resid 100 through 104 removed outlier: 3.574A pdb=" N LEU B 103 " --> pdb=" O GLY B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 185 Processing helix chain 'B' and resid 201 through 215 removed outlier: 3.515A pdb=" N ILE B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 237 through 251 removed outlier: 4.116A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 276 removed outlier: 4.052A pdb=" N VAL B 268 " --> pdb=" O SER B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 290 through 299 removed outlier: 3.932A pdb=" N ARG B 296 " --> pdb=" O TYR B 292 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU B 297 " --> pdb=" O LEU B 293 " (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: 3.579A pdb=" N ALA B 362 " --> pdb=" O ASN B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.896A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.610A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 408 removed outlier: 3.925A pdb=" N GLN B 408 " --> pdb=" O ALA B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 431 removed outlier: 3.548A pdb=" N GLN B 420 " --> pdb=" O ALA B 416 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLN B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 464 through 478 Processing helix chain 'B' and resid 479 through 490 Processing helix chain 'B' and resid 493 through 511 removed outlier: 3.559A pdb=" N THR B 510 " --> pdb=" O SER B 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 19 Processing helix chain 'A' and resid 135 through 139 Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.541A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 181 Processing helix chain 'A' and resid 201 through 215 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 251 Proline residue: A 239 - end of helix removed outlier: 3.793A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.865A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.650A pdb=" N ALA A 285 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 299 removed outlier: 4.066A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) 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 362 removed outlier: 3.551A pdb=" N ALA A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 383 through 404 removed outlier: 4.087A pdb=" N GLY A 391 " --> pdb=" O LYS A 387 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLY A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.425A pdb=" N GLN A 408 " --> pdb=" O ALA A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.994A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 426 " --> pdb=" O ASP A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 Processing helix chain 'A' and resid 454 through 458 removed outlier: 4.013A pdb=" N ASP A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 462 No H-bonds generated for 'chain 'A' and resid 460 through 462' Processing helix chain 'A' and resid 463 through 479 removed outlier: 3.557A pdb=" N ALA A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.698A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 511 Processing helix chain 'X' and resid 5 through 25 removed outlier: 3.951A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA X 13 " --> pdb=" O GLY X 9 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.721A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N GLY X 43 " --> pdb=" O GLU X 39 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU X 44 " --> pdb=" O ILE X 40 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N VAL X 74 " --> pdb=" O ALA X 70 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE X 75 " --> pdb=" O GLU X 71 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA X 107 " --> pdb=" O ALA X 103 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE X 135 " --> pdb=" O GLY X 131 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 147 removed outlier: 3.547A pdb=" N ASP X 147 " --> pdb=" O ALA X 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 144 through 147' Processing helix chain 'X' and resid 148 through 153 removed outlier: 3.675A pdb=" N VAL X 153 " --> pdb=" O VAL X 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 103 removed outlier: 3.557A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.526A pdb=" N LYS G 9 " --> pdb=" O ASP G 5 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 58 removed outlier: 4.124A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL G 51 " --> pdb=" O THR G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.626A pdb=" N LEU G 94 " --> pdb=" O LEU G 90 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G 108 " --> pdb=" O THR G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.806A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.579A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.502A 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 197 through 203 removed outlier: 4.185A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.706A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 115 through 119 Processing helix chain 'F' and resid 130 through 137 removed outlier: 3.533A 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 198 through 200 No H-bonds generated for 'chain 'F' and resid 198 through 200' Processing helix chain 'F' and resid 212 through 233 removed outlier: 3.601A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.749A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.968A pdb=" N LEU F 278 " --> pdb=" O GLU F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 302 Processing helix chain 'F' and resid 305 through 312 Processing helix chain 'F' and resid 313 through 315 No H-bonds generated for 'chain 'F' and resid 313 through 315' Processing helix chain 'F' and resid 322 through 328 removed outlier: 3.626A pdb=" N LEU F 328 " --> pdb=" O GLN F 324 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 378 removed outlier: 4.378A pdb=" N ASP F 372 " --> pdb=" O GLN F 368 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ILE F 373 " --> pdb=" O GLU F 369 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE F 376 " --> pdb=" O ASP F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 379 through 382 removed outlier: 3.614A pdb=" N LEU F 382 " --> pdb=" O MET F 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 379 through 382' Processing helix chain 'F' and resid 383 through 400 removed outlier: 3.839A pdb=" N LEU F 388 " --> pdb=" O GLU F 384 " (cutoff:3.500A) 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 458 removed outlier: 3.586A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU F 454 " --> pdb=" O GLU F 450 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.514A 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 removed outlier: 3.545A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 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: 3.513A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.670A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.582A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU E 278 " --> pdb=" O GLU E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 302 Processing helix chain 'E' and resid 305 through 312 Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.577A pdb=" N ALA E 326 " --> pdb=" O SER E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 3.916A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE E 376 " --> pdb=" O ASP E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 385 through 400 removed outlier: 3.500A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG E 398 " --> pdb=" O ARG E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 419 through 432 Processing helix chain 'E' and resid 439 through 443 Processing helix chain 'E' and resid 448 through 459 Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'D' and resid 154 through 169 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 197 through 200 removed outlier: 4.176A pdb=" N ASP D 200 " --> pdb=" O ASN D 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 197 through 200' Processing helix chain 'D' and resid 212 through 218 Processing helix chain 'D' and resid 218 through 233 Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.652A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 Processing helix chain 'D' and resid 305 through 312 Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 378 removed outlier: 7.448A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.334A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.416A 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 385 through 400 removed outlier: 3.810A pdb=" N ALA D 391 " --> pdb=" O LYS D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 407 through 412 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 'I' and resid 4 through 8 Processing helix chain 'I' and resid 8 through 42 removed outlier: 3.942A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA I 20 " --> pdb=" O MET I 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 77 removed outlier: 3.540A pdb=" N LEU I 49 " --> pdb=" O LEU I 45 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 4.791A 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: 3.599A pdb=" N LYS J 34 " --> pdb=" O ILE J 30 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 78 removed outlier: 4.002A pdb=" N THR J 51 " --> pdb=" O PRO J 47 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) Proline residue: J 64 - end of helix Processing helix chain 'L' and resid 4 through 40 removed outlier: 3.653A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N MET L 11 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET L 16 " --> pdb=" O ALA L 12 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA L 21 " --> pdb=" O MET L 17 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 44 No H-bonds generated for 'chain 'L' and resid 42 through 44' Processing helix chain 'L' and resid 45 through 61 Processing helix chain 'L' and resid 61 through 77 removed outlier: 3.616A pdb=" N ILE L 66 " --> pdb=" O ALA L 62 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N MET L 75 " --> pdb=" O GLY L 71 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 40 removed outlier: 3.696A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N TYR M 10 " --> pdb=" O MET M 6 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA M 13 " --> pdb=" O LEU M 9 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU M 31 " --> pdb=" O GLY M 27 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 44 No H-bonds generated for 'chain 'M' and resid 42 through 44' Processing helix chain 'M' and resid 45 through 61 removed outlier: 4.127A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 76 removed outlier: 3.534A pdb=" N MET M 65 " --> pdb=" O ASP M 61 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE M 66 " --> pdb=" O ALA M 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 42 removed outlier: 4.901A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.546A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 removed outlier: 3.765A pdb=" N MET N 65 " --> pdb=" O ASP N 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 42 removed outlier: 3.573A pdb=" N TYR O 10 " --> pdb=" O MET O 6 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 4.144A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.846A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 77 removed outlier: 3.999A pdb=" N GLN P 52 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA P 62 " --> pdb=" O GLY P 58 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Proline residue: P 64 - end of helix removed outlier: 3.618A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 4.366A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLY Q 33 " --> pdb=" O GLY Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 61 removed outlier: 3.703A pdb=" N PHE Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 61 through 77 removed outlier: 3.534A pdb=" N ALA Q 67 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 4 through 40 removed outlier: 4.210A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET R 16 " --> pdb=" O ALA R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 44 No H-bonds generated for 'chain 'R' and resid 42 through 44' Processing helix chain 'R' and resid 45 through 61 removed outlier: 3.528A pdb=" N THR R 51 " --> pdb=" O PRO R 47 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 77 removed outlier: 3.668A pdb=" N MET R 65 " --> pdb=" O ASP R 61 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE R 66 " --> pdb=" O ALA R 62 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 42 removed outlier: 3.967A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.629A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing helix chain 'Y' and resid 2 through 25 Processing helix chain 'Y' and resid 25 through 139 removed outlier: 3.939A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS Y 51 " --> pdb=" O ALA Y 47 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS Y 52 " --> pdb=" O GLU Y 48 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Y 59 " --> pdb=" O ASP Y 55 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU Y 95 " --> pdb=" O LYS Y 91 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN Y 106 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 153 removed outlier: 3.791A pdb=" N ASP Y 147 " --> pdb=" O ALA Y 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.521A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 65 removed outlier: 3.785A pdb=" N MET a 46 " --> pdb=" O ASN a 42 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.807A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.587A pdb=" N MET a 118 " --> pdb=" O LEU a 114 " (cutoff:3.500A) 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 removed outlier: 3.517A pdb=" N GLU a 131 " --> pdb=" O PRO a 127 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.617A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY a 173 " --> pdb=" O LYS a 169 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LYS a 176 " --> pdb=" O GLY a 172 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLN a 181 " --> pdb=" O GLU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 185 through 187 No H-bonds generated for 'chain 'a' and resid 185 through 187' Processing helix chain 'a' and resid 188 through 228 removed outlier: 3.835A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY a 197 " --> pdb=" O LEU a 193 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.629A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN a 214 " --> pdb=" O ARG a 210 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 269 removed outlier: 4.547A pdb=" N TRP a 235 " --> pdb=" O TRP a 231 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ILE a 236 " --> pdb=" O TRP a 232 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.008A pdb=" N PHE a 244 " --> pdb=" O PRO a 240 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR a 250 " --> pdb=" O ILE a 246 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU a 251 " --> pdb=" O LEU a 247 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR a 260 " --> pdb=" O PHE a 256 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 105 through 106 Processing sheet with id=AA2, first strand: chain 'W' and resid 139 through 142 removed outlier: 4.167A pdb=" N MET W 157 " --> pdb=" O ALA W 154 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR B 60 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 35 removed outlier: 5.097A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU E 36 " --> pdb=" O ASN E 33 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 66 removed outlier: 4.021A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N SER C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 66 " --> pdb=" O SER C 70 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASP F 67 " --> pdb=" O GLN F 32 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLN F 32 " --> pdb=" O ASP F 67 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLN F 45 " --> pdb=" O ILE F 50 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ILE F 50 " --> pdb=" O GLN F 45 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 96 through 99 Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 108 Processing sheet with id=AA7, first strand: chain 'C' and resid 145 through 146 removed outlier: 4.576A pdb=" N ILE C 159 " --> pdb=" O VAL C 146 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 329 through 331 removed outlier: 7.736A pdb=" N ILE C 330 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AB1, first strand: chain 'B' and resid 107 through 109 Processing sheet with id=AB2, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.485A pdb=" N ILE B 159 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 329 through 332 removed outlier: 6.357A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR B 332 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLY B 169 " --> pdb=" O THR B 332 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 60 through 66 removed outlier: 3.510A pdb=" N LYS A 89 " --> pdb=" O SER A 54 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU D 36 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N VAL D 42 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE D 54 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB6, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.510A pdb=" N VAL A 108 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 260 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 107 through 109 removed outlier: 6.510A pdb=" N VAL A 108 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 260 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.078A pdb=" N VAL H 8 " --> pdb=" O MET H 15 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 19 through 27 current: chain 'H' and resid 67 through 72 Processing sheet with id=AB9, first strand: chain 'H' and resid 30 through 34 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 4 through 9 current: chain 'H' and resid 58 through 64 Processing sheet with id=AC1, first strand: chain 'G' and resid 132 through 136 removed outlier: 7.992A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.698A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.529A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU G 187 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.850A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.637A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL F 175 " --> pdb=" O PHE F 240 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.716A pdb=" N PHE F 139 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC6, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.448A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER E 174 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL E 205 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE E 176 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY E 207 " --> pdb=" O PHE E 176 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY E 178 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR E 173 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.448A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N SER E 174 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N VAL E 205 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE E 176 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N GLY E 207 " --> pdb=" O PHE E 176 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLY E 178 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR E 173 " --> pdb=" O ASP E 236 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.354A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AD1, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.152A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL D 175 " --> pdb=" O PHE D 240 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL D 237 " --> pdb=" O THR D 291 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N VAL D 293 " --> pdb=" O VAL D 237 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU D 239 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ALA D 295 " --> pdb=" O LEU D 239 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL D 241 " --> pdb=" O ALA D 295 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR D 297 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) 2229 hydrogen bonds defined for protein. 6462 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: 8.54 Time building geometry restraints manager: 4.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6312 1.30 - 1.43: 8660 1.43 - 1.56: 22103 1.56 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37459 Sorted by residual: bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.64e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.17e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.15e+01 bond pdb=" C5 ATP A 600 " pdb=" C6 ATP A 600 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP C 600 " pdb=" C6 ATP C 600 " ideal model delta sigma weight residual 1.409 1.479 -0.070 1.00e-02 1.00e+04 4.88e+01 ... (remaining 37454 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.00: 50424 4.00 - 8.00: 259 8.00 - 12.01: 20 12.01 - 16.01: 1 16.01 - 20.01: 7 Bond angle restraints: 50711 Sorted by residual: angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 119.86 20.01 1.00e+00 1.00e+00 4.00e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" N VAL A 377 " pdb=" CA VAL A 377 " pdb=" C VAL A 377 " ideal model delta sigma weight residual 111.81 95.24 16.57 8.60e-01 1.35e+00 3.71e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 121.06 18.81 1.00e+00 1.00e+00 3.54e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 119.14 17.69 1.00e+00 1.00e+00 3.13e+02 ... (remaining 50706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.90: 21817 27.90 - 55.79: 809 55.79 - 83.69: 95 83.69 - 111.58: 13 111.58 - 139.48: 3 Dihedral angle restraints: 22737 sinusoidal: 8965 harmonic: 13772 Sorted by residual: dihedral pdb=" O2A ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PA ADP F 500 " pdb=" PB ADP F 500 " ideal model delta sinusoidal sigma weight residual -60.00 79.48 -139.48 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP F 500 " pdb=" O3A ADP F 500 " pdb=" PB ADP F 500 " pdb=" PA ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 162.22 137.78 1 2.00e+01 2.50e-03 4.18e+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 71.62 -131.62 1 2.00e+01 2.50e-03 3.99e+01 ... (remaining 22734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 5438 0.086 - 0.172: 434 0.172 - 0.258: 28 0.258 - 0.345: 10 0.345 - 0.431: 4 Chirality restraints: 5914 Sorted by residual: chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA ILE A 222 " pdb=" N ILE A 222 " pdb=" C ILE A 222 " pdb=" CB ILE A 222 " both_signs ideal model delta sigma weight residual False 2.43 2.81 -0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CA GLU G 208 " pdb=" N GLU G 208 " pdb=" C GLU G 208 " pdb=" CB GLU G 208 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.27e+00 ... (remaining 5911 not shown) Planarity restraints: 6538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU J 36 " -0.026 2.00e-02 2.50e+03 5.18e-02 2.69e+01 pdb=" C LEU J 36 " 0.090 2.00e-02 2.50e+03 pdb=" O LEU J 36 " -0.033 2.00e-02 2.50e+03 pdb=" N GLU J 37 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 209 " 0.025 2.00e-02 2.50e+03 4.87e-02 2.37e+01 pdb=" C VAL A 209 " -0.084 2.00e-02 2.50e+03 pdb=" O VAL A 209 " 0.031 2.00e-02 2.50e+03 pdb=" N ARG A 210 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER a 27 " -0.020 2.00e-02 2.50e+03 4.02e-02 1.61e+01 pdb=" C SER a 27 " 0.069 2.00e-02 2.50e+03 pdb=" O SER a 27 " -0.026 2.00e-02 2.50e+03 pdb=" N LEU a 28 " -0.024 2.00e-02 2.50e+03 ... (remaining 6535 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 142 2.52 - 3.11: 29818 3.11 - 3.71: 55213 3.71 - 4.30: 80311 4.30 - 4.90: 136470 Nonbonded interactions: 301954 Sorted by model distance: nonbonded pdb=" O1 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.924 2.170 nonbonded pdb=" OG1 THR A 176 " pdb="MG MG A 601 " model vdw 1.926 2.170 nonbonded pdb=" O1G ATP C 600 " pdb="MG MG C 601 " model vdw 1.941 2.170 nonbonded pdb=" O2B ATP C 600 " pdb="MG MG C 601 " model vdw 1.945 2.170 nonbonded pdb=" O2G ATP A 600 " pdb="MG MG A 601 " model vdw 1.946 2.170 ... (remaining 301949 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 4 through 511 or resid 600 through 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and resid 4 through 601) } ncs_group { reference = (chain 'D' and resid 2 through 500) selection = (chain 'E' and resid 2 through 500) selection = (chain 'F' and resid 2 through 500) } ncs_group { reference = (chain 'I' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'J' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'L' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'M' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'N' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'Q' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'R' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 through 78)) selection = (chain 'S' and (resid 3 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 35.120 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.110 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 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 : 0.005 0.113 37459 Z= 0.301 Angle : 0.818 20.009 50711 Z= 0.542 Chirality : 0.049 0.431 5914 Planarity : 0.004 0.059 6538 Dihedral : 14.555 139.481 13927 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.63 % Rotamer: Outliers : 1.75 % Allowed : 8.03 % Favored : 90.21 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 5.03 % 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: -2.30 (0.11), residues: 4803 helix: -1.48 (0.09), residues: 2604 sheet: -0.59 (0.20), residues: 515 loop : -1.59 (0.14), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 64 TYR 0.020 0.001 TYR G 205 PHE 0.017 0.001 PHE a 85 TRP 0.015 0.001 TRP a 186 HIS 0.006 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00473 (37459) covalent geometry : angle 0.81762 (50711) hydrogen bonds : bond 0.16187 ( 2206) hydrogen bonds : angle 7.42848 ( 6462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 878 time to evaluate : 1.346 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: W 90 ASP cc_start: 0.8430 (m-30) cc_final: 0.8218 (m-30) REVERT: W 137 LYS cc_start: 0.8304 (tppt) cc_final: 0.8031 (tmtt) REVERT: C 10 GLU cc_start: 0.8264 (pm20) cc_final: 0.8025 (pm20) REVERT: C 364 ILE cc_start: 0.9199 (mt) cc_final: 0.8920 (mm) REVERT: B 513 TRP cc_start: 0.8772 (OUTLIER) cc_final: 0.5653 (m100) REVERT: A 236 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.8542 (t80) REVERT: A 484 GLN cc_start: 0.7841 (tp-100) cc_final: 0.7166 (pp30) REVERT: X 7 ILE cc_start: 0.8690 (tt) cc_final: 0.8461 (tp) REVERT: X 73 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8714 (tp40) REVERT: X 104 GLN cc_start: 0.8929 (tp-100) cc_final: 0.8694 (tm-30) REVERT: X 138 ARG cc_start: 0.5589 (OUTLIER) cc_final: 0.4002 (tpm-80) REVERT: X 139 SER cc_start: 0.4728 (p) cc_final: 0.4396 (p) REVERT: X 150 ASP cc_start: 0.8002 (m-30) cc_final: 0.7796 (p0) REVERT: H 15 MET cc_start: 0.7991 (mtp) cc_final: 0.7785 (mtt) REVERT: H 99 ARG cc_start: 0.8794 (ttp-110) cc_final: 0.8591 (ptm-80) REVERT: H 118 SER cc_start: 0.8858 (t) cc_final: 0.8355 (p) REVERT: H 134 THR cc_start: 0.8787 (t) cc_final: 0.8412 (p) REVERT: G 52 ILE cc_start: 0.8940 (mt) cc_final: 0.8732 (mm) REVERT: G 226 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.8532 (mt0) REVERT: F 347 LEU cc_start: 0.9175 (mt) cc_final: 0.8929 (mm) REVERT: E 192 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7695 (mt-10) REVERT: D 56 MET cc_start: 0.9285 (mmt) cc_final: 0.8753 (mmm) REVERT: I 54 PHE cc_start: 0.8323 (m-80) cc_final: 0.7952 (m-80) REVERT: I 60 VAL cc_start: 0.8332 (t) cc_final: 0.7879 (t) REVERT: I 68 VAL cc_start: 0.8510 (t) cc_final: 0.8282 (m) REVERT: I 73 TYR cc_start: 0.7418 (t80) cc_final: 0.5956 (m-80) REVERT: J 11 MET cc_start: 0.8187 (tpp) cc_final: 0.7873 (tpp) REVERT: J 73 TYR cc_start: 0.8310 (t80) cc_final: 0.8024 (t80) REVERT: L 11 MET cc_start: 0.7914 (tpt) cc_final: 0.7643 (tmm) REVERT: L 17 MET cc_start: 0.7914 (mtm) cc_final: 0.6810 (ptt) REVERT: L 57 MET cc_start: 0.8567 (tmm) cc_final: 0.8233 (tmm) REVERT: M 34 LYS cc_start: 0.8468 (mmtm) cc_final: 0.8092 (mmmm) REVERT: M 76 PHE cc_start: 0.7732 (m-80) cc_final: 0.7110 (m-10) REVERT: N 7 ASP cc_start: 0.5856 (t0) cc_final: 0.5288 (m-30) REVERT: O 31 LEU cc_start: 0.8960 (tp) cc_final: 0.8479 (tp) REVERT: O 42 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8482 (mp10) REVERT: O 68 VAL cc_start: 0.8594 (t) cc_final: 0.8269 (m) REVERT: P 31 LEU cc_start: 0.8297 (tp) cc_final: 0.7897 (tp) REVERT: P 54 PHE cc_start: 0.8329 (m-80) cc_final: 0.7941 (m-80) REVERT: P 68 VAL cc_start: 0.7966 (t) cc_final: 0.7745 (t) REVERT: P 72 LEU cc_start: 0.7470 (mt) cc_final: 0.6944 (pp) REVERT: P 73 TYR cc_start: 0.5165 (t80) cc_final: 0.4551 (m-10) REVERT: P 78 VAL cc_start: 0.7857 (t) cc_final: 0.7525 (p) REVERT: Q 7 ASP cc_start: 0.6474 (t0) cc_final: 0.6175 (m-30) REVERT: Q 11 MET cc_start: 0.8195 (tpt) cc_final: 0.7731 (tpp) REVERT: Q 17 MET cc_start: 0.7938 (mtm) cc_final: 0.6821 (ppp) REVERT: Q 54 PHE cc_start: 0.8954 (m-80) cc_final: 0.8581 (m-80) REVERT: Q 55 ILE cc_start: 0.8824 (mt) cc_final: 0.8594 (mp) REVERT: Q 57 MET cc_start: 0.9021 (tmm) cc_final: 0.8701 (tmm) REVERT: R 11 MET cc_start: 0.7083 (tpt) cc_final: 0.6742 (tpp) REVERT: S 8 LEU cc_start: 0.8255 (tm) cc_final: 0.8023 (pp) REVERT: S 46 ILE cc_start: 0.8078 (mt) cc_final: 0.7863 (mt) REVERT: Y 39 GLU cc_start: 0.8764 (tt0) cc_final: 0.8474 (tt0) REVERT: Y 80 ASN cc_start: 0.8791 (m-40) cc_final: 0.8458 (m110) REVERT: Y 83 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8280 (ttp80) REVERT: Y 151 LYS cc_start: 0.9229 (tttt) cc_final: 0.8957 (tppt) REVERT: a 80 GLU cc_start: 0.8481 (pt0) cc_final: 0.8123 (pt0) REVERT: a 168 MET cc_start: 0.8333 (mmt) cc_final: 0.8081 (mmm) REVERT: a 262 VAL cc_start: 0.9020 (t) cc_final: 0.8807 (t) outliers start: 67 outliers final: 31 residues processed: 938 average time/residue: 0.2486 time to fit residues: 370.9954 Evaluate side-chains 643 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 607 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 493 ASN Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain X residue 135 ILE Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 226 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain a residue 15 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 0.0670 chunk 455 optimal weight: 1.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 470 optimal weight: 0.0870 overall best weight: 1.2302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 21 HIS ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN B 186 GLN B 399 GLN B 493 ASN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 333 GLN A 344 ASN X 37 GLN X 73 GLN X 85 GLN G 54 HIS G 91 ASN G 252 ASN G 265 ASN G 269 GLN E 351 GLN E 441 GLN D 19 GLN D 279 GLN J 42 GLN O 3 ASN R 42 GLN S 3 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS a 234 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.099036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.068660 restraints weight = 79465.075| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.37 r_work: 0.2819 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 37459 Z= 0.165 Angle : 0.687 13.365 50711 Z= 0.350 Chirality : 0.045 0.260 5914 Planarity : 0.004 0.054 6538 Dihedral : 7.932 136.546 5397 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.83 % Allowed : 12.56 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: -0.33 (0.12), residues: 4803 helix: 0.36 (0.10), residues: 2617 sheet: -0.32 (0.21), residues: 509 loop : -0.94 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 129 TYR 0.020 0.001 TYR Q 10 PHE 0.023 0.002 PHE I 76 TRP 0.019 0.001 TRP a 186 HIS 0.006 0.001 HIS B 479 Details of bonding type rmsd covalent geometry : bond 0.00363 (37459) covalent geometry : angle 0.68680 (50711) hydrogen bonds : bond 0.05472 ( 2206) hydrogen bonds : angle 4.94161 ( 6462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 768 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 660 time to evaluate : 1.219 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: W 120 GLN cc_start: 0.8353 (mt0) cc_final: 0.7792 (pt0) REVERT: W 123 LYS cc_start: 0.9200 (mtmt) cc_final: 0.8634 (mtmm) REVERT: W 137 LYS cc_start: 0.8408 (tppt) cc_final: 0.8111 (tmtt) REVERT: C 10 GLU cc_start: 0.8423 (pm20) cc_final: 0.8144 (pm20) REVERT: C 39 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8765 (pt) REVERT: C 316 GLU cc_start: 0.8664 (tp30) cc_final: 0.8420 (tm-30) REVERT: C 364 ILE cc_start: 0.9270 (mt) cc_final: 0.8978 (mm) REVERT: C 401 ARG cc_start: 0.8333 (ttm-80) cc_final: 0.7571 (mmt90) REVERT: B 76 MET cc_start: 0.9292 (mmm) cc_final: 0.8872 (mmm) REVERT: B 170 ASP cc_start: 0.8756 (m-30) cc_final: 0.8168 (m-30) REVERT: B 418 ARG cc_start: 0.9035 (mmm160) cc_final: 0.8464 (ttp-170) REVERT: B 497 GLU cc_start: 0.8504 (tp30) cc_final: 0.8243 (tp30) REVERT: B 513 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.6979 (m100) REVERT: A 484 GLN cc_start: 0.8559 (tp-100) cc_final: 0.8152 (pp30) REVERT: A 488 GLN cc_start: 0.8855 (mt0) cc_final: 0.8647 (mt0) REVERT: X 7 ILE cc_start: 0.8441 (tt) cc_final: 0.8156 (tp) REVERT: X 73 GLN cc_start: 0.9078 (tp40) cc_final: 0.8838 (tp40) REVERT: X 78 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8664 (tm-30) REVERT: X 82 ARG cc_start: 0.9043 (tpp-160) cc_final: 0.8789 (tpp-160) REVERT: X 104 GLN cc_start: 0.9009 (tp-100) cc_final: 0.8795 (tm-30) REVERT: X 138 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.6747 (tmm160) REVERT: X 150 ASP cc_start: 0.8127 (m-30) cc_final: 0.7901 (p0) REVERT: H 15 MET cc_start: 0.8863 (mtp) cc_final: 0.8656 (mtm) REVERT: H 87 GLN cc_start: 0.8990 (mm-40) cc_final: 0.8781 (tp40) REVERT: H 118 SER cc_start: 0.9235 (t) cc_final: 0.8876 (p) REVERT: G 52 ILE cc_start: 0.9330 (mt) cc_final: 0.9095 (mm) REVERT: G 205 TYR cc_start: 0.9389 (m-80) cc_final: 0.9179 (m-80) REVERT: G 243 MET cc_start: 0.9059 (ttp) cc_final: 0.8802 (ttt) REVERT: F 141 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9010 (mtpp) REVERT: F 159 MET cc_start: 0.9508 (ttm) cc_final: 0.9258 (ttp) REVERT: F 160 MET cc_start: 0.9291 (mmm) cc_final: 0.9040 (mmm) REVERT: E 192 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8375 (mt-10) REVERT: E 275 MET cc_start: 0.9352 (tpp) cc_final: 0.8821 (tpp) REVERT: E 330 ILE cc_start: 0.9253 (OUTLIER) cc_final: 0.9041 (mp) REVERT: E 340 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8534 (p) REVERT: E 366 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8258 (mmm-85) REVERT: I 17 MET cc_start: 0.8033 (ptm) cc_final: 0.6821 (ppp) REVERT: I 65 MET cc_start: 0.9101 (mmp) cc_final: 0.8866 (mmp) REVERT: I 73 TYR cc_start: 0.7386 (t80) cc_final: 0.6150 (m-80) REVERT: J 34 LYS cc_start: 0.7500 (mmtp) cc_final: 0.7155 (mttp) REVERT: J 41 ARG cc_start: 0.8694 (ttm110) cc_final: 0.8220 (ttm-80) REVERT: L 54 PHE cc_start: 0.8453 (m-80) cc_final: 0.8141 (m-80) REVERT: M 34 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7673 (mmmm) REVERT: M 37 GLU cc_start: 0.8817 (OUTLIER) cc_final: 0.8552 (pt0) REVERT: N 7 ASP cc_start: 0.6302 (t0) cc_final: 0.6020 (t0) REVERT: N 10 TYR cc_start: 0.7763 (m-10) cc_final: 0.6714 (m-10) REVERT: N 53 PHE cc_start: 0.8685 (t80) cc_final: 0.8168 (t80) REVERT: O 36 LEU cc_start: 0.8512 (tt) cc_final: 0.8245 (tt) REVERT: O 42 GLN cc_start: 0.8360 (mm-40) cc_final: 0.7836 (mp10) REVERT: P 17 MET cc_start: 0.8411 (ptm) cc_final: 0.8154 (ptm) REVERT: P 54 PHE cc_start: 0.8556 (m-80) cc_final: 0.8202 (m-80) REVERT: P 72 LEU cc_start: 0.7413 (mt) cc_final: 0.6840 (pp) REVERT: P 73 TYR cc_start: 0.5030 (t80) cc_final: 0.4202 (m-10) REVERT: Q 11 MET cc_start: 0.8271 (tpt) cc_final: 0.7806 (tpp) REVERT: Q 16 MET cc_start: 0.7842 (tpt) cc_final: 0.7396 (tpp) REVERT: Q 17 MET cc_start: 0.8440 (mtm) cc_final: 0.7672 (mpp) REVERT: Q 22 ILE cc_start: 0.7828 (mm) cc_final: 0.7515 (mm) REVERT: Q 42 GLN cc_start: 0.7535 (mt0) cc_final: 0.7295 (mt0) REVERT: Q 55 ILE cc_start: 0.8533 (mt) cc_final: 0.8210 (mm) REVERT: Q 65 MET cc_start: 0.7441 (mtt) cc_final: 0.6883 (ptm) REVERT: R 11 MET cc_start: 0.7114 (tpt) cc_final: 0.6667 (tpp) REVERT: R 37 GLU cc_start: 0.8620 (pt0) cc_final: 0.8241 (pt0) REVERT: S 8 LEU cc_start: 0.7992 (tm) cc_final: 0.7544 (tt) REVERT: Y 29 LEU cc_start: 0.8600 (pp) cc_final: 0.8277 (mm) REVERT: Y 36 ARG cc_start: 0.8406 (tpp80) cc_final: 0.8136 (tpp80) REVERT: Y 39 GLU cc_start: 0.8937 (tt0) cc_final: 0.8503 (tt0) REVERT: Y 80 ASN cc_start: 0.8994 (m-40) cc_final: 0.8772 (m110) REVERT: a 30 ASP cc_start: 0.6721 (t0) cc_final: 0.6371 (t0) REVERT: a 46 MET cc_start: 0.7669 (tpp) cc_final: 0.7365 (tpp) REVERT: a 80 GLU cc_start: 0.8851 (pt0) cc_final: 0.8353 (pt0) REVERT: a 131 GLU cc_start: 0.7657 (tp30) cc_final: 0.7231 (tp30) REVERT: a 151 LEU cc_start: 0.8992 (mm) cc_final: 0.8695 (tt) REVERT: a 168 MET cc_start: 0.8539 (mmt) cc_final: 0.8273 (mmm) REVERT: a 196 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7481 (mp0) outliers start: 108 outliers final: 47 residues processed: 737 average time/residue: 0.2217 time to fit residues: 266.6417 Evaluate side-chains 625 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 571 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 48 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 141 LYS Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain Y residue 129 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 464 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 163 optimal weight: 0.9980 chunk 346 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 258 optimal weight: 4.9990 chunk 315 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 115 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN B 479 HIS ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 24 GLN F 343 GLN J 42 GLN N 5 ASN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 GLN ** a 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** a 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.066492 restraints weight = 79198.011| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.34 r_work: 0.2774 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 37459 Z= 0.155 Angle : 0.629 11.356 50711 Z= 0.318 Chirality : 0.044 0.223 5914 Planarity : 0.004 0.048 6538 Dihedral : 7.245 125.303 5367 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.90 % Allowed : 14.15 % Favored : 82.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.35 (0.12), residues: 4803 helix: 1.00 (0.10), residues: 2627 sheet: -0.04 (0.22), residues: 519 loop : -0.80 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG O 50 TYR 0.026 0.001 TYR C 474 PHE 0.022 0.001 PHE N 53 TRP 0.017 0.001 TRP X 26 HIS 0.004 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00348 (37459) covalent geometry : angle 0.62862 (50711) hydrogen bonds : bond 0.04991 ( 2206) hydrogen bonds : angle 4.62082 ( 6462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 606 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 16 ASP cc_start: 0.8832 (t0) cc_final: 0.8614 (t0) REVERT: W 94 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8654 (mm110) REVERT: W 119 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8353 (tm-30) REVERT: W 123 LYS cc_start: 0.9078 (mtmt) cc_final: 0.8615 (mtmt) REVERT: W 130 LYS cc_start: 0.8971 (mttp) cc_final: 0.8764 (mtmm) REVERT: W 137 LYS cc_start: 0.8355 (tppt) cc_final: 0.8068 (tmtt) REVERT: C 39 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8700 (pt) REVERT: C 401 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7587 (mmt90) REVERT: B 76 MET cc_start: 0.9351 (mmm) cc_final: 0.8902 (mmm) REVERT: B 170 ASP cc_start: 0.8732 (m-30) cc_final: 0.8225 (m-30) REVERT: B 304 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8755 (m) REVERT: B 513 TRP cc_start: 0.9028 (OUTLIER) cc_final: 0.7391 (m100) REVERT: A 484 GLN cc_start: 0.8388 (tp-100) cc_final: 0.8001 (pp30) REVERT: A 488 GLN cc_start: 0.8738 (mt0) cc_final: 0.8500 (mt0) REVERT: X 78 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8560 (tm-30) REVERT: X 82 ARG cc_start: 0.9046 (tpp-160) cc_final: 0.8769 (tpp-160) REVERT: X 104 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8735 (tm-30) REVERT: X 138 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.6872 (tmm160) REVERT: X 150 ASP cc_start: 0.8256 (m-30) cc_final: 0.7966 (p0) REVERT: H 22 LYS cc_start: 0.8733 (pttt) cc_final: 0.8490 (pttt) REVERT: H 118 SER cc_start: 0.9249 (t) cc_final: 0.8964 (p) REVERT: H 134 THR cc_start: 0.8664 (t) cc_final: 0.8371 (p) REVERT: G 52 ILE cc_start: 0.9368 (mt) cc_final: 0.9104 (mm) REVERT: G 155 MET cc_start: 0.8859 (mmm) cc_final: 0.8648 (mmp) REVERT: G 243 MET cc_start: 0.9004 (ttp) cc_final: 0.8732 (ttp) REVERT: F 160 MET cc_start: 0.9315 (mmm) cc_final: 0.9060 (mmm) REVERT: F 342 ARG cc_start: 0.9125 (tpp-160) cc_final: 0.8581 (ttm-80) REVERT: E 192 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8391 (mt-10) REVERT: E 298 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.9004 (t) REVERT: E 340 THR cc_start: 0.8813 (m) cc_final: 0.8606 (p) REVERT: E 457 LYS cc_start: 0.8871 (tmmt) cc_final: 0.8180 (mtpt) REVERT: D 81 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8666 (mmtp) REVERT: I 17 MET cc_start: 0.8169 (ptm) cc_final: 0.6980 (ppp) REVERT: I 54 PHE cc_start: 0.8054 (m-80) cc_final: 0.7828 (m-80) REVERT: I 65 MET cc_start: 0.9089 (mmp) cc_final: 0.8799 (mmp) REVERT: I 73 TYR cc_start: 0.7230 (t80) cc_final: 0.5919 (m-80) REVERT: J 17 MET cc_start: 0.8414 (mmp) cc_final: 0.7946 (mmp) REVERT: J 37 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8508 (tp30) REVERT: J 41 ARG cc_start: 0.8791 (ttm110) cc_final: 0.8119 (ttm170) REVERT: J 65 MET cc_start: 0.8349 (mtp) cc_final: 0.8004 (mmp) REVERT: L 11 MET cc_start: 0.8005 (tmm) cc_final: 0.7470 (tpp) REVERT: L 53 PHE cc_start: 0.8829 (t80) cc_final: 0.8538 (t80) REVERT: L 57 MET cc_start: 0.8199 (ttp) cc_final: 0.7827 (tmm) REVERT: L 61 ASP cc_start: 0.8962 (m-30) cc_final: 0.8377 (m-30) REVERT: M 34 LYS cc_start: 0.8399 (mmtm) cc_final: 0.7965 (mmmm) REVERT: M 55 ILE cc_start: 0.8895 (mm) cc_final: 0.8623 (mt) REVERT: M 57 MET cc_start: 0.8834 (tmm) cc_final: 0.8548 (tmm) REVERT: M 61 ASP cc_start: 0.8423 (p0) cc_final: 0.7962 (p0) REVERT: M 66 ILE cc_start: 0.8956 (mm) cc_final: 0.8542 (mt) REVERT: N 7 ASP cc_start: 0.7034 (t0) cc_final: 0.6747 (t0) REVERT: N 57 MET cc_start: 0.9375 (tpp) cc_final: 0.9171 (tpp) REVERT: O 48 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8901 (tp) REVERT: O 75 MET cc_start: 0.8262 (tmm) cc_final: 0.7819 (tmm) REVERT: P 72 LEU cc_start: 0.7494 (mt) cc_final: 0.6935 (pp) REVERT: P 73 TYR cc_start: 0.5205 (t80) cc_final: 0.4176 (m-10) REVERT: Q 9 LEU cc_start: 0.8567 (mm) cc_final: 0.8313 (mm) REVERT: Q 17 MET cc_start: 0.8589 (mtm) cc_final: 0.7458 (tpp) REVERT: Q 35 PHE cc_start: 0.8398 (t80) cc_final: 0.7915 (t80) REVERT: Q 54 PHE cc_start: 0.8932 (m-80) cc_final: 0.8677 (m-80) REVERT: Q 55 ILE cc_start: 0.8635 (mt) cc_final: 0.8350 (mt) REVERT: Q 65 MET cc_start: 0.7423 (mtt) cc_final: 0.6914 (ptm) REVERT: R 11 MET cc_start: 0.7226 (tpt) cc_final: 0.6729 (tpp) REVERT: R 37 GLU cc_start: 0.8722 (pt0) cc_final: 0.8367 (pt0) REVERT: S 8 LEU cc_start: 0.8017 (tm) cc_final: 0.7672 (tm) REVERT: Y 29 LEU cc_start: 0.8500 (pp) cc_final: 0.8123 (mm) REVERT: Y 36 ARG cc_start: 0.8437 (tpp80) cc_final: 0.7905 (tpp80) REVERT: a 30 ASP cc_start: 0.6864 (t0) cc_final: 0.6440 (t0) REVERT: a 46 MET cc_start: 0.7669 (tpp) cc_final: 0.7263 (tpp) REVERT: a 76 GLN cc_start: 0.8125 (pt0) cc_final: 0.7780 (pt0) REVERT: a 80 GLU cc_start: 0.8951 (pt0) cc_final: 0.8565 (pt0) REVERT: a 140 ARG cc_start: 0.7618 (ptt90) cc_final: 0.7341 (ptt180) REVERT: a 151 LEU cc_start: 0.9017 (mm) cc_final: 0.8662 (tp) REVERT: a 168 MET cc_start: 0.8458 (mmt) cc_final: 0.8164 (mmm) REVERT: a 196 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7347 (mm-30) outliers start: 111 outliers final: 63 residues processed: 686 average time/residue: 0.2269 time to fit residues: 255.1225 Evaluate side-chains 632 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 561 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 110 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 48 LEU Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 7 ASP Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 86 VAL Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 209 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 282 optimal weight: 6.9990 chunk 202 optimal weight: 0.9990 chunk 470 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 473 optimal weight: 4.9990 chunk 443 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 347 optimal weight: 0.2980 chunk 80 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 94 GLN B 358 ASN ** B 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 14 GLN H 24 GLN J 52 GLN O 52 GLN ** S 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 80 ASN Y 123 GLN a 9 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.065890 restraints weight = 78367.848| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 2.33 r_work: 0.2765 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 37459 Z= 0.144 Angle : 0.597 10.325 50711 Z= 0.302 Chirality : 0.043 0.284 5914 Planarity : 0.004 0.046 6538 Dihedral : 6.955 121.829 5363 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.85 % Allowed : 15.07 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.64 (0.12), residues: 4803 helix: 1.28 (0.10), residues: 2623 sheet: 0.08 (0.22), residues: 528 loop : -0.76 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 115 TYR 0.021 0.001 TYR C 474 PHE 0.029 0.001 PHE E 189 TRP 0.016 0.001 TRP a 39 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00328 (37459) covalent geometry : angle 0.59656 (50711) hydrogen bonds : bond 0.04640 ( 2206) hydrogen bonds : angle 4.48055 ( 6462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 710 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 601 time to evaluate : 1.412 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: W 16 ASP cc_start: 0.8830 (t0) cc_final: 0.8546 (t0) REVERT: W 94 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8625 (mt0) REVERT: W 130 LYS cc_start: 0.9005 (mttp) cc_final: 0.8803 (mtmm) REVERT: W 137 LYS cc_start: 0.8357 (tppt) cc_final: 0.8047 (tmtt) REVERT: W 156 ASP cc_start: 0.7702 (m-30) cc_final: 0.7426 (t0) REVERT: C 39 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8607 (pt) REVERT: C 352 GLN cc_start: 0.8452 (tt0) cc_final: 0.8096 (pt0) REVERT: B 170 ASP cc_start: 0.8719 (m-30) cc_final: 0.8212 (m-30) REVERT: B 304 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8802 (m) REVERT: B 418 ARG cc_start: 0.8855 (mmm160) cc_final: 0.8633 (tpp-160) REVERT: B 513 TRP cc_start: 0.9000 (OUTLIER) cc_final: 0.6587 (m100) REVERT: X 30 MET cc_start: 0.8546 (mtp) cc_final: 0.8275 (mpp) REVERT: X 73 GLN cc_start: 0.8978 (tp40) cc_final: 0.8670 (tp40) REVERT: X 78 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8550 (tm-30) REVERT: X 82 ARG cc_start: 0.9031 (tpp-160) cc_final: 0.8768 (tpp-160) REVERT: X 138 ARG cc_start: 0.7626 (OUTLIER) cc_final: 0.6969 (tmm160) REVERT: X 150 ASP cc_start: 0.8284 (m-30) cc_final: 0.7974 (p0) REVERT: H 22 LYS cc_start: 0.8652 (pttt) cc_final: 0.8450 (pttt) REVERT: H 129 ARG cc_start: 0.7779 (mtm110) cc_final: 0.7448 (mtm110) REVERT: H 132 GLU cc_start: 0.8642 (pp20) cc_final: 0.8235 (pp20) REVERT: H 134 THR cc_start: 0.8647 (t) cc_final: 0.8425 (p) REVERT: G 155 MET cc_start: 0.8889 (mmm) cc_final: 0.8683 (mmp) REVERT: F 160 MET cc_start: 0.9291 (mmm) cc_final: 0.9019 (mmm) REVERT: F 342 ARG cc_start: 0.9101 (tpp-160) cc_final: 0.8650 (ttm-80) REVERT: E 192 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8394 (mt-10) REVERT: E 298 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8973 (t) REVERT: E 340 THR cc_start: 0.8763 (m) cc_final: 0.8540 (p) REVERT: E 368 GLN cc_start: 0.8787 (tp40) cc_final: 0.8585 (tp40) REVERT: E 457 LYS cc_start: 0.8854 (tmmt) cc_final: 0.8143 (mtpt) REVERT: D 81 LYS cc_start: 0.9090 (ttmm) cc_final: 0.8680 (mmmm) REVERT: I 11 MET cc_start: 0.8545 (tpt) cc_final: 0.8318 (mmt) REVERT: I 17 MET cc_start: 0.8116 (ptm) cc_final: 0.6956 (ppp) REVERT: I 50 ARG cc_start: 0.8374 (ttp-110) cc_final: 0.7900 (mtm-85) REVERT: I 65 MET cc_start: 0.9073 (mmp) cc_final: 0.8854 (mmp) REVERT: I 73 TYR cc_start: 0.7256 (t80) cc_final: 0.5884 (m-80) REVERT: J 6 MET cc_start: 0.6895 (mmp) cc_final: 0.6286 (mmp) REVERT: J 37 GLU cc_start: 0.8794 (tt0) cc_final: 0.8381 (tp30) REVERT: J 41 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8214 (ttm170) REVERT: J 65 MET cc_start: 0.8557 (mtp) cc_final: 0.8316 (mmp) REVERT: L 11 MET cc_start: 0.7966 (tmm) cc_final: 0.7604 (tpp) REVERT: L 53 PHE cc_start: 0.8904 (t80) cc_final: 0.8585 (t80) REVERT: L 57 MET cc_start: 0.8289 (ttp) cc_final: 0.7851 (tmm) REVERT: L 61 ASP cc_start: 0.9009 (m-30) cc_final: 0.8359 (m-30) REVERT: M 34 LYS cc_start: 0.8451 (mmtm) cc_final: 0.8015 (mmmm) REVERT: M 55 ILE cc_start: 0.9062 (mm) cc_final: 0.8859 (mt) REVERT: M 57 MET cc_start: 0.8947 (tmm) cc_final: 0.8647 (tmm) REVERT: M 61 ASP cc_start: 0.8346 (p0) cc_final: 0.8007 (p0) REVERT: N 57 MET cc_start: 0.9426 (tpp) cc_final: 0.8891 (tpp) REVERT: N 61 ASP cc_start: 0.7853 (t70) cc_final: 0.7626 (p0) REVERT: O 17 MET cc_start: 0.8230 (ptp) cc_final: 0.7982 (ptm) REVERT: O 42 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7763 (mp10) REVERT: O 50 ARG cc_start: 0.8901 (ttp-110) cc_final: 0.8545 (ttm110) REVERT: O 65 MET cc_start: 0.9177 (mmp) cc_final: 0.8862 (mmm) REVERT: O 75 MET cc_start: 0.8207 (tmm) cc_final: 0.7830 (tmm) REVERT: P 65 MET cc_start: 0.8575 (mmp) cc_final: 0.8290 (mmm) REVERT: P 73 TYR cc_start: 0.5224 (t80) cc_final: 0.4474 (m-10) REVERT: Q 35 PHE cc_start: 0.8552 (t80) cc_final: 0.8306 (t80) REVERT: Q 53 PHE cc_start: 0.8388 (t80) cc_final: 0.8188 (t80) REVERT: Q 54 PHE cc_start: 0.8929 (m-80) cc_final: 0.8696 (m-80) REVERT: Q 55 ILE cc_start: 0.8600 (mt) cc_final: 0.8346 (mt) REVERT: Q 65 MET cc_start: 0.7404 (mtt) cc_final: 0.6911 (ptm) REVERT: R 11 MET cc_start: 0.7300 (tpt) cc_final: 0.6682 (tpp) REVERT: R 37 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: S 8 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7689 (tm) REVERT: S 65 MET cc_start: 0.8537 (mmt) cc_final: 0.8315 (mmm) REVERT: Y 29 LEU cc_start: 0.8569 (pp) cc_final: 0.8164 (mm) REVERT: Y 36 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7984 (tpp80) REVERT: Y 39 GLU cc_start: 0.8907 (tt0) cc_final: 0.8644 (tt0) REVERT: a 30 ASP cc_start: 0.7056 (t0) cc_final: 0.6732 (t0) REVERT: a 46 MET cc_start: 0.7736 (tpp) cc_final: 0.7308 (tpp) REVERT: a 76 GLN cc_start: 0.8156 (pt0) cc_final: 0.7788 (pt0) REVERT: a 80 GLU cc_start: 0.8951 (pt0) cc_final: 0.8556 (pt0) REVERT: a 94 TYR cc_start: 0.8330 (t80) cc_final: 0.8065 (t80) REVERT: a 131 GLU cc_start: 0.7982 (tp30) cc_final: 0.7657 (tp30) REVERT: a 140 ARG cc_start: 0.7715 (ptt90) cc_final: 0.7502 (ptt180) REVERT: a 151 LEU cc_start: 0.8961 (mm) cc_final: 0.8662 (mm) REVERT: a 167 LYS cc_start: 0.8606 (tttt) cc_final: 0.8026 (tptp) REVERT: a 196 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7520 (mm-30) outliers start: 109 outliers final: 72 residues processed: 672 average time/residue: 0.2288 time to fit residues: 251.5693 Evaluate side-chains 637 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 557 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 7 ASP Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 209 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 277 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 338 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 367 optimal weight: 5.9990 chunk 406 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 82 ASN W 120 GLN C 172 GLN C 423 HIS C 479 HIS B 511 GLN A 488 GLN A 511 GLN X 85 GLN H 14 GLN H 24 GLN G 126 ASN E 361 GLN I 52 GLN J 42 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 GLN ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.092123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.061757 restraints weight = 78715.641| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.31 r_work: 0.2674 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 37459 Z= 0.230 Angle : 0.668 11.636 50711 Z= 0.339 Chirality : 0.046 0.237 5914 Planarity : 0.004 0.047 6538 Dihedral : 7.034 122.200 5357 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.92 % Allowed : 15.44 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.63 (0.12), residues: 4803 helix: 1.25 (0.10), residues: 2635 sheet: -0.02 (0.22), residues: 525 loop : -0.72 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 41 TYR 0.022 0.002 TYR a 263 PHE 0.026 0.002 PHE E 189 TRP 0.016 0.002 TRP Y 26 HIS 0.003 0.001 HIS W 97 Details of bonding type rmsd covalent geometry : bond 0.00537 (37459) covalent geometry : angle 0.66758 (50711) hydrogen bonds : bond 0.05142 ( 2206) hydrogen bonds : angle 4.59737 ( 6462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 592 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 16 ASP cc_start: 0.8907 (t0) cc_final: 0.8566 (t0) REVERT: W 30 MET cc_start: 0.8592 (ttp) cc_final: 0.8355 (ttp) REVERT: W 67 GLN cc_start: 0.8878 (mt0) cc_final: 0.7901 (mp10) REVERT: W 137 LYS cc_start: 0.8387 (tppt) cc_final: 0.7935 (tmtt) REVERT: W 156 ASP cc_start: 0.7861 (m-30) cc_final: 0.7501 (t0) REVERT: C 384 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8085 (pttt) REVERT: C 413 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8058 (tp) REVERT: C 474 TYR cc_start: 0.7469 (t80) cc_final: 0.7155 (t80) REVERT: C 484 GLN cc_start: 0.9044 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 170 ASP cc_start: 0.8782 (m-30) cc_final: 0.8261 (m-30) REVERT: B 236 TYR cc_start: 0.9163 (OUTLIER) cc_final: 0.7335 (t80) REVERT: B 418 ARG cc_start: 0.8921 (mmm160) cc_final: 0.8333 (tpp-160) REVERT: A 402 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8252 (tm-30) REVERT: X 73 GLN cc_start: 0.9092 (tp40) cc_final: 0.8791 (tp40) REVERT: X 78 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8539 (tm-30) REVERT: X 82 ARG cc_start: 0.9035 (tpp-160) cc_final: 0.8768 (tpp-160) REVERT: X 104 GLN cc_start: 0.8939 (tp-100) cc_final: 0.8728 (tm-30) REVERT: X 138 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.6844 (tmm160) REVERT: X 150 ASP cc_start: 0.8293 (m-30) cc_final: 0.7996 (p0) REVERT: H 129 ARG cc_start: 0.7955 (mtm110) cc_final: 0.7677 (mtm110) REVERT: H 132 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8303 (pp20) REVERT: G 243 MET cc_start: 0.9108 (ttp) cc_final: 0.8852 (ttp) REVERT: F 160 MET cc_start: 0.9338 (mmm) cc_final: 0.9074 (mmm) REVERT: F 342 ARG cc_start: 0.9220 (tpp-160) cc_final: 0.8860 (ttm-80) REVERT: E 192 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8337 (mt-10) REVERT: E 298 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.8990 (t) REVERT: E 340 THR cc_start: 0.8688 (m) cc_final: 0.8352 (p) REVERT: I 11 MET cc_start: 0.8422 (tpt) cc_final: 0.8194 (mmt) REVERT: I 17 MET cc_start: 0.8012 (ptm) cc_final: 0.7036 (ppp) REVERT: I 65 MET cc_start: 0.9076 (mmp) cc_final: 0.8483 (mmp) REVERT: J 6 MET cc_start: 0.7056 (mmp) cc_final: 0.6528 (mmp) REVERT: J 11 MET cc_start: 0.7152 (tpt) cc_final: 0.6868 (tpt) REVERT: J 37 GLU cc_start: 0.8871 (tt0) cc_final: 0.8442 (tp30) REVERT: J 41 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8321 (ttm170) REVERT: J 42 GLN cc_start: 0.8535 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: J 65 MET cc_start: 0.8722 (mtp) cc_final: 0.8499 (mmp) REVERT: L 57 MET cc_start: 0.8439 (ttp) cc_final: 0.8086 (tmm) REVERT: L 61 ASP cc_start: 0.9079 (m-30) cc_final: 0.8336 (m-30) REVERT: M 34 LYS cc_start: 0.8716 (mmtm) cc_final: 0.8187 (mmmm) REVERT: M 57 MET cc_start: 0.9044 (tmm) cc_final: 0.8677 (tmm) REVERT: N 7 ASP cc_start: 0.6711 (t0) cc_final: 0.6085 (m-30) REVERT: N 57 MET cc_start: 0.9486 (tpp) cc_final: 0.8686 (tpt) REVERT: N 61 ASP cc_start: 0.8177 (t70) cc_final: 0.7812 (p0) REVERT: O 50 ARG cc_start: 0.8999 (ttp-110) cc_final: 0.8764 (ttp-110) REVERT: O 65 MET cc_start: 0.9206 (mmp) cc_final: 0.8767 (mmm) REVERT: O 75 MET cc_start: 0.8121 (tmm) cc_final: 0.7903 (tmm) REVERT: P 57 MET cc_start: 0.8575 (tmm) cc_final: 0.8225 (tmm) REVERT: P 73 TYR cc_start: 0.5260 (t80) cc_final: 0.4425 (m-10) REVERT: Q 17 MET cc_start: 0.8703 (mtm) cc_final: 0.7862 (mpp) REVERT: Q 55 ILE cc_start: 0.8692 (mt) cc_final: 0.8452 (mt) REVERT: Q 57 MET cc_start: 0.8815 (tmm) cc_final: 0.8272 (tmm) REVERT: Q 65 MET cc_start: 0.7604 (mtt) cc_final: 0.7108 (ptm) REVERT: Q 76 PHE cc_start: 0.8075 (m-80) cc_final: 0.7830 (m-10) REVERT: R 11 MET cc_start: 0.7876 (tpt) cc_final: 0.7453 (tpp) REVERT: R 34 LYS cc_start: 0.8702 (tppt) cc_final: 0.8452 (tppt) REVERT: R 37 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8621 (pt0) REVERT: S 65 MET cc_start: 0.8703 (mmt) cc_final: 0.8459 (mmm) REVERT: Y 29 LEU cc_start: 0.8616 (pp) cc_final: 0.8217 (mm) REVERT: Y 36 ARG cc_start: 0.8422 (tpp80) cc_final: 0.8176 (tpp80) REVERT: Y 39 GLU cc_start: 0.8922 (tt0) cc_final: 0.8669 (tt0) REVERT: Y 83 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8318 (ttp80) REVERT: a 30 ASP cc_start: 0.6996 (t0) cc_final: 0.6388 (t70) REVERT: a 32 GLN cc_start: 0.7832 (pm20) cc_final: 0.7534 (pm20) REVERT: a 46 MET cc_start: 0.7920 (tpp) cc_final: 0.7502 (tpp) REVERT: a 131 GLU cc_start: 0.8196 (tp30) cc_final: 0.7908 (tp30) REVERT: a 167 LYS cc_start: 0.8735 (tttt) cc_final: 0.8115 (tptp) REVERT: a 168 MET cc_start: 0.8167 (mmt) cc_final: 0.7966 (mmm) REVERT: a 196 GLU cc_start: 0.8088 (mm-30) cc_final: 0.7722 (mm-30) REVERT: a 236 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8910 (mp) outliers start: 150 outliers final: 91 residues processed: 694 average time/residue: 0.2339 time to fit residues: 263.8714 Evaluate side-chains 650 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 550 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 61 ILE Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 129 VAL Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 166 ILE Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain R residue 15 VAL Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain S residue 74 VAL Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 93 MET Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain a residue 236 ILE Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 133 optimal weight: 0.4980 chunk 462 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 473 optimal weight: 2.9990 chunk 64 optimal weight: 8.9990 chunk 17 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 402 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 445 optimal weight: 9.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 119 GLN C 172 GLN B 358 ASN B 511 GLN A 27 ASN D 243 ASN O 52 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 123 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.064023 restraints weight = 78061.303| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.33 r_work: 0.2721 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37459 Z= 0.126 Angle : 0.602 11.559 50711 Z= 0.302 Chirality : 0.043 0.225 5914 Planarity : 0.004 0.048 6538 Dihedral : 6.697 117.125 5355 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.69 % Allowed : 17.37 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.93 (0.12), residues: 4803 helix: 1.53 (0.10), residues: 2624 sheet: 0.13 (0.23), residues: 511 loop : -0.65 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Y 115 TYR 0.012 0.001 TYR X 24 PHE 0.029 0.001 PHE E 189 TRP 0.020 0.001 TRP X 26 HIS 0.007 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00278 (37459) covalent geometry : angle 0.60193 (50711) hydrogen bonds : bond 0.04434 ( 2206) hydrogen bonds : angle 4.41032 ( 6462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 590 time to evaluate : 1.412 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: W 16 ASP cc_start: 0.8880 (t0) cc_final: 0.8532 (t0) REVERT: W 30 MET cc_start: 0.8674 (ttm) cc_final: 0.8468 (ttp) REVERT: W 67 GLN cc_start: 0.8859 (mt0) cc_final: 0.7998 (mp10) REVERT: W 94 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: W 123 LYS cc_start: 0.9113 (mtmt) cc_final: 0.8530 (mtmt) REVERT: W 137 LYS cc_start: 0.8401 (tppt) cc_final: 0.7993 (tmtt) REVERT: W 156 ASP cc_start: 0.7834 (m-30) cc_final: 0.7513 (t0) REVERT: C 39 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8538 (pt) REVERT: C 352 GLN cc_start: 0.8347 (tt0) cc_final: 0.8069 (pt0) REVERT: C 384 LYS cc_start: 0.8500 (ptmt) cc_final: 0.8031 (pttt) REVERT: C 474 TYR cc_start: 0.7604 (t80) cc_final: 0.7348 (t80) REVERT: C 484 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 170 ASP cc_start: 0.8744 (m-30) cc_final: 0.8280 (m-30) REVERT: B 418 ARG cc_start: 0.8952 (mmm160) cc_final: 0.8275 (mtt-85) REVERT: X 29 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7705 (mm) REVERT: X 73 GLN cc_start: 0.9033 (tp40) cc_final: 0.8787 (tp40) REVERT: X 78 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8512 (tm-30) REVERT: X 82 ARG cc_start: 0.9038 (tpp-160) cc_final: 0.8804 (tpp-160) REVERT: X 138 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.6947 (tmm160) REVERT: X 150 ASP cc_start: 0.8228 (m-30) cc_final: 0.7949 (p0) REVERT: H 132 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: G 243 MET cc_start: 0.9085 (ttp) cc_final: 0.8831 (ttp) REVERT: F 42 VAL cc_start: 0.8839 (OUTLIER) cc_final: 0.8521 (t) REVERT: F 160 MET cc_start: 0.9324 (mmm) cc_final: 0.9096 (mmm) REVERT: F 342 ARG cc_start: 0.9129 (tpp-160) cc_final: 0.8778 (ttm-80) REVERT: E 31 VAL cc_start: 0.9058 (OUTLIER) cc_final: 0.8858 (p) REVERT: E 192 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8300 (mt-10) REVERT: E 298 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8984 (t) REVERT: E 340 THR cc_start: 0.8702 (m) cc_final: 0.8408 (p) REVERT: I 17 MET cc_start: 0.7876 (ptm) cc_final: 0.6781 (ppp) REVERT: I 65 MET cc_start: 0.9025 (mmp) cc_final: 0.8696 (mmp) REVERT: J 6 MET cc_start: 0.6946 (mmp) cc_final: 0.6444 (mmp) REVERT: J 11 MET cc_start: 0.7511 (tpt) cc_final: 0.6711 (tpp) REVERT: J 17 MET cc_start: 0.8784 (mmp) cc_final: 0.8489 (mmp) REVERT: J 37 GLU cc_start: 0.8792 (tt0) cc_final: 0.8408 (tp30) REVERT: J 41 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8405 (ttm170) REVERT: L 57 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8069 (tmm) REVERT: L 61 ASP cc_start: 0.8976 (m-30) cc_final: 0.8331 (m-30) REVERT: M 34 LYS cc_start: 0.8725 (mmtm) cc_final: 0.8175 (mmmm) REVERT: N 57 MET cc_start: 0.9302 (tpp) cc_final: 0.9096 (tpp) REVERT: O 50 ARG cc_start: 0.8959 (ttp-110) cc_final: 0.8703 (ttp-110) REVERT: O 52 GLN cc_start: 0.8824 (mm110) cc_final: 0.8406 (mm-40) REVERT: O 55 ILE cc_start: 0.9149 (mm) cc_final: 0.8816 (mt) REVERT: O 65 MET cc_start: 0.9185 (mmp) cc_final: 0.8971 (mmm) REVERT: O 68 VAL cc_start: 0.8871 (t) cc_final: 0.8596 (m) REVERT: P 57 MET cc_start: 0.8569 (tmm) cc_final: 0.8156 (tmm) REVERT: P 73 TYR cc_start: 0.5225 (t80) cc_final: 0.4436 (m-10) REVERT: Q 41 ARG cc_start: 0.8662 (ttm-80) cc_final: 0.8449 (ttm-80) REVERT: Q 55 ILE cc_start: 0.8700 (mt) cc_final: 0.8485 (mt) REVERT: Q 57 MET cc_start: 0.8915 (tmm) cc_final: 0.8602 (tmm) REVERT: Q 65 MET cc_start: 0.7528 (mtt) cc_final: 0.7096 (ptm) REVERT: Q 76 PHE cc_start: 0.8061 (m-80) cc_final: 0.7810 (m-10) REVERT: R 9 LEU cc_start: 0.8146 (pp) cc_final: 0.7757 (mt) REVERT: R 11 MET cc_start: 0.7896 (tpt) cc_final: 0.7456 (tpp) REVERT: R 34 LYS cc_start: 0.8663 (tppt) cc_final: 0.8425 (tppt) REVERT: R 37 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8592 (pt0) REVERT: Y 29 LEU cc_start: 0.8645 (pp) cc_final: 0.8106 (mm) REVERT: Y 36 ARG cc_start: 0.8392 (tpp80) cc_final: 0.7995 (tpp80) REVERT: Y 39 GLU cc_start: 0.8915 (tt0) cc_final: 0.8467 (pp20) REVERT: Y 83 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (ttp80) REVERT: Y 115 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8521 (ttp80) REVERT: a 30 ASP cc_start: 0.7092 (t0) cc_final: 0.6687 (t0) REVERT: a 94 TYR cc_start: 0.8492 (t80) cc_final: 0.8031 (t80) REVERT: a 131 GLU cc_start: 0.8244 (tp30) cc_final: 0.7996 (tp30) REVERT: a 167 LYS cc_start: 0.8717 (tttt) cc_final: 0.8125 (tptp) REVERT: a 196 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7694 (mm-30) outliers start: 103 outliers final: 69 residues processed: 661 average time/residue: 0.2256 time to fit residues: 242.9482 Evaluate side-chains 643 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 563 time to evaluate : 1.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain L residue 57 MET Chi-restraints excluded: chain M residue 26 ILE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 49 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 29 VAL Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 209 LEU Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 302 optimal weight: 6.9990 chunk 205 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 228 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 356 optimal weight: 5.9990 chunk 222 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 119 GLN C 443 GLN B 488 GLN B 511 GLN H 24 GLN D 243 ASN J 42 GLN S 52 GLN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 15 HIS ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.091774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.061628 restraints weight = 78651.951| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.31 r_work: 0.2666 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2537 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 37459 Z= 0.216 Angle : 0.659 13.483 50711 Z= 0.331 Chirality : 0.046 0.345 5914 Planarity : 0.004 0.045 6538 Dihedral : 6.775 116.501 5354 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.09 % Allowed : 17.50 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 0.91 (0.12), residues: 4803 helix: 1.51 (0.10), residues: 2629 sheet: 0.09 (0.22), residues: 518 loop : -0.62 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 98 TYR 0.024 0.001 TYR a 263 PHE 0.025 0.002 PHE Y 14 TRP 0.020 0.001 TRP Y 26 HIS 0.004 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00514 (37459) covalent geometry : angle 0.65851 (50711) hydrogen bonds : bond 0.04827 ( 2206) hydrogen bonds : angle 4.49817 ( 6462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 565 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 16 ASP cc_start: 0.8931 (t0) cc_final: 0.8551 (t0) REVERT: W 67 GLN cc_start: 0.8931 (mt0) cc_final: 0.8120 (mp10) REVERT: W 94 GLN cc_start: 0.8618 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: W 123 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8597 (mtmt) REVERT: W 130 LYS cc_start: 0.9090 (mtmm) cc_final: 0.8878 (mtmm) REVERT: W 137 LYS cc_start: 0.8426 (tppt) cc_final: 0.8047 (tmtt) REVERT: W 156 ASP cc_start: 0.7897 (m-30) cc_final: 0.7528 (t0) REVERT: C 384 LYS cc_start: 0.8510 (ptmt) cc_final: 0.8041 (pttt) REVERT: C 413 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8099 (tp) REVERT: C 474 TYR cc_start: 0.7538 (t80) cc_final: 0.7078 (t80) REVERT: C 484 GLN cc_start: 0.9089 (tm-30) cc_final: 0.8517 (tm-30) REVERT: B 13 LYS cc_start: 0.8582 (mmmm) cc_final: 0.8309 (mmmm) REVERT: B 170 ASP cc_start: 0.8792 (m-30) cc_final: 0.8317 (m-30) REVERT: B 418 ARG cc_start: 0.8937 (mmm160) cc_final: 0.8239 (mtt-85) REVERT: X 30 MET cc_start: 0.8661 (mmp) cc_final: 0.8298 (mmm) REVERT: X 73 GLN cc_start: 0.9018 (tp40) cc_final: 0.8764 (tp40) REVERT: X 78 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8474 (tm-30) REVERT: X 82 ARG cc_start: 0.9054 (tpp-160) cc_final: 0.8808 (tpp-160) REVERT: X 138 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.6929 (tmm160) REVERT: X 150 ASP cc_start: 0.8229 (m-30) cc_final: 0.7960 (p0) REVERT: H 129 ARG cc_start: 0.7920 (mtm110) cc_final: 0.7610 (mtm110) REVERT: H 132 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8308 (pp20) REVERT: G 116 MET cc_start: 0.9202 (mmm) cc_final: 0.8959 (mmm) REVERT: G 243 MET cc_start: 0.9115 (ttp) cc_final: 0.8851 (ttp) REVERT: F 160 MET cc_start: 0.9371 (mmm) cc_final: 0.9131 (mmm) REVERT: F 342 ARG cc_start: 0.9207 (tpp-160) cc_final: 0.8898 (ttm-80) REVERT: E 192 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8326 (mt-10) REVERT: E 298 VAL cc_start: 0.9239 (OUTLIER) cc_final: 0.8995 (t) REVERT: E 340 THR cc_start: 0.8704 (m) cc_final: 0.8378 (p) REVERT: I 11 MET cc_start: 0.8519 (tpt) cc_final: 0.8298 (mmt) REVERT: I 17 MET cc_start: 0.7943 (ptm) cc_final: 0.7121 (ppp) REVERT: I 65 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8430 (mmp) REVERT: J 6 MET cc_start: 0.7015 (mmp) cc_final: 0.6522 (mmp) REVERT: J 17 MET cc_start: 0.8905 (mmp) cc_final: 0.8703 (mmp) REVERT: J 37 GLU cc_start: 0.8861 (tt0) cc_final: 0.8519 (tp30) REVERT: J 41 ARG cc_start: 0.8747 (ttm110) cc_final: 0.8423 (ttm170) REVERT: M 34 LYS cc_start: 0.8897 (mmtm) cc_final: 0.8685 (mmtm) REVERT: M 57 MET cc_start: 0.9085 (tmm) cc_final: 0.8871 (tmm) REVERT: M 61 ASP cc_start: 0.8605 (t0) cc_final: 0.7871 (t0) REVERT: M 65 MET cc_start: 0.8785 (mtt) cc_final: 0.8452 (mmm) REVERT: M 75 MET cc_start: 0.9324 (ttt) cc_final: 0.8767 (tmm) REVERT: O 42 GLN cc_start: 0.8199 (mm110) cc_final: 0.7910 (mp10) REVERT: O 50 ARG cc_start: 0.8986 (ttp-110) cc_final: 0.8733 (ttp-110) REVERT: O 52 GLN cc_start: 0.8952 (mm110) cc_final: 0.8620 (mm-40) REVERT: O 55 ILE cc_start: 0.9195 (mm) cc_final: 0.8902 (mt) REVERT: O 68 VAL cc_start: 0.9010 (t) cc_final: 0.8809 (p) REVERT: P 57 MET cc_start: 0.8609 (tmm) cc_final: 0.8238 (tmm) REVERT: P 73 TYR cc_start: 0.5255 (t80) cc_final: 0.4448 (m-10) REVERT: Q 17 MET cc_start: 0.8812 (mtm) cc_final: 0.8009 (mpp) REVERT: Q 55 ILE cc_start: 0.8785 (mt) cc_final: 0.8536 (mt) REVERT: Q 57 MET cc_start: 0.8953 (tmm) cc_final: 0.8646 (tmm) REVERT: Q 65 MET cc_start: 0.7653 (mtt) cc_final: 0.7241 (ptm) REVERT: Q 76 PHE cc_start: 0.8127 (m-80) cc_final: 0.7859 (m-10) REVERT: R 11 MET cc_start: 0.7963 (tpt) cc_final: 0.7492 (tpp) REVERT: R 34 LYS cc_start: 0.8730 (tppt) cc_final: 0.8521 (tppt) REVERT: S 8 LEU cc_start: 0.8934 (tp) cc_final: 0.8434 (pp) REVERT: Y 29 LEU cc_start: 0.8651 (pp) cc_final: 0.8209 (mm) REVERT: Y 39 GLU cc_start: 0.8974 (tt0) cc_final: 0.8534 (pp20) REVERT: Y 83 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8342 (ttp80) REVERT: Y 98 ARG cc_start: 0.8481 (tpp80) cc_final: 0.7846 (ttm-80) REVERT: Y 123 GLN cc_start: 0.8979 (mt0) cc_final: 0.8511 (mt0) REVERT: a 30 ASP cc_start: 0.7016 (t0) cc_final: 0.6720 (t0) REVERT: a 94 TYR cc_start: 0.8454 (t80) cc_final: 0.7815 (t80) REVERT: a 118 MET cc_start: 0.9279 (mmp) cc_final: 0.9023 (tpp) REVERT: a 131 GLU cc_start: 0.8396 (tp30) cc_final: 0.8127 (tp30) REVERT: a 167 LYS cc_start: 0.8810 (tttt) cc_final: 0.8191 (tptp) REVERT: a 196 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7793 (mm-30) outliers start: 118 outliers final: 85 residues processed: 649 average time/residue: 0.2309 time to fit residues: 244.0777 Evaluate side-chains 644 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 552 time to evaluate : 1.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 68 LEU Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 119 GLN Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 177 THR Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 373 ILE Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 428 LYS Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 446 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 22 ILE Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 246 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 55 optimal weight: 0.7980 chunk 252 optimal weight: 0.9980 chunk 147 optimal weight: 0.7980 chunk 287 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 334 optimal weight: 7.9990 chunk 337 optimal weight: 0.9980 chunk 292 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN A 294 HIS H 14 GLN H 24 GLN G 57 HIS D 243 ASN ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.094125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.064229 restraints weight = 77833.699| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.31 r_work: 0.2727 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2597 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 37459 Z= 0.122 Angle : 0.614 11.264 50711 Z= 0.306 Chirality : 0.043 0.277 5914 Planarity : 0.004 0.047 6538 Dihedral : 6.512 111.232 5354 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.62 % Allowed : 18.42 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.09 (0.12), residues: 4803 helix: 1.70 (0.10), residues: 2620 sheet: 0.16 (0.23), residues: 519 loop : -0.61 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 98 TYR 0.023 0.001 TYR a 263 PHE 0.025 0.001 PHE E 189 TRP 0.020 0.001 TRP Y 26 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00267 (37459) covalent geometry : angle 0.61391 (50711) hydrogen bonds : bond 0.04282 ( 2206) hydrogen bonds : angle 4.34358 ( 6462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 697 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 597 time to evaluate : 1.325 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: W 16 ASP cc_start: 0.8884 (t0) cc_final: 0.8494 (t0) REVERT: W 67 GLN cc_start: 0.8889 (mt0) cc_final: 0.8003 (mm110) REVERT: W 94 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8211 (mt0) REVERT: W 137 LYS cc_start: 0.8348 (tppt) cc_final: 0.8001 (tmtt) REVERT: W 156 ASP cc_start: 0.7868 (m-30) cc_final: 0.7516 (t0) REVERT: C 39 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8544 (pt) REVERT: C 181 ASP cc_start: 0.9098 (t0) cc_final: 0.8807 (m-30) REVERT: C 352 GLN cc_start: 0.8321 (tt0) cc_final: 0.7975 (pt0) REVERT: C 384 LYS cc_start: 0.8449 (ptmt) cc_final: 0.7989 (pttt) REVERT: C 484 GLN cc_start: 0.9065 (tm-30) cc_final: 0.8494 (tm-30) REVERT: B 13 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8305 (mmmm) REVERT: B 170 ASP cc_start: 0.8732 (m-30) cc_final: 0.8300 (m-30) REVERT: B 343 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8663 (p) REVERT: B 418 ARG cc_start: 0.8970 (mmm160) cc_final: 0.8289 (mtt-85) REVERT: X 30 MET cc_start: 0.8566 (mmp) cc_final: 0.8248 (mmm) REVERT: X 78 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8503 (tm-30) REVERT: X 82 ARG cc_start: 0.8996 (tpp-160) cc_final: 0.8772 (tpp-160) REVERT: X 138 ARG cc_start: 0.7447 (OUTLIER) cc_final: 0.6890 (ptt180) REVERT: X 150 ASP cc_start: 0.8225 (m-30) cc_final: 0.7968 (p0) REVERT: H 132 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.8240 (pp20) REVERT: G 116 MET cc_start: 0.9157 (mmm) cc_final: 0.8903 (mmm) REVERT: G 243 MET cc_start: 0.9072 (ttp) cc_final: 0.8830 (ttp) REVERT: F 42 VAL cc_start: 0.8728 (OUTLIER) cc_final: 0.8508 (t) REVERT: F 342 ARG cc_start: 0.9162 (tpp-160) cc_final: 0.8846 (ttm-80) REVERT: F 445 MET cc_start: 0.9404 (mmm) cc_final: 0.9158 (mmt) REVERT: E 31 VAL cc_start: 0.9060 (OUTLIER) cc_final: 0.8850 (p) REVERT: E 192 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8255 (mt-10) REVERT: E 298 VAL cc_start: 0.9189 (OUTLIER) cc_final: 0.8948 (t) REVERT: E 340 THR cc_start: 0.8709 (m) cc_final: 0.8411 (p) REVERT: E 432 GLU cc_start: 0.8639 (pt0) cc_final: 0.8156 (pp20) REVERT: I 11 MET cc_start: 0.8487 (tpt) cc_final: 0.8220 (mmt) REVERT: I 17 MET cc_start: 0.7805 (ptm) cc_final: 0.7112 (ppp) REVERT: I 65 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8446 (mmt) REVERT: J 6 MET cc_start: 0.7084 (mmp) cc_final: 0.6598 (mmp) REVERT: J 37 GLU cc_start: 0.8831 (tt0) cc_final: 0.8530 (tp30) REVERT: J 41 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8432 (ttm170) REVERT: L 61 ASP cc_start: 0.9023 (m-30) cc_final: 0.8796 (m-30) REVERT: M 4 LEU cc_start: 0.3993 (OUTLIER) cc_final: 0.3705 (tp) REVERT: M 61 ASP cc_start: 0.8614 (t0) cc_final: 0.7276 (t70) REVERT: N 74 VAL cc_start: 0.8719 (t) cc_final: 0.8441 (p) REVERT: O 42 GLN cc_start: 0.8131 (mm110) cc_final: 0.7850 (mp10) REVERT: O 50 ARG cc_start: 0.8960 (ttp-110) cc_final: 0.8694 (ttp-110) REVERT: O 51 THR cc_start: 0.9217 (p) cc_final: 0.8963 (p) REVERT: O 55 ILE cc_start: 0.9193 (mm) cc_final: 0.8891 (mt) REVERT: O 68 VAL cc_start: 0.8889 (t) cc_final: 0.8687 (p) REVERT: P 57 MET cc_start: 0.8497 (tmm) cc_final: 0.8240 (tmm) REVERT: P 73 TYR cc_start: 0.5218 (t80) cc_final: 0.4508 (m-10) REVERT: Q 55 ILE cc_start: 0.8780 (mt) cc_final: 0.8572 (mt) REVERT: Q 65 MET cc_start: 0.7526 (mtt) cc_final: 0.7121 (ptm) REVERT: Q 76 PHE cc_start: 0.8065 (m-80) cc_final: 0.7796 (m-10) REVERT: R 9 LEU cc_start: 0.8098 (pp) cc_final: 0.7789 (mp) REVERT: R 11 MET cc_start: 0.7970 (tpt) cc_final: 0.7503 (tpp) REVERT: S 11 MET cc_start: 0.8068 (mmm) cc_final: 0.7742 (tpp) REVERT: S 16 MET cc_start: 0.8823 (ttp) cc_final: 0.8567 (ttm) REVERT: Y 29 LEU cc_start: 0.8808 (pp) cc_final: 0.8388 (mm) REVERT: Y 39 GLU cc_start: 0.8921 (tt0) cc_final: 0.8653 (pp20) REVERT: Y 80 ASN cc_start: 0.9079 (m-40) cc_final: 0.8813 (m110) REVERT: Y 83 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.8348 (ttp80) REVERT: Y 98 ARG cc_start: 0.8496 (tpp80) cc_final: 0.7872 (ttm-80) REVERT: Y 123 GLN cc_start: 0.8995 (mt0) cc_final: 0.8544 (mt0) REVERT: a 30 ASP cc_start: 0.6988 (t0) cc_final: 0.6750 (t0) REVERT: a 94 TYR cc_start: 0.8590 (t80) cc_final: 0.7914 (t80) REVERT: a 118 MET cc_start: 0.9319 (mmp) cc_final: 0.9054 (tpp) REVERT: a 131 GLU cc_start: 0.8351 (tp30) cc_final: 0.8074 (tp30) REVERT: a 167 LYS cc_start: 0.8810 (tttt) cc_final: 0.8190 (tptp) REVERT: a 196 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7711 (mm-30) outliers start: 100 outliers final: 66 residues processed: 669 average time/residue: 0.2206 time to fit residues: 242.0830 Evaluate side-chains 642 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 565 time to evaluate : 1.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 97 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 7 optimal weight: 5.9990 chunk 380 optimal weight: 6.9990 chunk 353 optimal weight: 0.9980 chunk 470 optimal weight: 1.9990 chunk 345 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 428 optimal weight: 3.9990 chunk 210 optimal weight: 0.9980 chunk 123 optimal weight: 7.9990 chunk 388 optimal weight: 1.9990 chunk 472 optimal weight: 5.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 423 HIS ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN A 511 GLN H 24 GLN G 57 HIS D 243 ASN S 52 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.092450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062328 restraints weight = 78614.363| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.32 r_work: 0.2685 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2555 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 37459 Z= 0.180 Angle : 0.647 11.449 50711 Z= 0.323 Chirality : 0.045 0.255 5914 Planarity : 0.004 0.047 6538 Dihedral : 6.530 110.264 5352 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.56 % Allowed : 18.63 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.09 (0.12), residues: 4803 helix: 1.64 (0.10), residues: 2631 sheet: 0.17 (0.23), residues: 512 loop : -0.54 (0.16), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 98 TYR 0.023 0.001 TYR a 263 PHE 0.023 0.001 PHE Y 14 TRP 0.029 0.002 TRP Y 26 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00428 (37459) covalent geometry : angle 0.64656 (50711) hydrogen bonds : bond 0.04576 ( 2206) hydrogen bonds : angle 4.41764 ( 6462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 572 time to evaluate : 1.382 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: W 16 ASP cc_start: 0.8915 (t0) cc_final: 0.8516 (t0) REVERT: W 30 MET cc_start: 0.8612 (ttp) cc_final: 0.8035 (ttp) REVERT: W 67 GLN cc_start: 0.8936 (mt0) cc_final: 0.8061 (mm110) REVERT: W 94 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: W 119 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8776 (tm-30) REVERT: W 123 LYS cc_start: 0.9071 (mtmt) cc_final: 0.8795 (mtmm) REVERT: W 137 LYS cc_start: 0.8423 (tppt) cc_final: 0.8065 (tmtt) REVERT: W 156 ASP cc_start: 0.7921 (m-30) cc_final: 0.7547 (t0) REVERT: C 352 GLN cc_start: 0.8524 (tt0) cc_final: 0.8129 (pt0) REVERT: C 384 LYS cc_start: 0.8474 (ptmt) cc_final: 0.8016 (pttt) REVERT: C 482 LEU cc_start: 0.6885 (OUTLIER) cc_final: 0.6485 (pt) REVERT: C 484 GLN cc_start: 0.9056 (tm-30) cc_final: 0.8485 (tm-30) REVERT: B 13 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8300 (mmmm) REVERT: B 103 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9003 (pp) REVERT: B 170 ASP cc_start: 0.8752 (m-30) cc_final: 0.8306 (m-30) REVERT: B 343 THR cc_start: 0.9212 (OUTLIER) cc_final: 0.8658 (p) REVERT: B 418 ARG cc_start: 0.8940 (mmm160) cc_final: 0.8243 (mtt-85) REVERT: B 511 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8951 (mm-40) REVERT: X 30 MET cc_start: 0.8557 (mmp) cc_final: 0.8130 (ptt) REVERT: X 78 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8466 (tm-30) REVERT: X 82 ARG cc_start: 0.9061 (tpp-160) cc_final: 0.8844 (tpp-160) REVERT: X 150 ASP cc_start: 0.8219 (m-30) cc_final: 0.7967 (p0) REVERT: H 132 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8253 (pp20) REVERT: G 116 MET cc_start: 0.9174 (mmm) cc_final: 0.8931 (mmm) REVERT: G 243 MET cc_start: 0.9087 (ttp) cc_final: 0.8841 (ttp) REVERT: F 342 ARG cc_start: 0.9196 (tpp-160) cc_final: 0.8889 (ttm-80) REVERT: E 192 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8318 (mt-10) REVERT: E 298 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8976 (t) REVERT: E 340 THR cc_start: 0.8678 (m) cc_final: 0.8358 (p) REVERT: E 432 GLU cc_start: 0.8616 (pt0) cc_final: 0.8132 (pp20) REVERT: I 11 MET cc_start: 0.8463 (tpt) cc_final: 0.8195 (mmt) REVERT: I 17 MET cc_start: 0.7811 (ptm) cc_final: 0.7178 (ppp) REVERT: I 65 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8437 (mmt) REVERT: J 6 MET cc_start: 0.7113 (mmp) cc_final: 0.6641 (mmp) REVERT: J 37 GLU cc_start: 0.8803 (tt0) cc_final: 0.8540 (tp30) REVERT: J 41 ARG cc_start: 0.8712 (ttm110) cc_final: 0.8409 (ttm170) REVERT: L 61 ASP cc_start: 0.9110 (m-30) cc_final: 0.8832 (m-30) REVERT: M 75 MET cc_start: 0.9354 (ttt) cc_final: 0.8810 (tmm) REVERT: O 42 GLN cc_start: 0.8189 (mm110) cc_final: 0.7920 (mp10) REVERT: O 50 ARG cc_start: 0.8946 (ttp-110) cc_final: 0.8687 (ttp-110) REVERT: O 51 THR cc_start: 0.9239 (p) cc_final: 0.8990 (p) REVERT: O 55 ILE cc_start: 0.9248 (mm) cc_final: 0.8940 (mt) REVERT: O 68 VAL cc_start: 0.9009 (t) cc_final: 0.8794 (p) REVERT: P 57 MET cc_start: 0.8541 (tmm) cc_final: 0.8279 (tmm) REVERT: P 73 TYR cc_start: 0.5276 (t80) cc_final: 0.4540 (m-10) REVERT: Q 41 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8493 (ttp-110) REVERT: Q 55 ILE cc_start: 0.8746 (mt) cc_final: 0.8502 (mt) REVERT: Q 61 ASP cc_start: 0.8399 (m-30) cc_final: 0.7895 (m-30) REVERT: Q 65 MET cc_start: 0.7639 (mtt) cc_final: 0.7267 (ptm) REVERT: Q 76 PHE cc_start: 0.8105 (m-80) cc_final: 0.7821 (m-10) REVERT: R 11 MET cc_start: 0.8185 (tpt) cc_final: 0.7760 (tpp) REVERT: S 11 MET cc_start: 0.8206 (mmm) cc_final: 0.7785 (tpp) REVERT: Y 29 LEU cc_start: 0.8770 (pp) cc_final: 0.8369 (mm) REVERT: Y 39 GLU cc_start: 0.8916 (tt0) cc_final: 0.8645 (pp20) REVERT: Y 80 ASN cc_start: 0.9086 (m-40) cc_final: 0.8809 (m110) REVERT: Y 83 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8378 (ttp80) REVERT: Y 98 ARG cc_start: 0.8512 (tpp80) cc_final: 0.7910 (ttm-80) REVERT: Y 123 GLN cc_start: 0.8996 (mt0) cc_final: 0.8557 (mt0) REVERT: a 30 ASP cc_start: 0.7006 (t0) cc_final: 0.6779 (t0) REVERT: a 94 TYR cc_start: 0.8599 (t80) cc_final: 0.7638 (t80) REVERT: a 118 MET cc_start: 0.9355 (mmp) cc_final: 0.9104 (tpp) REVERT: a 131 GLU cc_start: 0.8377 (tp30) cc_final: 0.8089 (tp30) REVERT: a 167 LYS cc_start: 0.8826 (tttt) cc_final: 0.8201 (tptp) REVERT: a 196 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7831 (mm-30) outliers start: 98 outliers final: 77 residues processed: 640 average time/residue: 0.2300 time to fit residues: 240.6646 Evaluate side-chains 640 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 554 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 511 GLN Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain J residue 22 ILE Chi-restraints excluded: chain J residue 30 ILE Chi-restraints excluded: chain J residue 34 LYS Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 75 MET Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 246 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 226 optimal weight: 4.9990 chunk 357 optimal weight: 0.9990 chunk 387 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 398 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 137 optimal weight: 0.5980 chunk 417 optimal weight: 1.9990 chunk 419 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 468 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN X 73 GLN D 243 ASN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.063245 restraints weight = 78166.234| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 2.31 r_work: 0.2704 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 37459 Z= 0.145 Angle : 0.629 10.592 50711 Z= 0.314 Chirality : 0.044 0.238 5914 Planarity : 0.004 0.047 6538 Dihedral : 6.436 105.989 5352 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.43 % Allowed : 18.89 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.12), residues: 4803 helix: 1.69 (0.10), residues: 2634 sheet: 0.19 (0.23), residues: 518 loop : -0.52 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG X 98 TYR 0.026 0.001 TYR a 263 PHE 0.023 0.001 PHE M 53 TRP 0.044 0.001 TRP Y 26 HIS 0.006 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00335 (37459) covalent geometry : angle 0.62877 (50711) hydrogen bonds : bond 0.04400 ( 2206) hydrogen bonds : angle 4.36972 ( 6462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9606 Ramachandran restraints generated. 4803 Oldfield, 0 Emsley, 4803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 569 time to evaluate : 1.447 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: W 16 ASP cc_start: 0.8904 (t0) cc_final: 0.8504 (t0) REVERT: W 67 GLN cc_start: 0.8871 (mt0) cc_final: 0.7944 (mm110) REVERT: W 94 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: W 119 GLN cc_start: 0.9167 (tm-30) cc_final: 0.8810 (tm-30) REVERT: W 123 LYS cc_start: 0.9066 (mtmt) cc_final: 0.8794 (mtmm) REVERT: W 137 LYS cc_start: 0.8315 (tppt) cc_final: 0.7938 (tmtt) REVERT: W 156 ASP cc_start: 0.7921 (m-30) cc_final: 0.7536 (t0) REVERT: C 39 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8723 (pt) REVERT: C 181 ASP cc_start: 0.9120 (t0) cc_final: 0.8916 (m-30) REVERT: C 352 GLN cc_start: 0.8347 (tt0) cc_final: 0.7985 (pt0) REVERT: C 384 LYS cc_start: 0.8409 (ptmt) cc_final: 0.7945 (pttt) REVERT: C 482 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6503 (pt) REVERT: C 484 GLN cc_start: 0.9049 (tm-30) cc_final: 0.8478 (tm-30) REVERT: B 13 LYS cc_start: 0.8618 (mmmm) cc_final: 0.8336 (mmmm) REVERT: B 103 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8947 (pp) REVERT: B 170 ASP cc_start: 0.8740 (m-30) cc_final: 0.8301 (m-30) REVERT: B 343 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8657 (p) REVERT: B 418 ARG cc_start: 0.8968 (mmm160) cc_final: 0.8302 (mtt-85) REVERT: B 484 GLN cc_start: 0.8933 (tp40) cc_final: 0.8724 (tp40) REVERT: X 30 MET cc_start: 0.8536 (mmp) cc_final: 0.8244 (mmm) REVERT: X 78 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8456 (tm-30) REVERT: X 82 ARG cc_start: 0.9012 (tpp-160) cc_final: 0.8804 (tpp-160) REVERT: X 138 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6882 (ptt180) REVERT: X 150 ASP cc_start: 0.8198 (m-30) cc_final: 0.7966 (p0) REVERT: H 132 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8245 (pp20) REVERT: G 116 MET cc_start: 0.9180 (mmm) cc_final: 0.8940 (mmm) REVERT: G 243 MET cc_start: 0.9093 (ttp) cc_final: 0.8844 (ttp) REVERT: F 42 VAL cc_start: 0.8795 (OUTLIER) cc_final: 0.8522 (t) REVERT: F 342 ARG cc_start: 0.9195 (tpp-160) cc_final: 0.8890 (ttm-80) REVERT: F 445 MET cc_start: 0.9416 (mmm) cc_final: 0.9149 (mmt) REVERT: E 31 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8840 (p) REVERT: E 192 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8284 (mt-10) REVERT: E 298 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8948 (t) REVERT: E 340 THR cc_start: 0.8692 (m) cc_final: 0.8382 (p) REVERT: E 432 GLU cc_start: 0.8572 (pt0) cc_final: 0.8106 (pp20) REVERT: D 88 MET cc_start: 0.9608 (mtm) cc_final: 0.9175 (mtm) REVERT: I 11 MET cc_start: 0.8537 (tpt) cc_final: 0.8333 (mmp) REVERT: I 17 MET cc_start: 0.7788 (ptm) cc_final: 0.7190 (ppp) REVERT: I 65 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8428 (mmt) REVERT: J 6 MET cc_start: 0.7143 (mmp) cc_final: 0.6510 (mmm) REVERT: J 37 GLU cc_start: 0.8782 (tt0) cc_final: 0.8561 (tp30) REVERT: J 41 ARG cc_start: 0.8700 (ttm110) cc_final: 0.8471 (ttm170) REVERT: L 61 ASP cc_start: 0.9110 (m-30) cc_final: 0.8730 (m-30) REVERT: M 61 ASP cc_start: 0.9075 (t0) cc_final: 0.8230 (t70) REVERT: M 75 MET cc_start: 0.9331 (ttt) cc_final: 0.8835 (tmm) REVERT: N 74 VAL cc_start: 0.8762 (t) cc_final: 0.8479 (p) REVERT: O 17 MET cc_start: 0.8579 (ptm) cc_final: 0.8317 (ptm) REVERT: O 50 ARG cc_start: 0.8937 (ttp-110) cc_final: 0.8675 (ttp-110) REVERT: O 51 THR cc_start: 0.9256 (p) cc_final: 0.9008 (p) REVERT: O 55 ILE cc_start: 0.9235 (mm) cc_final: 0.8943 (mt) REVERT: P 57 MET cc_start: 0.8562 (tmm) cc_final: 0.8299 (tmm) REVERT: P 73 TYR cc_start: 0.5277 (t80) cc_final: 0.4500 (m-10) REVERT: Q 11 MET cc_start: 0.8262 (tpt) cc_final: 0.7884 (tpp) REVERT: Q 37 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8890 (tm-30) REVERT: Q 41 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8480 (ttp-110) REVERT: Q 57 MET cc_start: 0.9009 (tmm) cc_final: 0.8259 (tmm) REVERT: Q 61 ASP cc_start: 0.8418 (m-30) cc_final: 0.7758 (m-30) REVERT: Q 65 MET cc_start: 0.7495 (mtt) cc_final: 0.7066 (ptm) REVERT: Q 76 PHE cc_start: 0.8079 (m-80) cc_final: 0.7781 (m-10) REVERT: R 11 MET cc_start: 0.8165 (tpt) cc_final: 0.7792 (tpp) REVERT: S 11 MET cc_start: 0.8160 (mmm) cc_final: 0.7755 (tpp) REVERT: S 57 MET cc_start: 0.8874 (tmm) cc_final: 0.8498 (tmm) REVERT: Y 39 GLU cc_start: 0.8921 (tt0) cc_final: 0.8648 (pp20) REVERT: Y 80 ASN cc_start: 0.9042 (m-40) cc_final: 0.8756 (m110) REVERT: Y 83 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.8369 (ttp80) REVERT: Y 98 ARG cc_start: 0.8521 (tpp80) cc_final: 0.7970 (ttm-80) REVERT: Y 123 GLN cc_start: 0.8977 (mt0) cc_final: 0.8537 (mt0) REVERT: a 30 ASP cc_start: 0.7015 (t0) cc_final: 0.6797 (t0) REVERT: a 94 TYR cc_start: 0.8595 (t80) cc_final: 0.7782 (t80) REVERT: a 118 MET cc_start: 0.9350 (mmp) cc_final: 0.9097 (tpp) REVERT: a 131 GLU cc_start: 0.8493 (tp30) cc_final: 0.8153 (tp30) REVERT: a 151 LEU cc_start: 0.8755 (mm) cc_final: 0.8547 (tp) REVERT: a 167 LYS cc_start: 0.8812 (tttt) cc_final: 0.8184 (tptp) outliers start: 93 outliers final: 71 residues processed: 634 average time/residue: 0.2265 time to fit residues: 234.7322 Evaluate side-chains 644 residues out of total 3846 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 561 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 3 PHE Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 6 VAL Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 43 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 94 GLN Chi-restraints excluded: chain W residue 138 LEU Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 136 VAL Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 327 LEU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 343 THR Chi-restraints excluded: chain B residue 372 ILE Chi-restraints excluded: chain B residue 374 VAL Chi-restraints excluded: chain B residue 399 GLN Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 368 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain X residue 51 HIS Chi-restraints excluded: chain X residue 74 VAL Chi-restraints excluded: chain X residue 138 ARG Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 50 ILE Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 98 LYS Chi-restraints excluded: chain H residue 120 GLU Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 55 LEU Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 167 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 125 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 36 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 65 MET Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 63 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain S residue 70 LEU Chi-restraints excluded: chain Y residue 62 THR Chi-restraints excluded: chain Y residue 83 ARG Chi-restraints excluded: chain Y residue 124 VAL Chi-restraints excluded: chain a residue 14 HIS Chi-restraints excluded: chain a residue 16 LEU Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 185 HIS Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 252 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 370 optimal weight: 2.9990 chunk 251 optimal weight: 2.9990 chunk 249 optimal weight: 0.8980 chunk 315 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 258 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 273 optimal weight: 0.0770 chunk 339 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 511 GLN X 73 GLN H 24 GLN D 243 ASN S 52 GLN ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 234 GLN a 252 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.063408 restraints weight = 78016.697| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 2.30 r_work: 0.2711 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2581 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.5033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 37459 Z= 0.140 Angle : 0.634 10.435 50711 Z= 0.316 Chirality : 0.044 0.230 5914 Planarity : 0.004 0.051 6538 Dihedral : 6.321 102.095 5352 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.33 % Allowed : 18.92 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % 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: 1.16 (0.12), residues: 4803 helix: 1.71 (0.10), residues: 2634 sheet: 0.13 (0.22), residues: 534 loop : -0.50 (0.16), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG a 210 TYR 0.026 0.001 TYR a 263 PHE 0.022 0.001 PHE M 53 TRP 0.055 0.002 TRP Y 26 HIS 0.005 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00322 (37459) covalent geometry : angle 0.63353 (50711) hydrogen bonds : bond 0.04316 ( 2206) hydrogen bonds : angle 4.34744 ( 6462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12223.48 seconds wall clock time: 208 minutes 33.98 seconds (12513.98 seconds total)