Starting phenix.real_space_refine on Sat Mar 7 02:25:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oqt_20169/03_2026/6oqt_20169_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oqt_20169/03_2026/6oqt_20169.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6oqt_20169/03_2026/6oqt_20169.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oqt_20169/03_2026/6oqt_20169.map" model { file = "/net/cci-nas-00/data/ceres_data/6oqt_20169/03_2026/6oqt_20169_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oqt_20169/03_2026/6oqt_20169_neut.cif" } 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 23485 2.51 5 N 6317 2.21 5 O 6968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 273 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: 36971 Number of models: 1 Model: "" Number of chains: 28 Chain: "W" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1320 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 3, 'TRANS': 169} Chain: "C" Number of atoms: 3869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 512, 3869 Classifications: {'peptide': 512} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 493} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3871 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 489} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "X" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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: "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: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} 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: "Y" Number of atoms: 1210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1210 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 153} 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: "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: "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: "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: 9.10, per 1000 atoms: 0.25 Number of scatterers: 36971 At special positions: 0 Unit cell: (176.956, 219.037, 138.112, 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 6968 8.00 N 6317 7.00 C 23485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.10 Conformation dependent library (CDL) restraints added in 1.6 seconds 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8818 Finding SS restraints... Secondary structure from input PDB file: 205 helices and 26 sheets defined 61.6% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'W' and resid 7 through 21 Processing helix chain 'W' and resid 23 through 38 Processing helix chain 'W' and resid 40 through 47 removed outlier: 3.563A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 removed outlier: 3.901A pdb=" N GLU W 58 " --> pdb=" O GLU W 54 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL W 63 " --> pdb=" O SER W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 70 through 82 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: 3.804A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 removed outlier: 3.683A pdb=" N LYS W 130 " --> pdb=" O ALA W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 162 through 172 removed outlier: 3.688A 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 100 through 104 removed outlier: 3.620A pdb=" N LEU C 103 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.654A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.671A pdb=" N MET C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 185 Processing helix chain 'C' and resid 186 through 189 Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.557A pdb=" N ILE C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) 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 237 Processing helix chain 'C' and resid 237 through 251 removed outlier: 3.669A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 265 through 277 removed outlier: 3.534A pdb=" N ALA C 269 " --> pdb=" O LYS C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 287 through 288 No H-bonds generated for 'chain 'C' and resid 287 through 288' Processing helix chain 'C' and resid 289 through 299 removed outlier: 3.736A pdb=" N ARG C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.640A 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 Processing helix chain 'C' and resid 339 through 349 removed outlier: 3.608A pdb=" N ASN C 344 " --> pdb=" O PHE C 340 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 362 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 383 through 404 removed outlier: 3.773A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR C 395 " --> pdb=" O GLY C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 413 removed outlier: 3.854A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA C 410 " --> pdb=" O SER C 407 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER C 411 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 4.354A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 426 " --> pdb=" O ASP C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 Processing helix chain 'C' and resid 454 through 459 removed outlier: 4.409A pdb=" N ASP C 458 " --> pdb=" O TYR C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 462 No H-bonds generated for 'chain 'C' and resid 460 through 462' Processing helix chain 'C' and resid 463 through 479 removed outlier: 3.603A pdb=" N ARG C 477 " --> pdb=" O ALA C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 479 through 490 removed outlier: 3.653A pdb=" N GLN C 488 " --> pdb=" O GLN C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 Processing helix chain 'B' and resid 4 through 18 removed outlier: 3.643A pdb=" N ILE B 12 " --> pdb=" O ILE B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 174 through 186 removed outlier: 3.752A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 216 through 219 removed outlier: 3.857A pdb=" N ALA B 219 " --> pdb=" O GLY B 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 216 through 219' Processing helix chain 'B' and resid 231 through 252 Proline residue: B 239 - end of helix removed outlier: 3.670A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 252 " --> pdb=" O TYR B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 276 Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 287 through 288 No H-bonds generated for 'chain 'B' and resid 287 through 288' Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.838A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.665A 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 333 through 336 Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 356 through 362 Processing helix chain 'B' and resid 377 through 382 removed outlier: 3.792A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 removed outlier: 3.527A pdb=" N GLY B 391 " --> pdb=" O LYS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.712A pdb=" N GLU B 402 " --> pdb=" O ALA B 398 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 432 Processing helix chain 'B' and resid 440 through 453 Processing helix chain 'B' and resid 463 through 478 Processing helix chain 'B' and resid 479 through 487 Processing helix chain 'B' and resid 493 through 511 Processing helix chain 'A' and resid 6 through 20 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.629A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.573A pdb=" N SER A 155 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 Processing helix chain 'A' and resid 186 through 189 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 252 Proline residue: A 239 - end of helix removed outlier: 3.715A pdb=" N TYR A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.651A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 289 through 299 removed outlier: 3.605A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.578A 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 333 through 336 Processing helix chain 'A' and resid 339 through 346 Processing helix chain 'A' and resid 356 through 362 removed outlier: 3.542A pdb=" N ALA A 362 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 382 removed outlier: 3.568A pdb=" N ALA A 380 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 392 through 407 removed outlier: 3.760A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.667A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 453 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: 3.628A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.626A pdb=" N MET A 483 " --> pdb=" O HIS A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 removed outlier: 3.566A pdb=" N LYS A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'X' and resid 5 through 25 removed outlier: 3.530A pdb=" N ALA X 11 " --> pdb=" O ILE X 7 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU X 16 " --> pdb=" O ILE X 12 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N PHE X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 136 removed outlier: 3.541A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG X 36 " --> pdb=" O ALA X 32 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS X 51 " --> pdb=" O ALA X 47 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU X 54 " --> pdb=" O ALA X 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER X 60 " --> pdb=" O LEU X 56 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE X 76 " --> pdb=" O ALA X 72 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN X 96 " --> pdb=" O ALA X 92 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLU X 119 " --> pdb=" O ARG X 115 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL X 129 " --> pdb=" O ALA X 125 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA X 132 " --> pdb=" O ALA X 128 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 146 Processing helix chain 'X' and resid 147 through 156 removed outlier: 3.806A pdb=" N LEU X 156 " --> pdb=" O LEU X 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 103 removed outlier: 3.694A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.546A 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 'H' and resid 129 through 134 removed outlier: 3.714A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.658A pdb=" N ALA G 39 " --> pdb=" O GLN G 35 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 58 removed outlier: 4.069A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS G 57 " --> pdb=" O GLY G 53 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY G 58 " --> pdb=" O HIS G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 89 through 108 removed outlier: 3.566A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 129 removed outlier: 3.816A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.641A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.285A 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 198 through 203 removed outlier: 3.890A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 283 removed outlier: 3.630A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP G 216 " --> pdb=" O LYS G 212 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL G 244 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU G 259 " --> pdb=" O SER G 255 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 removed outlier: 3.539A pdb=" N LEU F 84 " --> pdb=" O LYS F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 115 through 119 removed outlier: 3.627A pdb=" N LEU F 119 " --> pdb=" O TYR F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 137 Processing helix chain 'F' and resid 156 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: 3.623A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N MET F 226 " --> pdb=" O THR F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.870A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA F 256 " --> pdb=" O THR F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 259 No H-bonds generated for 'chain 'F' and resid 257 through 259' Processing helix chain 'F' and resid 270 through 280 removed outlier: 3.965A 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 327 Processing helix chain 'F' and resid 345 through 370 removed outlier: 7.340A pdb=" N GLN F 351 " --> pdb=" O LEU F 347 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N GLU F 352 " --> pdb=" O VAL F 348 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS F 353 " --> pdb=" O VAL F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 379 through 382 Processing helix chain 'F' and resid 385 through 400 Processing helix chain 'F' and resid 404 through 406 No H-bonds generated for 'chain 'F' and resid 404 through 406' Processing helix chain 'F' and resid 407 through 412 Processing helix chain 'F' and resid 419 through 433 removed outlier: 3.727A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY F 426 " --> pdb=" O ASP F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'F' and resid 448 through 457 removed outlier: 3.724A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 196 through 197 No H-bonds generated for 'chain 'E' and resid 196 through 197' 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: 5.066A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.582A pdb=" N GLY E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.756A 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 313 removed outlier: 3.646A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 removed outlier: 3.512A 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: 4.391A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.599A 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 383 through 400 removed outlier: 3.627A pdb=" N LEU E 388 " --> pdb=" O GLU E 384 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL E 389 " --> pdb=" O GLU E 385 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 391 " --> pdb=" O LYS E 387 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS E 395 " --> pdb=" O ALA E 391 " (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 458 removed outlier: 3.925A pdb=" N GLU E 454 " --> pdb=" O GLU E 450 " (cutoff:3.500A) 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 170 Processing helix chain 'D' and resid 182 through 196 Processing helix chain 'D' and resid 198 through 200 No H-bonds generated for 'chain 'D' and resid 198 through 200' Processing helix chain 'D' and resid 212 through 233 removed outlier: 3.662A pdb=" N ARG D 216 " --> pdb=" O PRO D 212 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.584A 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 299 through 302 removed outlier: 3.725A pdb=" N ASP D 302 " --> pdb=" O PRO D 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 299 through 302' 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: 7.368A pdb=" N GLN D 351 " --> pdb=" O LEU D 347 " (cutoff:3.500A) removed outlier: 9.075A pdb=" N GLU D 352 " --> pdb=" O VAL D 348 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N HIS D 353 " --> pdb=" O VAL D 349 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.294A 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 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 444 Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.517A pdb=" N ALA D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 4.851A pdb=" N TYR J 10 " --> pdb=" O MET J 6 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N MET J 11 " --> pdb=" O ASP J 7 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.123A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 Processing helix chain 'L' and resid 6 through 42 removed outlier: 3.639A pdb=" N TYR L 10 " --> pdb=" O MET L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 Processing helix chain 'L' and resid 61 through 78 removed outlier: 3.614A pdb=" N VAL L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 42 removed outlier: 3.976A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN M 42 " --> pdb=" O GLY M 38 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 77 removed outlier: 4.026A pdb=" N GLY M 58 " --> pdb=" O PHE M 54 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE M 63 " --> pdb=" O LEU M 59 " (cutoff:3.500A) Proline residue: M 64 - end of helix Processing helix chain 'N' and resid 4 through 42 removed outlier: 3.910A pdb=" N LEU N 9 " --> pdb=" O ASN N 5 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N TYR N 10 " --> pdb=" O MET N 6 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG N 41 " --> pdb=" O GLU N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 4.065A pdb=" N LEU N 59 " --> pdb=" O ILE N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 61 through 77 Processing helix chain 'O' and resid 7 through 42 removed outlier: 3.515A pdb=" N MET O 11 " --> pdb=" O ASP O 7 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA O 20 " --> pdb=" O MET O 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.582A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 77 Processing helix chain 'P' and resid 5 through 42 removed outlier: 3.828A pdb=" N LEU P 9 " --> pdb=" O ASN P 5 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR P 10 " --> pdb=" O MET P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 61 removed outlier: 3.751A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) Processing helix chain 'P' and resid 61 through 77 removed outlier: 3.673A pdb=" N LEU P 70 " --> pdb=" O ILE P 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 6 Processing helix chain 'Q' and resid 7 through 42 removed outlier: 4.064A pdb=" N MET Q 11 " --> pdb=" O ASP Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 4.035A pdb=" N GLY Q 58 " --> pdb=" O PHE Q 54 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ILE Q 63 " --> pdb=" O LEU Q 59 " (cutoff:3.500A) Proline residue: Q 64 - end of helix Processing helix chain 'R' and resid 5 through 42 removed outlier: 3.720A pdb=" N LEU R 9 " --> pdb=" O ASN R 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 77 removed outlier: 3.631A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA R 62 " --> pdb=" O GLY R 58 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE R 63 " --> pdb=" O LEU R 59 " (cutoff:3.500A) Proline residue: R 64 - end of helix Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.764A pdb=" N ILE Y 12 " --> pdb=" O LEU Y 8 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA Y 13 " --> pdb=" O GLY Y 9 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 140 removed outlier: 3.779A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR Y 62 " --> pdb=" O LYS Y 58 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ASP Y 63 " --> pdb=" O ALA Y 59 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP Y 88 " --> pdb=" O SER Y 84 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN Y 96 " --> pdb=" O ALA Y 92 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN Y 106 " --> pdb=" O VAL Y 102 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA Y 107 " --> pdb=" O ALA Y 103 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU Y 108 " --> pdb=" O GLN Y 104 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU Y 110 " --> pdb=" O GLN Y 106 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL Y 129 " --> pdb=" O ALA Y 125 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 156 removed outlier: 3.606A pdb=" N ASP Y 147 " --> pdb=" O ALA Y 143 " (cutoff:3.500A) Processing helix chain 'a' and resid 7 through 16 removed outlier: 3.699A pdb=" N LEU a 16 " --> pdb=" O ILE a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 65 removed outlier: 3.840A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 94 removed outlier: 3.727A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET a 93 " --> pdb=" O SER a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 119 removed outlier: 4.136A pdb=" N ASP a 119 " --> pdb=" O MET a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 124 through 133 removed outlier: 3.587A 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: 3.516A pdb=" N ILE a 159 " --> pdb=" O LEU a 155 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS a 169 " --> pdb=" O SER a 165 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.202A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (cutoff:3.500A) removed outlier: 3.889A 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: 4.080A pdb=" N ILE a 194 " --> pdb=" O PRO a 190 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.565A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) Processing helix chain 'a' and resid 233 through 269 removed outlier: 4.102A pdb=" N LEU a 237 " --> pdb=" O SER a 233 " (cutoff:3.500A) Proline residue: a 240 - end of helix removed outlier: 4.167A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE a 256 " --> pdb=" O GLN a 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 8 through 42 removed outlier: 3.525A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 3.514A pdb=" N GLY I 58 " --> pdb=" O PHE I 54 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 removed outlier: 3.583A pdb=" N ILE I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 42 removed outlier: 4.549A pdb=" N LEU S 9 " --> pdb=" O ASN S 5 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS S 34 " --> pdb=" O ILE S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.992A pdb=" N THR S 51 " --> pdb=" O PRO S 47 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP S 61 " --> pdb=" O MET S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 77 Processing sheet with id=AA1, first strand: chain 'W' and resid 135 through 142 removed outlier: 6.735A pdb=" N ALA W 106 " --> pdb=" O LYS W 137 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ASN W 139 " --> pdb=" O ALA W 106 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL W 108 " --> pdb=" O ASN W 139 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LYS W 141 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N VAL W 110 " --> pdb=" O LYS W 141 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 35 removed outlier: 13.387A pdb=" N ALA B 25 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N GLY B 92 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ASN B 27 " --> pdb=" O CYS B 90 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR B 91 " --> pdb=" O MET B 52 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASP F 27 " --> pdb=" O VAL F 42 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA F 28 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 59 through 67 removed outlier: 4.201A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER C 70 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N VAL C 74 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA C 63 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU D 36 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 107 through 109 removed outlier: 6.535A pdb=" N LYS C 192 " --> pdb=" O LEU C 257 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N ILE C 259 " --> pdb=" O LYS C 192 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ILE C 194 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ASP C 261 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N VAL C 196 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 331 removed outlier: 6.378A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA8, first strand: chain 'B' and resid 107 through 108 Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.456A pdb=" N ILE B 159 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 329 through 331 removed outlier: 6.404A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 168 " --> pdb=" O LEU B 355 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 59 through 66 removed outlier: 3.698A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N GLN E 45 " --> pdb=" O ILE E 50 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE E 50 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ASP E 14 " --> pdb=" O VAL E 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AB4, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.613A pdb=" N TYR A 260 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 107 through 109 removed outlier: 3.613A pdb=" N TYR A 260 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 30 through 34 removed outlier: 7.164A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 30 through 34 removed outlier: 6.426A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ALA H 44 " --> pdb=" O GLU G 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 132 through 136 removed outlier: 8.280A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 8.773A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.499A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE G 175 " --> pdb=" O SER G 179 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N SER G 179 " --> pdb=" O ILE G 175 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 76 through 79 removed outlier: 4.804A pdb=" N GLU F 105 " --> pdb=" O VAL F 79 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 87 through 88 removed outlier: 6.073A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER F 174 " --> pdb=" O SER F 203 " (cutoff:3.500A) removed outlier: 8.284A pdb=" N VAL F 205 " --> pdb=" O SER F 174 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE F 176 " --> pdb=" O VAL F 205 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N GLY F 207 " --> pdb=" O PHE F 176 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY F 178 " --> pdb=" O GLY F 207 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.694A pdb=" N PHE F 139 " --> pdb=" O LEU F 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 76 through 78 Processing sheet with id=AC4, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.389A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N SER E 174 " --> pdb=" O SER E 203 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N VAL E 205 " --> pdb=" O SER E 174 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N PHE E 176 " --> pdb=" O VAL E 205 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N GLY E 207 " --> pdb=" O PHE E 176 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLY E 178 " --> pdb=" O GLY E 207 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL E 175 " --> pdb=" O PHE E 240 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 125 through 126 removed outlier: 4.401A pdb=" N PHE E 139 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 76 through 78 Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.253A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS D 144 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N VAL D 319 " --> pdb=" O LYS D 144 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N GLY D 146 " --> pdb=" O VAL D 319 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 27 through 28 2276 hydrogen bonds defined for protein. 6579 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: 8.53 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6333 1.30 - 1.42: 8611 1.42 - 1.55: 22200 1.55 - 1.68: 24 1.68 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.21e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.09e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.459 -0.071 1.00e-02 1.00e+04 5.01e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.471 -0.062 1.00e-02 1.00e+04 3.85e+01 bond pdb=" C VAL F 205 " pdb=" O VAL F 205 " ideal model delta sigma weight residual 1.237 1.170 0.066 1.07e-02 8.73e+03 3.84e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.24: 50563 4.24 - 8.47: 212 8.47 - 12.71: 16 12.71 - 16.94: 2 16.94 - 21.18: 4 Bond angle restraints: 50797 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 139.87 118.69 21.18 1.00e+00 1.00e+00 4.49e+02 angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 118.75 21.12 1.00e+00 1.00e+00 4.46e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 119.39 20.48 1.00e+00 1.00e+00 4.19e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 117.42 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PA ATP B 600 " pdb=" O3A ATP B 600 " pdb=" PB ATP B 600 " ideal model delta sigma weight residual 136.83 120.69 16.14 1.00e+00 1.00e+00 2.61e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.39: 22024 29.39 - 58.77: 675 58.77 - 88.16: 85 88.16 - 117.54: 5 117.54 - 146.93: 5 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" O1B ADP D 500 " pdb=" O3A ADP D 500 " pdb=" PB ADP D 500 " pdb=" PA ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 153.07 146.93 1 2.00e+01 2.50e-03 4.41e+01 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 85.51 -145.51 1 2.00e+01 2.50e-03 4.38e+01 dihedral pdb=" C5' ADP D 500 " pdb=" O5' ADP D 500 " pdb=" PA ADP D 500 " pdb=" O2A ADP D 500 " ideal model delta sinusoidal sigma weight residual 300.00 166.99 133.02 1 2.00e+01 2.50e-03 4.04e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 5534 0.094 - 0.188: 362 0.188 - 0.282: 18 0.282 - 0.376: 4 0.376 - 0.469: 2 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA GLN B 511 " pdb=" N GLN B 511 " pdb=" C GLN B 511 " pdb=" CB GLN B 511 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.51e+00 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 ASP C 261 " pdb=" N ASP C 261 " pdb=" C ASP C 261 " pdb=" CB ASP C 261 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C ALA D 264 " -0.084 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.030 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 261 " -0.022 2.00e-02 2.50e+03 4.36e-02 1.90e+01 pdb=" C ASP A 261 " 0.075 2.00e-02 2.50e+03 pdb=" O ASP A 261 " -0.027 2.00e-02 2.50e+03 pdb=" N ASP A 262 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 264 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C ALA E 264 " -0.074 2.00e-02 2.50e+03 pdb=" O ALA E 264 " 0.027 2.00e-02 2.50e+03 pdb=" N VAL E 265 " 0.026 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.41: 46 2.41 - 3.03: 24225 3.03 - 3.65: 53397 3.65 - 4.28: 83831 4.28 - 4.90: 141878 Nonbonded interactions: 303377 Sorted by model distance: nonbonded pdb=" O2G ATP C 600 " pdb="MG MG C 601 " model vdw 1.781 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.852 2.170 nonbonded pdb=" OG1 THR C 176 " pdb="MG MG C 601 " model vdw 1.860 2.170 nonbonded pdb=" O3 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.870 2.170 nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.888 2.170 ... (remaining 303372 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 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 601)) selection = (chain 'B' and (resid 4 through 511 or resid 600 through 601)) selection = (chain 'C' and (resid 4 through 408 or (resid 409 through 410 and (name N or nam \ e CA or name C or name O or name CB )) or resid 411 through 511 or resid 600 thr \ ough 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 78) selection = (chain 'J' and resid 3 through 78) selection = (chain 'L' and resid 3 through 78) selection = (chain 'M' and resid 3 through 78) selection = (chain 'N' and resid 3 through 78) selection = (chain 'O' and resid 3 through 78) selection = (chain 'P' and resid 3 through 78) selection = (chain 'Q' and resid 3 through 78) selection = chain 'R' selection = (chain 'S' and resid 3 through 78) } ncs_group { reference = chain 'X' selection = chain 'Y' } 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: 0.030 Extract box with map and model: 0.620 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 35.720 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.090 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 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 : 0.008 0.114 37528 Z= 0.403 Angle : 0.855 21.180 50797 Z= 0.552 Chirality : 0.050 0.469 5920 Planarity : 0.004 0.049 6550 Dihedral : 14.495 146.931 13976 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.96 % Allowed : 7.35 % Favored : 90.69 % Cbeta Deviations : 0.02 % 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: -2.11 (0.11), residues: 4807 helix: -1.46 (0.09), residues: 2654 sheet: -0.52 (0.20), residues: 538 loop : -1.26 (0.14), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 61 TYR 0.022 0.002 TYR B 236 PHE 0.018 0.002 PHE F 139 TRP 0.017 0.001 TRP a 39 HIS 0.011 0.001 HIS F 437 Details of bonding type rmsd covalent geometry : bond 0.00777 (37528) covalent geometry : angle 0.85519 (50797) hydrogen bonds : bond 0.15753 ( 2253) hydrogen bonds : angle 6.98676 ( 6579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 750 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: C 236 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.7769 (t80) REVERT: C 408 GLN cc_start: 0.8751 (pt0) cc_final: 0.8549 (pm20) REVERT: C 422 ASP cc_start: 0.7872 (p0) cc_final: 0.7564 (p0) REVERT: B 2 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.5875 (pt0) REVERT: B 7 GLU cc_start: 0.8474 (tt0) cc_final: 0.8267 (tt0) REVERT: B 52 MET cc_start: 0.8998 (mtm) cc_final: 0.8675 (mtp) REVERT: B 236 TYR cc_start: 0.9321 (OUTLIER) cc_final: 0.8741 (t80) REVERT: B 484 GLN cc_start: 0.8597 (tp-100) cc_final: 0.8357 (tp40) REVERT: A 180 ILE cc_start: 0.9054 (pt) cc_final: 0.8840 (mm) REVERT: X 10 GLN cc_start: 0.8681 (tp40) cc_final: 0.8250 (tp40) REVERT: X 24 TYR cc_start: 0.8292 (m-80) cc_final: 0.7895 (m-10) REVERT: X 104 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7784 (tm-30) REVERT: X 115 ARG cc_start: 0.7886 (ttm110) cc_final: 0.7578 (mtm-85) REVERT: X 136 ILE cc_start: 0.7662 (OUTLIER) cc_final: 0.7133 (tt) REVERT: F 226 MET cc_start: 0.8982 (mtt) cc_final: 0.8699 (mtp) REVERT: F 437 HIS cc_start: 0.8983 (OUTLIER) cc_final: 0.8275 (p90) REVERT: E 322 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8178 (p) REVERT: D 116 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7156 (p90) REVERT: D 343 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: M 50 ARG cc_start: 0.8609 (ttm110) cc_final: 0.8266 (ttp-170) REVERT: M 75 MET cc_start: 0.9266 (ttp) cc_final: 0.8879 (ttm) REVERT: M 76 PHE cc_start: 0.8502 (m-80) cc_final: 0.8214 (m-10) REVERT: N 65 MET cc_start: 0.8804 (mmt) cc_final: 0.8548 (mmt) REVERT: O 6 MET cc_start: 0.8355 (ttm) cc_final: 0.8003 (mpp) REVERT: O 10 TYR cc_start: 0.8637 (m-80) cc_final: 0.8307 (m-80) REVERT: O 17 MET cc_start: 0.8431 (ttm) cc_final: 0.7908 (mtp) REVERT: O 63 ILE cc_start: 0.8933 (mm) cc_final: 0.8654 (mt) REVERT: O 73 TYR cc_start: 0.8768 (t80) cc_final: 0.8407 (t80) REVERT: P 10 TYR cc_start: 0.8997 (m-80) cc_final: 0.8757 (m-80) REVERT: P 51 THR cc_start: 0.8878 (p) cc_final: 0.8668 (p) REVERT: Q 10 TYR cc_start: 0.8666 (m-80) cc_final: 0.7981 (m-80) REVERT: R 51 THR cc_start: 0.9359 (m) cc_final: 0.9047 (p) REVERT: Y 2 ASN cc_start: 0.7874 (t0) cc_final: 0.6919 (t0) REVERT: Y 8 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8708 (tp) REVERT: Y 46 SER cc_start: 0.9172 (t) cc_final: 0.8823 (p) REVERT: Y 53 ASP cc_start: 0.8209 (m-30) cc_final: 0.7839 (m-30) REVERT: Y 64 GLN cc_start: 0.8948 (mp-120) cc_final: 0.8274 (pt0) REVERT: Y 80 ASN cc_start: 0.8581 (m-40) cc_final: 0.8002 (m-40) REVERT: Y 117 ARG cc_start: 0.8535 (ttt-90) cc_final: 0.8204 (ttt90) REVERT: a 9 GLN cc_start: 0.8851 (mt0) cc_final: 0.8531 (mm-40) REVERT: a 65 LYS cc_start: 0.8456 (mttt) cc_final: 0.8204 (ttpt) REVERT: a 131 GLU cc_start: 0.8381 (tt0) cc_final: 0.8076 (tt0) REVERT: a 141 VAL cc_start: 0.8614 (m) cc_final: 0.8156 (p) REVERT: a 196 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8220 (mp0) REVERT: I 16 MET cc_start: 0.8566 (ttm) cc_final: 0.8279 (ttt) REVERT: I 17 MET cc_start: 0.8364 (ptp) cc_final: 0.7832 (mtm) REVERT: I 37 GLU cc_start: 0.8751 (tp30) cc_final: 0.8419 (tp30) REVERT: I 57 MET cc_start: 0.9048 (tmm) cc_final: 0.8840 (tmm) REVERT: I 59 LEU cc_start: 0.8969 (mp) cc_final: 0.8693 (mp) REVERT: I 65 MET cc_start: 0.8737 (mtp) cc_final: 0.7588 (mtp) REVERT: S 34 LYS cc_start: 0.9033 (mmtm) cc_final: 0.8777 (mmmm) REVERT: S 44 ASP cc_start: 0.8726 (m-30) cc_final: 0.8371 (m-30) REVERT: S 57 MET cc_start: 0.9117 (tmt) cc_final: 0.8884 (tmm) REVERT: S 73 TYR cc_start: 0.8282 (t80) cc_final: 0.7674 (t80) outliers start: 75 outliers final: 32 residues processed: 813 average time/residue: 0.2370 time to fit residues: 306.5707 Evaluate side-chains 646 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 605 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 99 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 259 ILE Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 2 GLN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 510 THR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 377 VAL Chi-restraints excluded: chain X residue 136 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 281 SER Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 210 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 437 HIS Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 322 SER Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 56 LEU Chi-restraints excluded: chain a residue 149 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 432 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 4.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.0470 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9980 chunk 470 optimal weight: 0.8980 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN W 71 ASN C 123 HIS C 333 GLN C 369 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 147 GLN B 186 GLN B 333 GLN B 484 GLN B 488 GLN A 4 ASN A 65 ASN A 147 GLN A 344 ASN A 408 GLN X 10 GLN X 123 GLN H 104 HIS ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 GLN G 57 HIS G 64 HIS F 121 ASN F 279 GLN F 437 HIS E 7 GLN D 279 GLN J 3 ASN J 52 GLN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 132 HIS a 181 GLN S 52 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.061809 restraints weight = 78119.250| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.17 r_work: 0.2667 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37528 Z= 0.148 Angle : 0.624 7.792 50797 Z= 0.327 Chirality : 0.044 0.246 5920 Planarity : 0.004 0.054 6550 Dihedral : 8.269 140.060 5404 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.55 % Allowed : 10.71 % Favored : 86.73 % 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: -0.04 (0.12), residues: 4807 helix: 0.43 (0.10), residues: 2687 sheet: -0.28 (0.21), residues: 539 loop : -0.51 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG X 83 TYR 0.023 0.001 TYR B 236 PHE 0.022 0.001 PHE a 48 TRP 0.013 0.001 TRP B 513 HIS 0.006 0.001 HIS a 14 Details of bonding type rmsd covalent geometry : bond 0.00293 (37528) covalent geometry : angle 0.62355 (50797) hydrogen bonds : bond 0.05281 ( 2253) hydrogen bonds : angle 4.83709 ( 6579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 679 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 236 TYR cc_start: 0.9289 (OUTLIER) cc_final: 0.7723 (t80) REVERT: B 236 TYR cc_start: 0.9409 (OUTLIER) cc_final: 0.8980 (t80) REVERT: B 386 MET cc_start: 0.9246 (mmt) cc_final: 0.8983 (mmt) REVERT: B 484 GLN cc_start: 0.8795 (tp40) cc_final: 0.8504 (tp40) REVERT: A 356 GLU cc_start: 0.8520 (tp30) cc_final: 0.8317 (tp30) REVERT: A 483 MET cc_start: 0.9176 (mmp) cc_final: 0.8965 (mmm) REVERT: X 10 GLN cc_start: 0.9245 (tp-100) cc_final: 0.8956 (tp-100) REVERT: X 24 TYR cc_start: 0.8428 (m-80) cc_final: 0.7538 (m-10) REVERT: X 82 ARG cc_start: 0.8692 (tpp-160) cc_final: 0.8317 (tpp-160) REVERT: X 85 GLN cc_start: 0.7749 (mp10) cc_final: 0.7281 (mp10) REVERT: X 104 GLN cc_start: 0.8395 (tm-30) cc_final: 0.8190 (tm-30) REVERT: X 115 ARG cc_start: 0.8368 (ttm110) cc_final: 0.7990 (mtm-85) REVERT: H 49 MET cc_start: 0.9357 (mmt) cc_final: 0.9141 (mmm) REVERT: H 132 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7978 (pp20) REVERT: F 121 ASN cc_start: 0.8850 (OUTLIER) cc_final: 0.8212 (m-40) REVERT: E 200 ASP cc_start: 0.8952 (t0) cc_final: 0.8714 (t0) REVERT: D 116 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7031 (p90) REVERT: M 50 ARG cc_start: 0.8780 (ttm110) cc_final: 0.8409 (ttp-170) REVERT: M 75 MET cc_start: 0.9398 (ttp) cc_final: 0.9166 (ttm) REVERT: N 9 LEU cc_start: 0.9111 (mm) cc_final: 0.8847 (pt) REVERT: N 11 MET cc_start: 0.8728 (tpt) cc_final: 0.8495 (mmt) REVERT: N 51 THR cc_start: 0.9467 (m) cc_final: 0.9009 (p) REVERT: N 55 ILE cc_start: 0.9488 (mt) cc_final: 0.9284 (mt) REVERT: N 65 MET cc_start: 0.9011 (mmt) cc_final: 0.8654 (mmt) REVERT: O 6 MET cc_start: 0.8412 (ttm) cc_final: 0.7871 (mpp) REVERT: O 17 MET cc_start: 0.8527 (ttm) cc_final: 0.7990 (mtp) REVERT: O 42 GLN cc_start: 0.8184 (mp10) cc_final: 0.7814 (mp10) REVERT: O 63 ILE cc_start: 0.9057 (mm) cc_final: 0.8714 (mt) REVERT: O 73 TYR cc_start: 0.8797 (t80) cc_final: 0.8277 (t80) REVERT: P 10 TYR cc_start: 0.9150 (m-80) cc_final: 0.8873 (m-80) REVERT: Q 10 TYR cc_start: 0.8750 (m-80) cc_final: 0.7975 (m-80) REVERT: Q 37 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8912 (mm-30) REVERT: R 65 MET cc_start: 0.8755 (mmm) cc_final: 0.8521 (mmm) REVERT: Y 8 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8772 (tp) REVERT: Y 14 PHE cc_start: 0.8976 (t80) cc_final: 0.8729 (t80) REVERT: Y 46 SER cc_start: 0.8635 (t) cc_final: 0.8409 (p) REVERT: Y 49 ARG cc_start: 0.8058 (tmm-80) cc_final: 0.7621 (tmm-80) REVERT: Y 53 ASP cc_start: 0.8276 (m-30) cc_final: 0.7976 (m-30) REVERT: Y 55 ASP cc_start: 0.8063 (p0) cc_final: 0.7851 (p0) REVERT: Y 63 ASP cc_start: 0.8655 (m-30) cc_final: 0.8343 (t0) REVERT: Y 64 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8389 (mm-40) REVERT: Y 80 ASN cc_start: 0.8559 (m-40) cc_final: 0.8100 (m110) REVERT: Y 150 ASP cc_start: 0.9155 (m-30) cc_final: 0.8855 (m-30) REVERT: a 46 MET cc_start: 0.8762 (tpp) cc_final: 0.8176 (tpt) REVERT: a 115 MET cc_start: 0.8633 (mtm) cc_final: 0.8397 (mtm) REVERT: a 196 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8291 (mm-30) REVERT: a 216 TYR cc_start: 0.9328 (t80) cc_final: 0.8947 (t80) REVERT: I 6 MET cc_start: 0.8582 (ppp) cc_final: 0.8261 (pmm) REVERT: I 10 TYR cc_start: 0.8898 (m-80) cc_final: 0.8625 (m-80) REVERT: I 17 MET cc_start: 0.8985 (ptp) cc_final: 0.8574 (tmm) REVERT: I 26 ILE cc_start: 0.9542 (mt) cc_final: 0.9255 (mm) REVERT: I 51 THR cc_start: 0.9423 (m) cc_final: 0.9220 (p) REVERT: I 54 PHE cc_start: 0.9158 (m-80) cc_final: 0.8605 (m-80) REVERT: S 11 MET cc_start: 0.9443 (tpp) cc_final: 0.8899 (mmt) REVERT: S 34 LYS cc_start: 0.9254 (mmtm) cc_final: 0.9003 (mmmm) REVERT: S 73 TYR cc_start: 0.8439 (t80) cc_final: 0.7804 (t80) outliers start: 98 outliers final: 41 residues processed: 736 average time/residue: 0.2208 time to fit residues: 263.8625 Evaluate side-chains 654 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 606 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 46 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 0.9980 chunk 177 optimal weight: 10.0000 chunk 344 optimal weight: 7.9990 chunk 431 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 4 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 307 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN A 408 GLN X 64 GLN H 5 HIS H 104 HIS G 54 HIS G 57 HIS F 324 GLN F 368 GLN D 243 ASN O 52 GLN I 42 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.087626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.061178 restraints weight = 78023.533| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.23 r_work: 0.2653 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 37528 Z= 0.160 Angle : 0.588 11.880 50797 Z= 0.305 Chirality : 0.043 0.213 5920 Planarity : 0.004 0.045 6550 Dihedral : 7.482 123.812 5370 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.58 % Allowed : 12.07 % Favored : 85.35 % 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: 0.66 (0.12), residues: 4807 helix: 1.10 (0.10), residues: 2690 sheet: -0.21 (0.21), residues: 528 loop : -0.31 (0.16), residues: 1589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 83 TYR 0.017 0.001 TYR B 236 PHE 0.026 0.001 PHE I 53 TRP 0.012 0.001 TRP B 513 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00369 (37528) covalent geometry : angle 0.58841 (50797) hydrogen bonds : bond 0.04943 ( 2253) hydrogen bonds : angle 4.53336 ( 6579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 641 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9468 (mm) cc_final: 0.9187 (tt) REVERT: W 156 ASP cc_start: 0.7581 (p0) cc_final: 0.7340 (p0) REVERT: C 52 MET cc_start: 0.9191 (OUTLIER) cc_final: 0.8978 (mtm) REVERT: C 236 TYR cc_start: 0.9325 (OUTLIER) cc_final: 0.7707 (t80) REVERT: B 59 ARG cc_start: 0.9307 (OUTLIER) cc_final: 0.8373 (mtp180) REVERT: B 484 GLN cc_start: 0.8779 (tp40) cc_final: 0.8413 (tp40) REVERT: A 356 GLU cc_start: 0.8450 (tp30) cc_final: 0.8097 (tp30) REVERT: A 408 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8373 (mp10) REVERT: X 24 TYR cc_start: 0.8689 (m-80) cc_final: 0.8377 (m-10) REVERT: X 30 MET cc_start: 0.8435 (mmm) cc_final: 0.8111 (mmm) REVERT: X 82 ARG cc_start: 0.8561 (tpp-160) cc_final: 0.8351 (tpp-160) REVERT: X 83 ARG cc_start: 0.8080 (ttp80) cc_final: 0.7621 (ttp80) REVERT: X 85 GLN cc_start: 0.7678 (mp10) cc_final: 0.7278 (mp10) REVERT: X 98 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7692 (ttt180) REVERT: X 104 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8157 (tm-30) REVERT: X 115 ARG cc_start: 0.8318 (ttm110) cc_final: 0.7894 (mtm-85) REVERT: H 22 LYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8863 (ptpt) REVERT: H 49 MET cc_start: 0.9394 (mmt) cc_final: 0.9138 (mmm) REVERT: H 116 GLN cc_start: 0.8859 (mt0) cc_final: 0.8502 (mm-40) REVERT: H 129 ARG cc_start: 0.8498 (mtm110) cc_final: 0.7889 (mtm-85) REVERT: H 132 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7919 (pp20) REVERT: G 187 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8804 (pp) REVERT: F 211 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8684 (mm-30) REVERT: E 200 ASP cc_start: 0.8984 (t0) cc_final: 0.8683 (t0) REVERT: E 301 ASP cc_start: 0.9202 (t0) cc_final: 0.8875 (t0) REVERT: D 116 TYR cc_start: 0.8207 (OUTLIER) cc_final: 0.7110 (p90) REVERT: D 372 ASP cc_start: 0.8583 (p0) cc_final: 0.8167 (p0) REVERT: L 6 MET cc_start: 0.8086 (ppp) cc_final: 0.7403 (tmm) REVERT: M 50 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8321 (ttp-170) REVERT: M 52 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8776 (mm-40) REVERT: N 9 LEU cc_start: 0.9007 (mm) cc_final: 0.8802 (mt) REVERT: N 51 THR cc_start: 0.9408 (m) cc_final: 0.8962 (p) REVERT: N 52 GLN cc_start: 0.9203 (mm110) cc_final: 0.9000 (mm110) REVERT: N 55 ILE cc_start: 0.9392 (mt) cc_final: 0.9186 (mt) REVERT: O 17 MET cc_start: 0.8665 (ttm) cc_final: 0.8147 (mtp) REVERT: O 52 GLN cc_start: 0.9181 (mm110) cc_final: 0.8882 (mm-40) REVERT: O 57 MET cc_start: 0.9184 (tmm) cc_final: 0.8970 (tmm) REVERT: O 63 ILE cc_start: 0.8982 (mm) cc_final: 0.8623 (mt) REVERT: O 73 TYR cc_start: 0.8779 (t80) cc_final: 0.8308 (t80) REVERT: P 10 TYR cc_start: 0.8813 (m-80) cc_final: 0.8209 (m-80) REVERT: P 17 MET cc_start: 0.9148 (mtm) cc_final: 0.8775 (mpp) REVERT: Q 10 TYR cc_start: 0.8791 (m-80) cc_final: 0.8057 (m-80) REVERT: Q 65 MET cc_start: 0.8873 (mmm) cc_final: 0.8601 (mmm) REVERT: Y 8 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8789 (tp) REVERT: Y 14 PHE cc_start: 0.8968 (t80) cc_final: 0.8703 (t80) REVERT: Y 46 SER cc_start: 0.8496 (t) cc_final: 0.8214 (p) REVERT: Y 49 ARG cc_start: 0.8111 (tmm-80) cc_final: 0.7598 (tmm-80) REVERT: Y 53 ASP cc_start: 0.8415 (m-30) cc_final: 0.8157 (m-30) REVERT: Y 55 ASP cc_start: 0.8164 (p0) cc_final: 0.7909 (p0) REVERT: Y 63 ASP cc_start: 0.8714 (m-30) cc_final: 0.8302 (t70) REVERT: Y 80 ASN cc_start: 0.8524 (m-40) cc_final: 0.7675 (m110) REVERT: Y 83 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7147 (tmm-80) REVERT: Y 117 ARG cc_start: 0.8776 (ttt-90) cc_final: 0.8514 (ttt90) REVERT: Y 123 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8745 (mt0) REVERT: Y 150 ASP cc_start: 0.9223 (m-30) cc_final: 0.8906 (m-30) REVERT: a 9 GLN cc_start: 0.8917 (pm20) cc_final: 0.8569 (mm-40) REVERT: a 46 MET cc_start: 0.8708 (tpp) cc_final: 0.8162 (tpt) REVERT: a 196 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8294 (mm-30) REVERT: a 216 TYR cc_start: 0.9336 (t80) cc_final: 0.9057 (t80) REVERT: I 6 MET cc_start: 0.8636 (ppp) cc_final: 0.8161 (tmm) REVERT: I 10 TYR cc_start: 0.9076 (m-80) cc_final: 0.8378 (m-80) REVERT: I 17 MET cc_start: 0.9072 (ptp) cc_final: 0.8500 (mtt) REVERT: I 44 ASP cc_start: 0.8966 (p0) cc_final: 0.8680 (p0) REVERT: I 50 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8023 (ttp80) REVERT: I 54 PHE cc_start: 0.9148 (m-80) cc_final: 0.8576 (m-80) REVERT: I 68 VAL cc_start: 0.9355 (OUTLIER) cc_final: 0.8937 (p) REVERT: I 72 LEU cc_start: 0.9277 (mt) cc_final: 0.8931 (mp) REVERT: S 17 MET cc_start: 0.8878 (mtp) cc_final: 0.8624 (mtp) REVERT: S 34 LYS cc_start: 0.9187 (mmtm) cc_final: 0.8925 (mmmm) REVERT: S 44 ASP cc_start: 0.9024 (m-30) cc_final: 0.8800 (m-30) REVERT: S 72 LEU cc_start: 0.9091 (mt) cc_final: 0.8873 (mt) REVERT: S 73 TYR cc_start: 0.8378 (t80) cc_final: 0.7829 (t80) outliers start: 99 outliers final: 57 residues processed: 700 average time/residue: 0.2206 time to fit residues: 251.9544 Evaluate side-chains 672 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 602 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 158 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 37 GLU Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 37 GLU Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 78 VAL Chi-restraints excluded: chain Y residue 4 ASN Chi-restraints excluded: chain Y residue 8 LEU Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 123 GLN Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 267 optimal weight: 0.6980 chunk 362 optimal weight: 10.0000 chunk 137 optimal weight: 0.6980 chunk 153 optimal weight: 6.9990 chunk 331 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 394 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 379 optimal weight: 7.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN X 64 GLN H 104 HIS G 57 HIS F 121 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.088864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.062417 restraints weight = 77977.146| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.19 r_work: 0.2684 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37528 Z= 0.127 Angle : 0.553 12.419 50797 Z= 0.286 Chirality : 0.042 0.193 5920 Planarity : 0.004 0.046 6550 Dihedral : 7.077 116.408 5368 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.61 % Allowed : 12.85 % Favored : 84.54 % 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: 1.01 (0.12), residues: 4807 helix: 1.44 (0.10), residues: 2687 sheet: -0.22 (0.21), residues: 549 loop : -0.22 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 210 TYR 0.012 0.001 TYR P 10 PHE 0.031 0.001 PHE E 189 TRP 0.011 0.001 TRP B 513 HIS 0.005 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00279 (37528) covalent geometry : angle 0.55273 (50797) hydrogen bonds : bond 0.04493 ( 2253) hydrogen bonds : angle 4.35765 ( 6579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 637 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 4 ILE cc_start: 0.9443 (mm) cc_final: 0.9218 (tt) REVERT: W 156 ASP cc_start: 0.7598 (p0) cc_final: 0.7348 (p0) REVERT: C 52 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8962 (mtm) REVERT: C 236 TYR cc_start: 0.9330 (OUTLIER) cc_final: 0.7838 (t80) REVERT: B 386 MET cc_start: 0.9316 (mmt) cc_final: 0.9078 (mmt) REVERT: B 463 LYS cc_start: 0.8912 (mmtt) cc_final: 0.8522 (mmtm) REVERT: A 356 GLU cc_start: 0.8559 (tp30) cc_final: 0.8221 (tp30) REVERT: A 408 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8615 (pm20) REVERT: X 24 TYR cc_start: 0.8742 (m-80) cc_final: 0.8538 (m-10) REVERT: X 29 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9013 (mm) REVERT: X 78 GLN cc_start: 0.8899 (tp40) cc_final: 0.8602 (pp30) REVERT: X 83 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7589 (ttp80) REVERT: X 85 GLN cc_start: 0.7807 (mp10) cc_final: 0.7400 (mp10) REVERT: H 49 MET cc_start: 0.9365 (mmt) cc_final: 0.9153 (mmm) REVERT: H 116 GLN cc_start: 0.8946 (mt0) cc_final: 0.8643 (mm-40) REVERT: H 129 ARG cc_start: 0.8537 (mtm110) cc_final: 0.8334 (mtm-85) REVERT: G 187 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8849 (pp) REVERT: F 121 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8366 (m-40) REVERT: F 211 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8701 (mm-30) REVERT: E 200 ASP cc_start: 0.8937 (t0) cc_final: 0.8630 (t0) REVERT: E 301 ASP cc_start: 0.9150 (t0) cc_final: 0.8761 (t0) REVERT: D 116 TYR cc_start: 0.8325 (OUTLIER) cc_final: 0.7289 (p90) REVERT: D 372 ASP cc_start: 0.8539 (p0) cc_final: 0.8305 (p0) REVERT: M 50 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8392 (ttp-170) REVERT: M 52 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8736 (mm-40) REVERT: N 11 MET cc_start: 0.9013 (tpt) cc_final: 0.8785 (mmt) REVERT: N 51 THR cc_start: 0.9465 (m) cc_final: 0.9011 (p) REVERT: N 55 ILE cc_start: 0.9462 (mt) cc_final: 0.9249 (mt) REVERT: O 17 MET cc_start: 0.8556 (ttm) cc_final: 0.8236 (mtp) REVERT: O 42 GLN cc_start: 0.8304 (mp10) cc_final: 0.8000 (mp10) REVERT: O 46 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8574 (mt) REVERT: O 52 GLN cc_start: 0.9196 (mm110) cc_final: 0.8946 (mm-40) REVERT: O 57 MET cc_start: 0.9230 (tmm) cc_final: 0.9028 (tmm) REVERT: O 63 ILE cc_start: 0.9127 (mm) cc_final: 0.8749 (mt) REVERT: O 73 TYR cc_start: 0.8771 (t80) cc_final: 0.8311 (t80) REVERT: P 10 TYR cc_start: 0.8803 (m-80) cc_final: 0.8292 (m-80) REVERT: P 17 MET cc_start: 0.9086 (mtm) cc_final: 0.8717 (mpp) REVERT: P 64 PRO cc_start: 0.9211 (Cg_exo) cc_final: 0.8822 (Cg_endo) REVERT: Q 10 TYR cc_start: 0.8674 (m-80) cc_final: 0.8065 (m-80) REVERT: Q 65 MET cc_start: 0.8968 (mmm) cc_final: 0.8749 (mmm) REVERT: Q 73 TYR cc_start: 0.8512 (t80) cc_final: 0.8269 (t80) REVERT: Y 14 PHE cc_start: 0.8959 (t80) cc_final: 0.8757 (t80) REVERT: Y 55 ASP cc_start: 0.8062 (p0) cc_final: 0.7858 (p0) REVERT: Y 63 ASP cc_start: 0.8754 (m-30) cc_final: 0.8429 (t0) REVERT: Y 80 ASN cc_start: 0.8534 (m-40) cc_final: 0.8139 (m110) REVERT: Y 117 ARG cc_start: 0.8860 (ttt-90) cc_final: 0.8616 (ttt90) REVERT: a 46 MET cc_start: 0.8753 (tpp) cc_final: 0.8423 (tpt) REVERT: a 115 MET cc_start: 0.8347 (mtm) cc_final: 0.8101 (mtm) REVERT: a 124 ASP cc_start: 0.8576 (m-30) cc_final: 0.8358 (m-30) REVERT: a 196 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8265 (mm-30) REVERT: I 6 MET cc_start: 0.8603 (ppp) cc_final: 0.8325 (pmm) REVERT: I 10 TYR cc_start: 0.8944 (m-80) cc_final: 0.8722 (m-80) REVERT: I 17 MET cc_start: 0.8969 (ptp) cc_final: 0.8531 (mtt) REVERT: I 45 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8388 (mt) REVERT: I 50 ARG cc_start: 0.8509 (ttp80) cc_final: 0.8030 (ttp80) REVERT: I 54 PHE cc_start: 0.9100 (m-80) cc_final: 0.8561 (m-80) REVERT: I 68 VAL cc_start: 0.9376 (t) cc_final: 0.9117 (p) REVERT: S 11 MET cc_start: 0.9365 (tpp) cc_final: 0.9127 (mmt) REVERT: S 34 LYS cc_start: 0.9238 (mmtm) cc_final: 0.9007 (mmmm) REVERT: S 72 LEU cc_start: 0.9000 (mt) cc_final: 0.8798 (mt) REVERT: S 73 TYR cc_start: 0.8370 (t80) cc_final: 0.7884 (t80) outliers start: 100 outliers final: 58 residues processed: 689 average time/residue: 0.2208 time to fit residues: 249.0112 Evaluate side-chains 678 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 610 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 64 GLN Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 42 GLN Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 66 ILE Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 61 ASP Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 137 GLU Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain S residue 46 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 404 optimal weight: 8.9990 chunk 445 optimal weight: 8.9990 chunk 374 optimal weight: 3.9990 chunk 443 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 324 optimal weight: 3.9990 chunk 320 optimal weight: 0.6980 chunk 263 optimal weight: 0.9990 chunk 201 optimal weight: 1.9990 chunk 362 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 ASN A 408 GLN X 64 GLN H 104 HIS G 57 HIS ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.089005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.062521 restraints weight = 77791.463| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.19 r_work: 0.2685 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37528 Z= 0.130 Angle : 0.558 10.044 50797 Z= 0.286 Chirality : 0.042 0.201 5920 Planarity : 0.004 0.047 6550 Dihedral : 6.767 112.662 5363 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.61 % Allowed : 13.97 % Favored : 83.42 % 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: 1.22 (0.12), residues: 4807 helix: 1.64 (0.10), residues: 2691 sheet: -0.06 (0.22), residues: 529 loop : -0.22 (0.16), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 41 TYR 0.011 0.001 TYR G 44 PHE 0.033 0.001 PHE E 189 TRP 0.011 0.001 TRP B 513 HIS 0.006 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00294 (37528) covalent geometry : angle 0.55758 (50797) hydrogen bonds : bond 0.04358 ( 2253) hydrogen bonds : angle 4.26604 ( 6579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 630 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7602 (p0) cc_final: 0.7345 (p0) REVERT: C 52 MET cc_start: 0.9174 (OUTLIER) cc_final: 0.8974 (mtm) REVERT: C 230 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8553 (mt-10) REVERT: C 236 TYR cc_start: 0.9357 (OUTLIER) cc_final: 0.7943 (t80) REVERT: C 422 ASP cc_start: 0.8782 (p0) cc_final: 0.8568 (p0) REVERT: B 386 MET cc_start: 0.9315 (mmt) cc_final: 0.9053 (mmt) REVERT: B 463 LYS cc_start: 0.8932 (mmtt) cc_final: 0.8654 (mmtt) REVERT: A 356 GLU cc_start: 0.8598 (tp30) cc_final: 0.8338 (tp30) REVERT: A 408 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8330 (pm20) REVERT: X 7 ILE cc_start: 0.8620 (pt) cc_final: 0.8360 (mp) REVERT: X 78 GLN cc_start: 0.8864 (tp40) cc_final: 0.8615 (pp30) REVERT: X 82 ARG cc_start: 0.8511 (tpp-160) cc_final: 0.8224 (tpp-160) REVERT: X 85 GLN cc_start: 0.7701 (mp10) cc_final: 0.7233 (mp10) REVERT: X 115 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.7781 (mtm-85) REVERT: H 20 VAL cc_start: 0.9309 (t) cc_final: 0.8973 (p) REVERT: H 116 GLN cc_start: 0.8956 (mt0) cc_final: 0.8638 (mm-40) REVERT: G 187 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8809 (pp) REVERT: F 193 MET cc_start: 0.8663 (mmp) cc_final: 0.8330 (mmp) REVERT: F 211 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8710 (mm-30) REVERT: E 200 ASP cc_start: 0.8930 (t0) cc_final: 0.8642 (t0) REVERT: E 301 ASP cc_start: 0.9130 (t0) cc_final: 0.8777 (t0) REVERT: D 116 TYR cc_start: 0.8365 (OUTLIER) cc_final: 0.7274 (p90) REVERT: D 372 ASP cc_start: 0.8456 (p0) cc_final: 0.8172 (p0) REVERT: M 6 MET cc_start: 0.7367 (ttt) cc_final: 0.6715 (tpp) REVERT: M 50 ARG cc_start: 0.8771 (ttm110) cc_final: 0.8357 (ttp-170) REVERT: M 52 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8747 (mm-40) REVERT: N 11 MET cc_start: 0.9039 (tpt) cc_final: 0.8751 (mmt) REVERT: N 51 THR cc_start: 0.9464 (m) cc_final: 0.8996 (p) REVERT: N 55 ILE cc_start: 0.9440 (mt) cc_final: 0.9181 (mt) REVERT: O 17 MET cc_start: 0.8539 (ttm) cc_final: 0.8331 (mtp) REVERT: O 41 ARG cc_start: 0.8661 (ttp-170) cc_final: 0.8373 (ttp-170) REVERT: O 42 GLN cc_start: 0.8321 (mp10) cc_final: 0.7919 (mp10) REVERT: O 46 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8569 (mt) REVERT: O 52 GLN cc_start: 0.9221 (mm110) cc_final: 0.8977 (mm-40) REVERT: O 63 ILE cc_start: 0.9148 (mm) cc_final: 0.8793 (mt) REVERT: O 73 TYR cc_start: 0.8749 (t80) cc_final: 0.8293 (t80) REVERT: P 10 TYR cc_start: 0.8831 (m-80) cc_final: 0.8329 (m-80) REVERT: P 17 MET cc_start: 0.9060 (mtm) cc_final: 0.8728 (mpp) REVERT: P 64 PRO cc_start: 0.9228 (Cg_exo) cc_final: 0.8838 (Cg_endo) REVERT: Q 10 TYR cc_start: 0.8651 (m-80) cc_final: 0.8039 (m-80) REVERT: Q 65 MET cc_start: 0.8956 (mmm) cc_final: 0.8732 (mmm) REVERT: Y 14 PHE cc_start: 0.8957 (t80) cc_final: 0.8751 (t80) REVERT: Y 63 ASP cc_start: 0.8757 (m-30) cc_final: 0.8475 (t0) REVERT: Y 80 ASN cc_start: 0.8559 (m-40) cc_final: 0.8159 (m110) REVERT: Y 96 GLN cc_start: 0.8605 (mm-40) cc_final: 0.7882 (tm-30) REVERT: Y 117 ARG cc_start: 0.8860 (ttt-90) cc_final: 0.8621 (ttt90) REVERT: a 164 TYR cc_start: 0.8191 (m-80) cc_final: 0.7905 (m-80) REVERT: a 196 GLU cc_start: 0.8551 (mm-30) cc_final: 0.8036 (mm-30) REVERT: a 203 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8767 (mtpt) REVERT: I 6 MET cc_start: 0.8627 (ppp) cc_final: 0.8347 (pmm) REVERT: I 10 TYR cc_start: 0.8986 (m-80) cc_final: 0.8708 (m-80) REVERT: I 17 MET cc_start: 0.8924 (ptp) cc_final: 0.8674 (mtt) REVERT: I 45 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8261 (mt) REVERT: I 50 ARG cc_start: 0.8536 (ttp80) cc_final: 0.8080 (ttp80) REVERT: I 54 PHE cc_start: 0.9091 (m-80) cc_final: 0.8593 (m-80) REVERT: I 68 VAL cc_start: 0.9416 (t) cc_final: 0.9171 (p) REVERT: S 11 MET cc_start: 0.9380 (tpp) cc_final: 0.9132 (mmm) REVERT: S 34 LYS cc_start: 0.9240 (mmtm) cc_final: 0.9007 (mmmm) REVERT: S 72 LEU cc_start: 0.9000 (mt) cc_final: 0.8798 (mt) REVERT: S 73 TYR cc_start: 0.8344 (t80) cc_final: 0.7910 (t80) outliers start: 100 outliers final: 57 residues processed: 689 average time/residue: 0.2168 time to fit residues: 246.0163 Evaluate side-chains 669 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 602 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 64 GLN Chi-restraints excluded: chain X residue 115 ARG Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 211 GLU Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 61 ASP Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 70 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 326 optimal weight: 0.7980 chunk 395 optimal weight: 4.9990 chunk 425 optimal weight: 20.0000 chunk 154 optimal weight: 4.9990 chunk 416 optimal weight: 1.9990 chunk 422 optimal weight: 7.9990 chunk 225 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 456 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN X 64 GLN H 5 HIS H 104 HIS G 57 HIS F 121 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.060796 restraints weight = 78435.724| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.18 r_work: 0.2645 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 37528 Z= 0.202 Angle : 0.599 13.224 50797 Z= 0.308 Chirality : 0.044 0.195 5920 Planarity : 0.004 0.047 6550 Dihedral : 6.860 113.305 5363 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.95 % Allowed : 14.47 % Favored : 82.59 % 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: 1.17 (0.12), residues: 4807 helix: 1.65 (0.10), residues: 2686 sheet: -0.26 (0.21), residues: 548 loop : -0.26 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 83 TYR 0.022 0.001 TYR a 263 PHE 0.029 0.001 PHE E 189 TRP 0.011 0.001 TRP B 513 HIS 0.006 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00481 (37528) covalent geometry : angle 0.59945 (50797) hydrogen bonds : bond 0.04686 ( 2253) hydrogen bonds : angle 4.35428 ( 6579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 616 time to evaluate : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7644 (p0) cc_final: 0.7381 (p0) REVERT: C 230 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.8569 (mt-10) REVERT: B 418 ARG cc_start: 0.8344 (ttp-170) cc_final: 0.7932 (ttp-170) REVERT: B 460 GLU cc_start: 0.8531 (pm20) cc_final: 0.7680 (pm20) REVERT: B 463 LYS cc_start: 0.8927 (mmtt) cc_final: 0.8296 (mttm) REVERT: A 356 GLU cc_start: 0.8581 (tp30) cc_final: 0.8223 (tp30) REVERT: A 408 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8335 (pm20) REVERT: X 7 ILE cc_start: 0.8713 (pt) cc_final: 0.8493 (mp) REVERT: X 78 GLN cc_start: 0.8909 (tp40) cc_final: 0.8612 (pp30) REVERT: X 82 ARG cc_start: 0.8535 (tpp-160) cc_final: 0.8058 (tpp-160) REVERT: X 83 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7533 (ttp80) REVERT: X 85 GLN cc_start: 0.7737 (mp10) cc_final: 0.7053 (mt0) REVERT: X 98 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7744 (ttt180) REVERT: X 115 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7786 (mtm-85) REVERT: H 20 VAL cc_start: 0.9357 (t) cc_final: 0.9063 (p) REVERT: H 116 GLN cc_start: 0.8971 (mt0) cc_final: 0.8624 (mm-40) REVERT: H 129 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8255 (ttm110) REVERT: G 187 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8903 (pp) REVERT: F 58 SER cc_start: 0.9600 (OUTLIER) cc_final: 0.9284 (p) REVERT: E 200 ASP cc_start: 0.8966 (t0) cc_final: 0.8716 (t0) REVERT: E 301 ASP cc_start: 0.9170 (t0) cc_final: 0.8833 (t0) REVERT: D 116 TYR cc_start: 0.8473 (OUTLIER) cc_final: 0.7291 (p90) REVERT: D 343 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8392 (mp10) REVERT: D 372 ASP cc_start: 0.8528 (p0) cc_final: 0.8222 (p0) REVERT: D 379 MET cc_start: 0.8958 (tpt) cc_final: 0.8585 (tpt) REVERT: L 37 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8568 (tp30) REVERT: M 6 MET cc_start: 0.7445 (ttt) cc_final: 0.6800 (tpp) REVERT: M 50 ARG cc_start: 0.8805 (ttm110) cc_final: 0.8378 (ttp-170) REVERT: M 52 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8770 (mm-40) REVERT: N 11 MET cc_start: 0.9053 (tpt) cc_final: 0.8699 (mmt) REVERT: N 51 THR cc_start: 0.9479 (m) cc_final: 0.9014 (p) REVERT: N 55 ILE cc_start: 0.9432 (mt) cc_final: 0.9193 (mt) REVERT: N 75 MET cc_start: 0.9107 (ttp) cc_final: 0.8891 (ttt) REVERT: O 41 ARG cc_start: 0.8665 (ttp-170) cc_final: 0.8365 (ttp-170) REVERT: O 42 GLN cc_start: 0.8413 (mp10) cc_final: 0.7996 (mp10) REVERT: O 46 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8641 (mt) REVERT: O 52 GLN cc_start: 0.9271 (mm110) cc_final: 0.9007 (mm-40) REVERT: O 63 ILE cc_start: 0.9197 (mm) cc_final: 0.8849 (mt) REVERT: O 73 TYR cc_start: 0.8749 (t80) cc_final: 0.8268 (t80) REVERT: P 10 TYR cc_start: 0.8894 (m-80) cc_final: 0.8315 (m-80) REVERT: P 17 MET cc_start: 0.9003 (mtm) cc_final: 0.8695 (mpp) REVERT: P 64 PRO cc_start: 0.9212 (Cg_exo) cc_final: 0.8804 (Cg_endo) REVERT: Q 10 TYR cc_start: 0.8673 (m-80) cc_final: 0.8049 (m-80) REVERT: Q 65 MET cc_start: 0.9010 (mmm) cc_final: 0.8708 (mmm) REVERT: R 44 ASP cc_start: 0.8853 (t70) cc_final: 0.8508 (t70) REVERT: Y 1 MET cc_start: 0.5875 (tmm) cc_final: 0.5554 (tmm) REVERT: Y 8 LEU cc_start: 0.8976 (mt) cc_final: 0.8665 (tp) REVERT: Y 63 ASP cc_start: 0.8699 (m-30) cc_final: 0.8465 (t0) REVERT: Y 80 ASN cc_start: 0.8571 (m-40) cc_final: 0.8161 (m110) REVERT: Y 117 ARG cc_start: 0.8938 (ttt-90) cc_final: 0.8678 (ttt90) REVERT: a 9 GLN cc_start: 0.9017 (mp10) cc_final: 0.8683 (mm-40) REVERT: a 65 LYS cc_start: 0.8261 (mttt) cc_final: 0.8032 (mttt) REVERT: a 164 TYR cc_start: 0.8173 (m-80) cc_final: 0.7854 (m-80) REVERT: a 196 GLU cc_start: 0.8527 (mm-30) cc_final: 0.7994 (mm-30) REVERT: I 6 MET cc_start: 0.8663 (ppp) cc_final: 0.8393 (pmm) REVERT: I 10 TYR cc_start: 0.8994 (m-80) cc_final: 0.8688 (m-80) REVERT: I 17 MET cc_start: 0.8989 (ptp) cc_final: 0.8464 (mtt) REVERT: I 45 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8393 (mt) REVERT: I 50 ARG cc_start: 0.8524 (ttp80) cc_final: 0.8081 (ttp80) REVERT: I 54 PHE cc_start: 0.9101 (m-80) cc_final: 0.8608 (m-80) REVERT: I 68 VAL cc_start: 0.9418 (t) cc_final: 0.9040 (p) REVERT: I 72 LEU cc_start: 0.9249 (mt) cc_final: 0.8874 (mp) REVERT: S 11 MET cc_start: 0.9378 (tpp) cc_final: 0.9125 (mmm) REVERT: S 34 LYS cc_start: 0.9259 (mmtm) cc_final: 0.9033 (mmmm) REVERT: S 72 LEU cc_start: 0.8974 (mt) cc_final: 0.8763 (mt) REVERT: S 73 TYR cc_start: 0.8349 (t80) cc_final: 0.7844 (t80) outliers start: 113 outliers final: 75 residues processed: 683 average time/residue: 0.2142 time to fit residues: 240.0690 Evaluate side-chains 683 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 597 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 462 SER Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 295 SER Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 2 ASN Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 64 GLN Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain X residue 115 ARG Chi-restraints excluded: chain X residue 150 ASP Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 194 THR Chi-restraints excluded: chain F residue 275 MET Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 76 PHE Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 9 LEU Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain a residue 149 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain S residue 15 VAL Chi-restraints excluded: chain S residue 46 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 141 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 435 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 82 optimal weight: 0.0170 chunk 342 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 323 optimal weight: 0.9980 chunk 311 optimal weight: 3.9990 chunk 389 optimal weight: 0.9990 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS A 408 GLN X 64 GLN H 104 HIS G 57 HIS F 121 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.062816 restraints weight = 77650.586| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.22 r_work: 0.2695 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2568 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 37528 Z= 0.122 Angle : 0.567 12.110 50797 Z= 0.291 Chirality : 0.042 0.211 5920 Planarity : 0.004 0.048 6550 Dihedral : 6.551 106.977 5361 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.29 % Allowed : 15.85 % Favored : 81.86 % 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: 1.31 (0.12), residues: 4807 helix: 1.75 (0.10), residues: 2685 sheet: -0.11 (0.22), residues: 541 loop : -0.22 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG X 83 TYR 0.026 0.001 TYR a 263 PHE 0.036 0.001 PHE Y 14 TRP 0.015 0.001 TRP a 111 HIS 0.006 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00269 (37528) covalent geometry : angle 0.56749 (50797) hydrogen bonds : bond 0.04241 ( 2253) hydrogen bonds : angle 4.24593 ( 6579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 627 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7628 (p0) cc_final: 0.7364 (p0) REVERT: C 230 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8552 (mt-10) REVERT: C 422 ASP cc_start: 0.8769 (p0) cc_final: 0.8551 (p0) REVERT: B 386 MET cc_start: 0.9277 (mmt) cc_final: 0.8971 (mmt) REVERT: B 418 ARG cc_start: 0.8358 (ttp-170) cc_final: 0.7947 (ttp-170) REVERT: B 463 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8600 (mmtt) REVERT: A 356 GLU cc_start: 0.8627 (tp30) cc_final: 0.8247 (tp30) REVERT: A 408 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.8407 (pm20) REVERT: A 418 ARG cc_start: 0.8485 (tpp80) cc_final: 0.8224 (tpp-160) REVERT: X 7 ILE cc_start: 0.8589 (pt) cc_final: 0.8376 (mp) REVERT: X 30 MET cc_start: 0.8208 (mmm) cc_final: 0.7916 (mmm) REVERT: X 78 GLN cc_start: 0.8880 (tp40) cc_final: 0.8633 (pp30) REVERT: X 83 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7474 (ttp80) REVERT: X 98 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7792 (ttt180) REVERT: H 20 VAL cc_start: 0.9290 (t) cc_final: 0.8988 (p) REVERT: H 116 GLN cc_start: 0.8955 (mt0) cc_final: 0.8623 (mm-40) REVERT: G 187 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8836 (pp) REVERT: F 58 SER cc_start: 0.9590 (OUTLIER) cc_final: 0.9265 (p) REVERT: F 193 MET cc_start: 0.8664 (mmp) cc_final: 0.8328 (mmp) REVERT: E 200 ASP cc_start: 0.8950 (t0) cc_final: 0.8691 (t0) REVERT: E 301 ASP cc_start: 0.9132 (t0) cc_final: 0.8791 (t0) REVERT: D 97 MET cc_start: 0.9274 (mmm) cc_final: 0.9037 (mtt) REVERT: D 116 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7285 (p90) REVERT: D 343 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: D 372 ASP cc_start: 0.8447 (p0) cc_final: 0.8138 (p0) REVERT: D 379 MET cc_start: 0.8971 (tpt) cc_final: 0.8645 (tpt) REVERT: L 37 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.8553 (tp30) REVERT: M 6 MET cc_start: 0.7339 (ttt) cc_final: 0.6717 (tpp) REVERT: M 50 ARG cc_start: 0.8785 (ttm110) cc_final: 0.8350 (ttp-170) REVERT: M 52 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8760 (mm-40) REVERT: N 11 MET cc_start: 0.8959 (tpt) cc_final: 0.8622 (mmt) REVERT: N 42 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8639 (mm-40) REVERT: N 51 THR cc_start: 0.9463 (m) cc_final: 0.9018 (p) REVERT: N 55 ILE cc_start: 0.9432 (mt) cc_final: 0.9213 (mt) REVERT: O 41 ARG cc_start: 0.8612 (ttp-170) cc_final: 0.8304 (ttp-170) REVERT: O 42 GLN cc_start: 0.8276 (mp10) cc_final: 0.7901 (mp10) REVERT: O 46 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8618 (mt) REVERT: O 52 GLN cc_start: 0.9256 (mm110) cc_final: 0.8991 (mm-40) REVERT: O 63 ILE cc_start: 0.9249 (mm) cc_final: 0.8897 (mt) REVERT: O 73 TYR cc_start: 0.8746 (t80) cc_final: 0.8239 (t80) REVERT: P 10 TYR cc_start: 0.8863 (m-80) cc_final: 0.8320 (m-80) REVERT: P 17 MET cc_start: 0.8986 (mtm) cc_final: 0.8590 (mpp) REVERT: P 64 PRO cc_start: 0.9182 (Cg_exo) cc_final: 0.8763 (Cg_endo) REVERT: Q 10 TYR cc_start: 0.8594 (m-80) cc_final: 0.8010 (m-80) REVERT: Q 17 MET cc_start: 0.8906 (mtm) cc_final: 0.8396 (mtm) REVERT: Q 37 GLU cc_start: 0.9129 (tp30) cc_final: 0.8894 (tp30) REVERT: Q 65 MET cc_start: 0.8860 (mmm) cc_final: 0.8658 (mmm) REVERT: R 44 ASP cc_start: 0.8732 (t70) cc_final: 0.8401 (t70) REVERT: Y 1 MET cc_start: 0.5419 (tmm) cc_final: 0.5020 (tmm) REVERT: Y 63 ASP cc_start: 0.8674 (m-30) cc_final: 0.8436 (t0) REVERT: Y 73 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7355 (mm110) REVERT: Y 80 ASN cc_start: 0.8600 (m-40) cc_final: 0.8197 (m110) REVERT: Y 117 ARG cc_start: 0.8918 (ttt-90) cc_final: 0.8670 (ttt90) REVERT: Y 150 ASP cc_start: 0.9143 (m-30) cc_final: 0.8858 (m-30) REVERT: a 9 GLN cc_start: 0.9020 (mp10) cc_final: 0.8651 (mm-40) REVERT: a 65 LYS cc_start: 0.8253 (mttt) cc_final: 0.7908 (mttt) REVERT: a 66 LYS cc_start: 0.6710 (mmtm) cc_final: 0.6506 (mmtm) REVERT: a 155 LEU cc_start: 0.9056 (mm) cc_final: 0.8766 (mm) REVERT: a 164 TYR cc_start: 0.8181 (m-80) cc_final: 0.7879 (m-80) REVERT: a 196 GLU cc_start: 0.8510 (mm-30) cc_final: 0.7993 (mm-30) REVERT: I 10 TYR cc_start: 0.8985 (m-80) cc_final: 0.8682 (m-80) REVERT: I 50 ARG cc_start: 0.8548 (ttp80) cc_final: 0.8029 (ttp80) REVERT: I 54 PHE cc_start: 0.9072 (m-80) cc_final: 0.8589 (m-80) REVERT: I 68 VAL cc_start: 0.9378 (OUTLIER) cc_final: 0.9164 (p) REVERT: S 11 MET cc_start: 0.9344 (tpp) cc_final: 0.9024 (tpp) REVERT: S 72 LEU cc_start: 0.8939 (mt) cc_final: 0.8735 (mt) REVERT: S 73 TYR cc_start: 0.8226 (t80) cc_final: 0.7850 (t80) outliers start: 88 outliers final: 56 residues processed: 676 average time/residue: 0.2173 time to fit residues: 240.3591 Evaluate side-chains 669 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 602 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 76 PHE Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain S residue 46 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 40 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 332 optimal weight: 0.7980 chunk 317 optimal weight: 1.9990 chunk 434 optimal weight: 8.9990 chunk 132 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 351 optimal weight: 0.9990 chunk 330 optimal weight: 0.6980 chunk 249 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN A 408 GLN X 104 GLN H 104 HIS G 57 HIS F 121 ASN ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.089349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.062809 restraints weight = 77556.449| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.22 r_work: 0.2693 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 37528 Z= 0.128 Angle : 0.564 13.580 50797 Z= 0.288 Chirality : 0.042 0.208 5920 Planarity : 0.004 0.049 6550 Dihedral : 6.425 104.036 5360 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.16 % Allowed : 16.29 % Favored : 81.54 % 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: 1.37 (0.12), residues: 4807 helix: 1.80 (0.10), residues: 2686 sheet: -0.07 (0.22), residues: 542 loop : -0.20 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 115 TYR 0.016 0.001 TYR a 263 PHE 0.030 0.001 PHE I 53 TRP 0.013 0.001 TRP a 111 HIS 0.006 0.001 HIS G 57 Details of bonding type rmsd covalent geometry : bond 0.00292 (37528) covalent geometry : angle 0.56444 (50797) hydrogen bonds : bond 0.04188 ( 2253) hydrogen bonds : angle 4.23557 ( 6579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 615 time to evaluate : 1.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7624 (p0) cc_final: 0.7348 (p0) REVERT: C 230 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: C 422 ASP cc_start: 0.8766 (p0) cc_final: 0.8536 (p0) REVERT: B 418 ARG cc_start: 0.8331 (ttp-170) cc_final: 0.7950 (ttp-170) REVERT: B 463 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8445 (mmmt) REVERT: A 356 GLU cc_start: 0.8642 (tp30) cc_final: 0.8251 (tp30) REVERT: A 408 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8352 (pm20) REVERT: A 418 ARG cc_start: 0.8477 (tpp80) cc_final: 0.8216 (tpp-160) REVERT: X 30 MET cc_start: 0.8167 (mmm) cc_final: 0.7835 (mmm) REVERT: X 64 GLN cc_start: 0.7822 (tt0) cc_final: 0.7499 (pp30) REVERT: X 78 GLN cc_start: 0.8876 (tp40) cc_final: 0.8631 (pp30) REVERT: X 82 ARG cc_start: 0.8346 (tpp-160) cc_final: 0.7967 (tpp-160) REVERT: X 83 ARG cc_start: 0.8005 (ttp80) cc_final: 0.7446 (ttp80) REVERT: X 85 GLN cc_start: 0.7728 (mp10) cc_final: 0.7126 (mt0) REVERT: X 88 ASP cc_start: 0.8600 (m-30) cc_final: 0.8327 (m-30) REVERT: X 98 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7783 (ttt180) REVERT: X 113 ARG cc_start: 0.8499 (ttp-170) cc_final: 0.8225 (ttp80) REVERT: H 20 VAL cc_start: 0.9274 (t) cc_final: 0.8985 (p) REVERT: H 116 GLN cc_start: 0.8964 (mt0) cc_final: 0.8630 (mm-40) REVERT: G 187 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8824 (pp) REVERT: E 200 ASP cc_start: 0.8942 (t0) cc_final: 0.8713 (t0) REVERT: E 301 ASP cc_start: 0.9126 (t0) cc_final: 0.8788 (t0) REVERT: D 97 MET cc_start: 0.9290 (mmm) cc_final: 0.9063 (mtt) REVERT: D 116 TYR cc_start: 0.8452 (OUTLIER) cc_final: 0.7294 (p90) REVERT: D 343 GLN cc_start: 0.9257 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: D 372 ASP cc_start: 0.8444 (p0) cc_final: 0.8100 (p0) REVERT: D 379 MET cc_start: 0.8973 (tpt) cc_final: 0.8651 (tpt) REVERT: L 61 ASP cc_start: 0.9057 (m-30) cc_final: 0.8802 (m-30) REVERT: M 6 MET cc_start: 0.7356 (ttt) cc_final: 0.6724 (tpp) REVERT: M 50 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8377 (ttp-170) REVERT: M 52 GLN cc_start: 0.9192 (mm-40) cc_final: 0.8753 (mm-40) REVERT: N 11 MET cc_start: 0.8946 (tpt) cc_final: 0.8641 (mmt) REVERT: N 42 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8617 (mm-40) REVERT: N 51 THR cc_start: 0.9450 (m) cc_final: 0.8998 (p) REVERT: N 55 ILE cc_start: 0.9418 (mt) cc_final: 0.9192 (mt) REVERT: O 42 GLN cc_start: 0.8303 (mp10) cc_final: 0.7995 (mp10) REVERT: O 46 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8632 (mt) REVERT: O 52 GLN cc_start: 0.9273 (mm110) cc_final: 0.8993 (mm-40) REVERT: O 63 ILE cc_start: 0.9279 (mm) cc_final: 0.8950 (mt) REVERT: O 73 TYR cc_start: 0.8691 (t80) cc_final: 0.8178 (t80) REVERT: P 10 TYR cc_start: 0.8819 (m-80) cc_final: 0.8304 (m-80) REVERT: P 17 MET cc_start: 0.9013 (mtm) cc_final: 0.8778 (mpp) REVERT: Q 10 TYR cc_start: 0.8581 (m-80) cc_final: 0.7945 (m-80) REVERT: Q 37 GLU cc_start: 0.9094 (tp30) cc_final: 0.8832 (tp30) REVERT: Q 65 MET cc_start: 0.8887 (mmm) cc_final: 0.8594 (mmm) REVERT: R 44 ASP cc_start: 0.8763 (t70) cc_final: 0.8435 (t70) REVERT: Y 1 MET cc_start: 0.5223 (tmm) cc_final: 0.4908 (tmm) REVERT: Y 73 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7364 (mm110) REVERT: Y 80 ASN cc_start: 0.8562 (m-40) cc_final: 0.8164 (m110) REVERT: Y 117 ARG cc_start: 0.8896 (ttt-90) cc_final: 0.8646 (ttt90) REVERT: Y 147 ASP cc_start: 0.9092 (p0) cc_final: 0.8845 (p0) REVERT: Y 150 ASP cc_start: 0.9142 (m-30) cc_final: 0.8816 (m-30) REVERT: a 9 GLN cc_start: 0.9043 (mp10) cc_final: 0.8676 (mm-40) REVERT: a 65 LYS cc_start: 0.8353 (mttt) cc_final: 0.8063 (mttt) REVERT: a 155 LEU cc_start: 0.9048 (mm) cc_final: 0.8761 (mm) REVERT: a 164 TYR cc_start: 0.8131 (m-80) cc_final: 0.7816 (m-80) REVERT: a 196 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7983 (mm-30) REVERT: I 10 TYR cc_start: 0.8882 (m-80) cc_final: 0.8643 (m-80) REVERT: I 50 ARG cc_start: 0.8498 (ttp80) cc_final: 0.7940 (ttp80) REVERT: I 54 PHE cc_start: 0.9066 (m-80) cc_final: 0.8533 (m-80) REVERT: I 57 MET cc_start: 0.9225 (tmm) cc_final: 0.8263 (tmm) REVERT: I 61 ASP cc_start: 0.9039 (t70) cc_final: 0.8663 (p0) REVERT: S 11 MET cc_start: 0.9348 (tpp) cc_final: 0.9019 (tpp) REVERT: S 72 LEU cc_start: 0.8962 (mt) cc_final: 0.8760 (mt) REVERT: S 73 TYR cc_start: 0.8220 (t80) cc_final: 0.7858 (t80) outliers start: 83 outliers final: 58 residues processed: 661 average time/residue: 0.2174 time to fit residues: 236.2946 Evaluate side-chains 663 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 597 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 129 ARG Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 63 ILE Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 76 PHE Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain S residue 46 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 179 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 242 optimal weight: 7.9990 chunk 352 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 349 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 GLN A 408 GLN F 121 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.089668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.063308 restraints weight = 78684.496| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.17 r_work: 0.2696 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2569 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 37528 Z= 0.134 Angle : 0.576 13.021 50797 Z= 0.293 Chirality : 0.043 0.214 5920 Planarity : 0.004 0.050 6550 Dihedral : 6.357 103.200 5360 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.14 % Allowed : 16.76 % Favored : 81.10 % 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: 1.41 (0.12), residues: 4807 helix: 1.82 (0.10), residues: 2689 sheet: -0.03 (0.22), residues: 532 loop : -0.17 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 83 TYR 0.032 0.001 TYR a 263 PHE 0.030 0.001 PHE I 53 TRP 0.014 0.001 TRP a 111 HIS 0.006 0.001 HIS a 245 Details of bonding type rmsd covalent geometry : bond 0.00309 (37528) covalent geometry : angle 0.57634 (50797) hydrogen bonds : bond 0.04189 ( 2253) hydrogen bonds : angle 4.23174 ( 6579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 611 time to evaluate : 1.401 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: W 156 ASP cc_start: 0.7639 (p0) cc_final: 0.7365 (p0) REVERT: C 230 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8571 (mt-10) REVERT: C 422 ASP cc_start: 0.8785 (p0) cc_final: 0.8557 (p0) REVERT: B 418 ARG cc_start: 0.8357 (ttp-170) cc_final: 0.7969 (ttp-170) REVERT: B 463 LYS cc_start: 0.8845 (mmtt) cc_final: 0.8464 (mmmt) REVERT: A 356 GLU cc_start: 0.8666 (tp30) cc_final: 0.8326 (tp30) REVERT: A 408 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8212 (pm20) REVERT: A 418 ARG cc_start: 0.8513 (tpp80) cc_final: 0.8286 (tpp-160) REVERT: X 10 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8386 (tp-100) REVERT: X 30 MET cc_start: 0.8208 (mmm) cc_final: 0.7903 (mmm) REVERT: X 64 GLN cc_start: 0.7835 (tt0) cc_final: 0.7529 (pp30) REVERT: X 78 GLN cc_start: 0.8872 (tp40) cc_final: 0.8663 (pp30) REVERT: X 88 ASP cc_start: 0.8653 (m-30) cc_final: 0.8398 (m-30) REVERT: X 98 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7818 (ttt180) REVERT: X 113 ARG cc_start: 0.8520 (ttp-170) cc_final: 0.8239 (ttp80) REVERT: H 20 VAL cc_start: 0.9335 (t) cc_final: 0.9073 (p) REVERT: H 116 GLN cc_start: 0.8985 (mt0) cc_final: 0.8670 (mm-40) REVERT: G 187 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8845 (pp) REVERT: F 58 SER cc_start: 0.9589 (OUTLIER) cc_final: 0.9259 (p) REVERT: F 79 VAL cc_start: 0.9364 (OUTLIER) cc_final: 0.9053 (m) REVERT: F 193 MET cc_start: 0.8703 (mmp) cc_final: 0.8384 (mmp) REVERT: E 200 ASP cc_start: 0.8889 (t0) cc_final: 0.8658 (t0) REVERT: E 301 ASP cc_start: 0.9098 (t0) cc_final: 0.8759 (t0) REVERT: D 116 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.7333 (p90) REVERT: D 343 GLN cc_start: 0.9242 (OUTLIER) cc_final: 0.8378 (mp10) REVERT: D 372 ASP cc_start: 0.8433 (p0) cc_final: 0.8091 (p0) REVERT: D 379 MET cc_start: 0.9016 (tpt) cc_final: 0.8710 (tpt) REVERT: L 37 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: L 61 ASP cc_start: 0.9072 (m-30) cc_final: 0.8802 (m-30) REVERT: M 6 MET cc_start: 0.7303 (ttt) cc_final: 0.6772 (tpp) REVERT: M 7 ASP cc_start: 0.8258 (m-30) cc_final: 0.8050 (m-30) REVERT: M 50 ARG cc_start: 0.8817 (ttm110) cc_final: 0.8357 (ttp-170) REVERT: M 52 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8757 (mm-40) REVERT: N 11 MET cc_start: 0.8951 (tpt) cc_final: 0.8641 (mmt) REVERT: N 16 MET cc_start: 0.8737 (mmm) cc_final: 0.8516 (mmm) REVERT: N 42 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8628 (mm-40) REVERT: N 51 THR cc_start: 0.9441 (m) cc_final: 0.8972 (p) REVERT: N 52 GLN cc_start: 0.9448 (mm110) cc_final: 0.9225 (mm110) REVERT: N 55 ILE cc_start: 0.9418 (mt) cc_final: 0.9141 (mt) REVERT: O 16 MET cc_start: 0.8900 (ttp) cc_final: 0.8524 (tpp) REVERT: O 42 GLN cc_start: 0.8328 (mp10) cc_final: 0.7892 (mp10) REVERT: O 46 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8731 (mt) REVERT: O 52 GLN cc_start: 0.9274 (mm110) cc_final: 0.8985 (mm-40) REVERT: O 63 ILE cc_start: 0.9311 (mm) cc_final: 0.9002 (mt) REVERT: O 73 TYR cc_start: 0.8679 (t80) cc_final: 0.8148 (t80) REVERT: P 10 TYR cc_start: 0.8835 (m-80) cc_final: 0.8289 (m-80) REVERT: Q 10 TYR cc_start: 0.8577 (m-80) cc_final: 0.7947 (m-80) REVERT: Q 37 GLU cc_start: 0.9123 (tp30) cc_final: 0.8874 (tp30) REVERT: Q 61 ASP cc_start: 0.9109 (t0) cc_final: 0.8692 (t0) REVERT: Q 65 MET cc_start: 0.8847 (mmm) cc_final: 0.8525 (mmm) REVERT: R 44 ASP cc_start: 0.8741 (t70) cc_final: 0.8431 (t70) REVERT: Y 1 MET cc_start: 0.4903 (tmm) cc_final: 0.4611 (tmm) REVERT: Y 73 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7364 (mm110) REVERT: Y 80 ASN cc_start: 0.8607 (m-40) cc_final: 0.8202 (m110) REVERT: Y 117 ARG cc_start: 0.8934 (ttt-90) cc_final: 0.8687 (ttt90) REVERT: Y 147 ASP cc_start: 0.9104 (p0) cc_final: 0.8847 (p0) REVERT: Y 150 ASP cc_start: 0.9106 (m-30) cc_final: 0.8813 (m-30) REVERT: a 9 GLN cc_start: 0.9082 (mp10) cc_final: 0.8675 (mm-40) REVERT: a 65 LYS cc_start: 0.8388 (mttt) cc_final: 0.8138 (mttt) REVERT: a 155 LEU cc_start: 0.9033 (mm) cc_final: 0.8739 (mm) REVERT: a 164 TYR cc_start: 0.8148 (m-80) cc_final: 0.7841 (m-80) REVERT: a 196 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8012 (mm-30) REVERT: I 10 TYR cc_start: 0.8882 (m-80) cc_final: 0.8645 (m-80) REVERT: I 50 ARG cc_start: 0.8557 (ttp80) cc_final: 0.7978 (ttp80) REVERT: I 54 PHE cc_start: 0.9035 (m-80) cc_final: 0.8496 (m-80) REVERT: S 6 MET cc_start: 0.8776 (mmm) cc_final: 0.8575 (tpp) REVERT: S 11 MET cc_start: 0.9329 (tpp) cc_final: 0.9025 (tpp) REVERT: S 72 LEU cc_start: 0.8929 (mt) cc_final: 0.8720 (mt) REVERT: S 73 TYR cc_start: 0.8227 (t80) cc_final: 0.7882 (t80) outliers start: 82 outliers final: 59 residues processed: 660 average time/residue: 0.2173 time to fit residues: 236.4163 Evaluate side-chains 666 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 596 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 98 ARG Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 76 PHE Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 6 MET Chi-restraints excluded: chain a residue 99 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 317 optimal weight: 0.8980 chunk 283 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 289 optimal weight: 2.9990 chunk 281 optimal weight: 1.9990 chunk 258 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 395 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 432 optimal weight: 4.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN X 104 GLN F 121 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.062738 restraints weight = 77764.958| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.23 r_work: 0.2684 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 37528 Z= 0.141 Angle : 0.583 12.164 50797 Z= 0.297 Chirality : 0.043 0.255 5920 Planarity : 0.004 0.050 6550 Dihedral : 6.314 102.788 5360 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.09 % Allowed : 17.15 % Favored : 80.76 % 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: 1.43 (0.12), residues: 4807 helix: 1.83 (0.10), residues: 2687 sheet: 0.00 (0.22), residues: 522 loop : -0.17 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 83 TYR 0.019 0.001 TYR A 308 PHE 0.029 0.001 PHE I 53 TRP 0.017 0.001 TRP a 111 HIS 0.006 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00332 (37528) covalent geometry : angle 0.58290 (50797) hydrogen bonds : bond 0.04204 ( 2253) hydrogen bonds : angle 4.23608 ( 6579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9614 Ramachandran restraints generated. 4807 Oldfield, 0 Emsley, 4807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 610 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 156 ASP cc_start: 0.7630 (p0) cc_final: 0.7350 (p0) REVERT: C 230 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: C 422 ASP cc_start: 0.8781 (p0) cc_final: 0.8555 (p0) REVERT: B 418 ARG cc_start: 0.8314 (ttp-170) cc_final: 0.7949 (ttp-170) REVERT: B 463 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8444 (mmmt) REVERT: A 356 GLU cc_start: 0.8644 (tp30) cc_final: 0.8279 (tp30) REVERT: A 408 GLN cc_start: 0.8677 (OUTLIER) cc_final: 0.8173 (pm20) REVERT: A 418 ARG cc_start: 0.8458 (tpp80) cc_final: 0.8199 (tpp-160) REVERT: X 64 GLN cc_start: 0.7717 (tt0) cc_final: 0.7400 (pp30) REVERT: X 78 GLN cc_start: 0.8863 (tp40) cc_final: 0.8612 (pp30) REVERT: X 85 GLN cc_start: 0.7760 (mp10) cc_final: 0.7183 (mt0) REVERT: X 88 ASP cc_start: 0.8554 (m-30) cc_final: 0.8307 (m-30) REVERT: X 113 ARG cc_start: 0.8524 (ttp-170) cc_final: 0.8176 (ttp80) REVERT: H 20 VAL cc_start: 0.9325 (t) cc_final: 0.9052 (p) REVERT: H 116 GLN cc_start: 0.8973 (mt0) cc_final: 0.8640 (mm-40) REVERT: G 187 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8834 (pp) REVERT: F 58 SER cc_start: 0.9602 (OUTLIER) cc_final: 0.9255 (p) REVERT: F 79 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9061 (m) REVERT: E 200 ASP cc_start: 0.8935 (t0) cc_final: 0.8706 (t0) REVERT: E 301 ASP cc_start: 0.9096 (t0) cc_final: 0.8765 (t0) REVERT: D 116 TYR cc_start: 0.8469 (OUTLIER) cc_final: 0.7329 (p90) REVERT: D 343 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.8338 (mp10) REVERT: D 372 ASP cc_start: 0.8453 (p0) cc_final: 0.8103 (p0) REVERT: D 379 MET cc_start: 0.9019 (tpt) cc_final: 0.8703 (tpt) REVERT: L 37 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8631 (tp30) REVERT: L 57 MET cc_start: 0.9098 (tmm) cc_final: 0.8407 (tmm) REVERT: M 6 MET cc_start: 0.7424 (ttt) cc_final: 0.6930 (tpp) REVERT: M 50 ARG cc_start: 0.8807 (ttm110) cc_final: 0.8346 (ttp-170) REVERT: N 11 MET cc_start: 0.8964 (tpt) cc_final: 0.8671 (mmt) REVERT: N 42 GLN cc_start: 0.8873 (mm-40) cc_final: 0.8633 (mm-40) REVERT: N 50 ARG cc_start: 0.8932 (ttp80) cc_final: 0.8692 (ttp80) REVERT: N 51 THR cc_start: 0.9437 (m) cc_final: 0.8983 (p) REVERT: N 52 GLN cc_start: 0.9437 (mm110) cc_final: 0.9218 (mm110) REVERT: N 55 ILE cc_start: 0.9390 (mt) cc_final: 0.9111 (mt) REVERT: O 16 MET cc_start: 0.8897 (ttp) cc_final: 0.8540 (tpp) REVERT: O 17 MET cc_start: 0.9202 (mmm) cc_final: 0.8995 (mmm) REVERT: O 42 GLN cc_start: 0.8319 (mp10) cc_final: 0.7886 (mp10) REVERT: O 46 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8749 (mt) REVERT: O 52 GLN cc_start: 0.9285 (mm110) cc_final: 0.9025 (mm-40) REVERT: O 63 ILE cc_start: 0.9301 (mm) cc_final: 0.8996 (mt) REVERT: O 73 TYR cc_start: 0.8662 (t80) cc_final: 0.8152 (t80) REVERT: P 10 TYR cc_start: 0.8908 (m-80) cc_final: 0.8463 (m-80) REVERT: Q 10 TYR cc_start: 0.8594 (m-80) cc_final: 0.7967 (m-80) REVERT: Q 37 GLU cc_start: 0.9096 (tp30) cc_final: 0.8849 (tp30) REVERT: Q 61 ASP cc_start: 0.9129 (t0) cc_final: 0.8676 (t0) REVERT: Q 65 MET cc_start: 0.8857 (mmm) cc_final: 0.8544 (mmm) REVERT: R 44 ASP cc_start: 0.8795 (t70) cc_final: 0.8487 (t70) REVERT: Y 1 MET cc_start: 0.4707 (tmm) cc_final: 0.4250 (tmm) REVERT: Y 73 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7434 (mm110) REVERT: Y 80 ASN cc_start: 0.8558 (m-40) cc_final: 0.8167 (m110) REVERT: Y 117 ARG cc_start: 0.8915 (ttt-90) cc_final: 0.8663 (ttt90) REVERT: Y 147 ASP cc_start: 0.9120 (p0) cc_final: 0.8870 (p0) REVERT: Y 150 ASP cc_start: 0.9157 (m-30) cc_final: 0.8837 (m-30) REVERT: a 9 GLN cc_start: 0.9084 (mp10) cc_final: 0.8662 (mm-40) REVERT: a 65 LYS cc_start: 0.8329 (mttt) cc_final: 0.8084 (mttt) REVERT: a 155 LEU cc_start: 0.9037 (mm) cc_final: 0.8748 (mm) REVERT: a 164 TYR cc_start: 0.8207 (m-80) cc_final: 0.7845 (m-80) REVERT: a 196 GLU cc_start: 0.8517 (mm-30) cc_final: 0.7989 (mm-30) REVERT: I 10 TYR cc_start: 0.8943 (m-80) cc_final: 0.8663 (m-80) REVERT: I 16 MET cc_start: 0.8841 (ttp) cc_final: 0.8589 (ttt) REVERT: I 50 ARG cc_start: 0.8514 (ttp80) cc_final: 0.7938 (ttp80) REVERT: I 54 PHE cc_start: 0.9083 (m-80) cc_final: 0.8527 (m-80) REVERT: I 61 ASP cc_start: 0.8950 (t0) cc_final: 0.8531 (t70) REVERT: I 70 LEU cc_start: 0.8951 (tp) cc_final: 0.8687 (tp) REVERT: S 11 MET cc_start: 0.9383 (tpp) cc_final: 0.9055 (tpp) REVERT: S 72 LEU cc_start: 0.8980 (mt) cc_final: 0.8755 (mt) REVERT: S 73 TYR cc_start: 0.8220 (t80) cc_final: 0.7887 (t80) outliers start: 80 outliers final: 61 residues processed: 659 average time/residue: 0.2190 time to fit residues: 237.2875 Evaluate side-chains 663 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 592 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 501 LYS Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 476 ASP Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain X residue 46 SER Chi-restraints excluded: chain X residue 63 ASP Chi-restraints excluded: chain X residue 153 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain H residue 32 LEU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 145 LEU Chi-restraints excluded: chain G residue 187 LEU Chi-restraints excluded: chain G residue 190 LEU Chi-restraints excluded: chain G residue 198 LEU Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 58 SER Chi-restraints excluded: chain F residue 68 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 277 VAL Chi-restraints excluded: chain F residue 278 LEU Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain F residue 340 THR Chi-restraints excluded: chain F residue 385 GLU Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 194 THR Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain E residue 373 ILE Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain E residue 459 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 343 GLN Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain L residue 37 GLU Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain M residue 4 LEU Chi-restraints excluded: chain N residue 37 GLU Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 76 PHE Chi-restraints excluded: chain P residue 37 GLU Chi-restraints excluded: chain Q residue 46 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 68 VAL Chi-restraints excluded: chain R residue 46 ILE Chi-restraints excluded: chain Y residue 25 VAL Chi-restraints excluded: chain Y residue 60 SER Chi-restraints excluded: chain Y residue 73 GLN Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain a residue 99 LYS Chi-restraints excluded: chain I residue 8 LEU Chi-restraints excluded: chain I residue 52 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 473 random chunks: chunk 389 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 225 optimal weight: 5.9990 chunk 402 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 188 optimal weight: 4.9990 chunk 238 optimal weight: 4.9990 chunk 422 optimal weight: 2.9990 chunk 303 optimal weight: 0.8980 chunk 216 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 67 GLN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 ASN ** D 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 52 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.089247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.062563 restraints weight = 77974.462| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.25 r_work: 0.2682 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2553 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.230 37528 Z= 0.185 Angle : 0.679 59.177 50797 Z= 0.366 Chirality : 0.043 0.366 5920 Planarity : 0.004 0.069 6550 Dihedral : 6.312 102.793 5360 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.09 % Allowed : 17.18 % Favored : 80.74 % Cbeta Deviations : 0.02 % 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: 1.42 (0.12), residues: 4807 helix: 1.83 (0.10), residues: 2687 sheet: 0.01 (0.22), residues: 522 loop : -0.17 (0.16), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG X 83 TYR 0.075 0.001 TYR a 263 PHE 0.027 0.001 PHE I 53 TRP 0.016 0.001 TRP a 111 HIS 0.006 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00414 (37528) covalent geometry : angle 0.67895 (50797) hydrogen bonds : bond 0.04230 ( 2253) hydrogen bonds : angle 4.23924 ( 6579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11570.45 seconds wall clock time: 197 minutes 17.30 seconds (11837.30 seconds total)