Starting phenix.real_space_refine on Sat Mar 7 02:45:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6oqv_20171/03_2026/6oqv_20171_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6oqv_20171/03_2026/6oqv_20171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6oqv_20171/03_2026/6oqv_20171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6oqv_20171/03_2026/6oqv_20171.map" model { file = "/net/cci-nas-00/data/ceres_data/6oqv_20171/03_2026/6oqv_20171_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6oqv_20171/03_2026/6oqv_20171_neut.cif" } resolution = 3.3 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 277 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: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 3877 Classifications: {'peptide': 513} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 494} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3846 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} 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: 3849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 3849 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 491} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "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: "I" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "J" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "L" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "M" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "N" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "O" Number of atoms: 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: "S" Number of atoms: 557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 557 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 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: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.48, per 1000 atoms: 0.23 Number of scatterers: 36971 At special positions: 0 Unit cell: (184.509, 214.721, 132.717, 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: 2.75 Conformation dependent library (CDL) restraints added in 1.2 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: 210 helices and 25 sheets defined 61.9% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'W' and resid 3 through 21 Proline residue: W 9 - end of helix Processing helix chain 'W' and resid 23 through 39 removed outlier: 3.924A pdb=" N ASP W 29 " --> pdb=" O GLU W 25 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR W 38 " --> pdb=" O ALA W 34 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS W 39 " --> pdb=" O ALA W 35 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 49 removed outlier: 3.705A pdb=" N GLU W 45 " --> pdb=" O GLU W 41 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 removed outlier: 3.850A 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 104 removed outlier: 3.692A pdb=" N GLU W 93 " --> pdb=" O PRO W 89 " (cutoff:3.500A) Processing helix chain 'W' and resid 119 through 132 Processing helix chain 'W' and resid 163 through 172 removed outlier: 3.708A pdb=" N ARG W 169 " --> pdb=" O GLY W 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 18 removed outlier: 3.852A pdb=" N ILE C 8 " --> pdb=" O ASN C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 139 removed outlier: 3.623A pdb=" N ARG C 139 " --> pdb=" O VAL C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 157 removed outlier: 3.515A pdb=" N SER C 155 " --> pdb=" O LYS C 151 " (cutoff:3.500A) removed outlier: 3.953A 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: 3.903A pdb=" N ASN C 207 " --> pdb=" O SER C 203 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 219 removed outlier: 3.768A pdb=" N ALA C 219 " --> pdb=" O GLY C 216 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 216 through 219' Processing helix chain 'C' and resid 231 through 251 Proline residue: C 239 - end of helix removed outlier: 3.656A pdb=" N TYR C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE C 249 " --> pdb=" O MET C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 4.090A pdb=" N VAL C 268 " --> pdb=" O SER C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 removed outlier: 3.518A pdb=" N ALA C 285 " --> pdb=" O GLY C 282 " (cutoff:3.500A) 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: 3.657A pdb=" N HIS C 294 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG C 296 " --> pdb=" O TYR C 292 " (cutoff:3.500A) removed outlier: 3.868A 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: 3.742A pdb=" N SER C 347 " --> pdb=" O THR C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 377 through 382 removed outlier: 3.516A pdb=" N ALA C 380 " --> pdb=" O VAL C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 404 removed outlier: 4.033A pdb=" N GLY C 391 " --> pdb=" O LYS C 387 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ILE C 393 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 413 removed outlier: 4.006A pdb=" N GLN C 408 " --> pdb=" O ALA C 405 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N SER C 411 " --> pdb=" O GLN C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 431 removed outlier: 4.777A pdb=" N GLN C 420 " --> pdb=" O ALA C 416 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN C 425 " --> pdb=" O LEU C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 440 through 453 removed outlier: 3.590A pdb=" N ALA C 451 " --> pdb=" O VAL C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 458 removed outlier: 4.124A 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: 3.711A pdb=" N MET C 483 " --> pdb=" O HIS C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 511 removed outlier: 3.513A pdb=" N ALA C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 19 removed outlier: 3.506A pdb=" N SER B 9 " --> pdb=" O SER B 5 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N LYS B 13 " --> pdb=" O SER B 9 " (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 185 Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 201 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 231 through 251 Proline residue: B 239 - end of helix removed outlier: 3.745A pdb=" N TYR B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N PHE B 249 " --> pdb=" O MET B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 277 removed outlier: 3.777A pdb=" N GLN B 266 " --> pdb=" O ASP B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.873A pdb=" N HIS B 294 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 3.735A 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: 3.520A pdb=" N ALA B 380 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 391 Processing helix chain 'B' and resid 392 through 407 removed outlier: 3.736A pdb=" N ALA B 405 " --> pdb=" O ARG B 401 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N PHE B 406 " --> pdb=" O GLU B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 431 Processing helix chain 'B' and resid 440 through 453 removed outlier: 3.567A pdb=" N SER B 445 " --> pdb=" O VAL B 441 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA B 451 " --> pdb=" O VAL B 447 " (cutoff:3.500A) 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 510 Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 100 through 104 Processing helix chain 'A' and resid 135 through 139 removed outlier: 3.806A pdb=" N ARG A 139 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 157 removed outlier: 3.537A pdb=" N MET A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 185 removed outlier: 3.757A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 189 Processing helix chain 'A' and resid 201 through 215 removed outlier: 3.557A pdb=" N ILE A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 231 through 251 Proline residue: A 239 - end of helix removed outlier: 4.083A pdb=" N PHE A 249 " --> pdb=" O MET A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.665A pdb=" N GLN A 266 " --> pdb=" O ASP A 262 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL A 268 " --> pdb=" O SER A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.521A pdb=" N HIS A 294 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 296 " --> pdb=" O TYR A 292 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 339 through 347 Processing helix chain 'A' and resid 356 through 362 Processing helix chain 'A' and resid 377 through 382 removed outlier: 4.017A 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 408 removed outlier: 3.918A pdb=" N GLU A 402 " --> pdb=" O ALA A 398 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 405 " --> pdb=" O ARG A 401 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLN A 408 " --> pdb=" O ALA A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 432 removed outlier: 4.211A pdb=" N GLN A 420 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LYS A 432 " --> pdb=" O THR A 428 " (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: 3.728A pdb=" N ARG A 477 " --> pdb=" O ALA A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.658A pdb=" N GLU A 485 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN A 488 " --> pdb=" O GLN A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 Processing helix chain 'X' and resid 5 through 23 removed outlier: 3.841A pdb=" N GLY X 9 " --> pdb=" O ALA X 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 42 removed outlier: 3.750A pdb=" N ALA X 32 " --> pdb=" O PRO X 28 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 49 removed outlier: 4.341A pdb=" N ALA X 47 " --> pdb=" O GLY X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 137 removed outlier: 4.223A pdb=" N ASP X 55 " --> pdb=" O HIS X 51 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU X 56 " --> pdb=" O LYS X 52 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU X 77 " --> pdb=" O GLN X 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN X 78 " --> pdb=" O VAL X 74 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA X 79 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU X 97 " --> pdb=" O GLU X 93 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS X 100 " --> pdb=" O GLN X 96 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ALA X 103 " --> pdb=" O THR X 99 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU X 110 " --> pdb=" O GLN X 106 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA X 111 " --> pdb=" O ALA X 107 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS X 114 " --> pdb=" O GLU X 110 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ARG X 121 " --> pdb=" O ARG X 117 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS X 122 " --> pdb=" O GLU X 118 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLN X 123 " --> pdb=" O GLU X 119 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA X 125 " --> pdb=" O ARG X 121 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ILE X 126 " --> pdb=" O LYS X 122 " (cutoff:3.500A) Processing helix chain 'X' and resid 144 through 155 removed outlier: 4.089A pdb=" N ILE X 148 " --> pdb=" O ALA X 144 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA X 154 " --> pdb=" O ASP X 150 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLU X 155 " --> pdb=" O LYS X 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 104 removed outlier: 3.658A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA H 101 " --> pdb=" O ALA H 97 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU H 102 " --> pdb=" O LYS H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 129 through 134 removed outlier: 3.666A pdb=" N LEU H 133 " --> pdb=" O ARG H 129 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 40 removed outlier: 3.887A pdb=" N SER G 8 " --> pdb=" O LYS G 4 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 56 removed outlier: 3.757A pdb=" N ALA G 45 " --> pdb=" O SER G 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 68 removed outlier: 3.615A pdb=" N GLU G 68 " --> pdb=" O PRO G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 107 Processing helix chain 'G' and resid 118 through 128 removed outlier: 3.693A pdb=" N VAL G 122 " --> pdb=" O GLY G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 3.627A pdb=" N LEU G 148 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 4.746A 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: 4.041A pdb=" N SER G 202 " --> pdb=" O LYS G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 281 removed outlier: 3.579A pdb=" N LEU G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR G 217 " --> pdb=" O ALA G 213 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS G 258 " --> pdb=" O GLY G 254 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU G 262 " --> pdb=" O LYS G 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 115 through 119 removed outlier: 3.519A 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 168 removed outlier: 3.918A pdb=" N ILE F 168 " --> pdb=" O ARG F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 195 removed outlier: 3.569A pdb=" N GLY F 186 " --> pdb=" O ARG F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 196 through 197 No H-bonds generated for 'chain 'F' and resid 196 through 197' 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: 3.578A pdb=" N ARG F 216 " --> pdb=" O PRO F 212 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N ALA F 220 " --> pdb=" O ARG F 216 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU F 221 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N THR F 222 " --> pdb=" O ARG F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.916A pdb=" N THR F 248 " --> pdb=" O ILE F 244 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL F 254 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 4.238A 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: 4.029A 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 350 Processing helix chain 'F' and resid 350 through 369 Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 379 through 382 removed outlier: 3.652A pdb=" N LEU F 382 " --> pdb=" O MET F 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 379 through 382' Processing helix chain 'F' and resid 385 through 400 removed outlier: 3.717A pdb=" N LYS F 395 " --> pdb=" O ALA F 391 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG F 398 " --> pdb=" O ARG F 394 " (cutoff:3.500A) 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: 3.651A pdb=" N ARG F 425 " --> pdb=" O LYS F 421 " (cutoff:3.500A) removed outlier: 3.948A 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 458 removed outlier: 3.691A pdb=" N ALA F 452 " --> pdb=" O SER F 448 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS F 457 " --> pdb=" O VAL F 453 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS F 458 " --> pdb=" O GLU F 454 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 115 through 119 removed outlier: 3.584A pdb=" N LEU E 119 " --> pdb=" O TYR E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 137 Processing helix chain 'E' and resid 154 through 169 removed outlier: 3.504A pdb=" N ALA E 167 " --> pdb=" O ILE E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 198 through 200 No H-bonds generated for 'chain 'E' and resid 198 through 200' Processing helix chain 'E' and resid 212 through 233 removed outlier: 3.589A pdb=" N ARG E 216 " --> pdb=" O PRO E 212 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ALA E 220 " --> pdb=" O ARG E 216 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 259 removed outlier: 3.561A pdb=" N TYR E 247 " --> pdb=" O ASN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 removed outlier: 3.591A pdb=" N GLY E 276 " --> pdb=" O ALA E 272 " (cutoff:3.500A) removed outlier: 3.773A 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: 3.940A pdb=" N ALA E 313 " --> pdb=" O ALA E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 328 Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 350 through 378 removed outlier: 4.323A pdb=" N GLU E 369 " --> pdb=" O GLN E 365 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP E 372 " --> pdb=" O GLN E 368 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA E 375 " --> pdb=" O LYS E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 382 Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.731A pdb=" N VAL E 389 " --> pdb=" O GLU E 385 " (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: 4.245A 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: 5.023A pdb=" N ALA D 220 " --> pdb=" O ARG D 216 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 258 removed outlier: 3.608A pdb=" N TYR D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 280 removed outlier: 3.569A pdb=" N GLY D 276 " --> pdb=" O ALA D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 299 through 302 Processing helix chain 'D' and resid 305 through 312 removed outlier: 3.517A pdb=" N THR D 311 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 312 " --> pdb=" O PRO D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 315 No H-bonds generated for 'chain 'D' and resid 313 through 315' Processing helix chain 'D' and resid 322 through 328 Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 350 through 378 removed outlier: 3.698A pdb=" N GLU D 369 " --> pdb=" O GLN D 365 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP D 372 " --> pdb=" O GLN D 368 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE D 373 " --> pdb=" O GLU D 369 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE D 376 " --> pdb=" O ASP D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 379 through 382 Processing helix chain 'D' and resid 383 through 400 Processing helix chain 'D' and resid 407 through 412 Processing helix chain 'D' and resid 419 through 433 Processing helix chain 'D' and resid 439 through 444 Processing helix chain 'D' and resid 448 through 459 removed outlier: 3.613A pdb=" N ALA D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LYS D 458 " --> pdb=" O GLU D 454 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 Processing helix chain 'I' and resid 8 through 42 removed outlier: 3.615A pdb=" N ALA I 12 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE I 22 " --> pdb=" O GLY I 18 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 61 removed outlier: 4.108A pdb=" N LEU I 59 " --> pdb=" O ILE I 55 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL I 60 " --> pdb=" O VAL I 56 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP I 61 " --> pdb=" O MET I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 77 removed outlier: 3.586A pdb=" N ILE I 66 " --> pdb=" O ALA I 62 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N MET I 75 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 42 removed outlier: 3.661A pdb=" N LEU J 8 " --> pdb=" O LEU J 4 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 61 removed outlier: 4.148A pdb=" N LEU J 59 " --> pdb=" O ILE J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 77 removed outlier: 3.614A pdb=" N LEU J 72 " --> pdb=" O VAL J 68 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 42 removed outlier: 4.517A pdb=" N LEU L 8 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU L 9 " --> pdb=" O ASN L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 45 through 61 removed outlier: 3.525A pdb=" N LEU L 59 " --> pdb=" O ILE L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 61 through 77 Processing helix chain 'M' and resid 4 through 42 removed outlier: 4.045A pdb=" N LEU M 8 " --> pdb=" O LEU M 4 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA M 20 " --> pdb=" O MET M 16 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS M 34 " --> pdb=" O ILE M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 61 removed outlier: 4.789A pdb=" N LEU M 59 " --> pdb=" O ILE M 55 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL M 60 " --> pdb=" O VAL M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 78 Processing helix chain 'N' and resid 3 through 6 Processing helix chain 'N' and resid 7 through 42 removed outlier: 3.951A pdb=" N MET N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) Processing helix chain 'N' and resid 45 through 61 removed outlier: 3.630A pdb=" N GLY N 58 " --> pdb=" O PHE N 54 " (cutoff:3.500A) removed outlier: 3.696A 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 4 through 42 removed outlier: 3.835A pdb=" N LEU O 8 " --> pdb=" O LEU O 4 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU O 9 " --> pdb=" O ASN O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 61 removed outlier: 3.755A pdb=" N PHE O 54 " --> pdb=" O ARG O 50 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE O 55 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL O 56 " --> pdb=" O GLN O 52 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU O 59 " --> pdb=" O ILE O 55 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP O 61 " --> pdb=" O MET O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 76 removed outlier: 3.724A pdb=" N GLY O 69 " --> pdb=" O MET O 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 42 removed outlier: 3.510A pdb=" N TYR P 10 " --> pdb=" O MET P 6 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 63 removed outlier: 3.737A pdb=" N GLY P 58 " --> pdb=" O PHE P 54 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N LEU P 59 " --> pdb=" O ILE P 55 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL P 60 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP P 61 " --> pdb=" O MET P 57 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE P 63 " --> pdb=" O LEU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 77 removed outlier: 3.552A pdb=" N ALA P 67 " --> pdb=" O ILE P 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 42 removed outlier: 4.149A pdb=" N LEU Q 9 " --> pdb=" O ASN Q 5 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR Q 10 " --> pdb=" O MET Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 77 removed outlier: 4.046A pdb=" N LEU Q 59 " --> pdb=" O ILE Q 55 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA Q 62 " --> pdb=" O GLY Q 58 " (cutoff:3.500A) removed outlier: 4.813A 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 4 through 42 removed outlier: 3.875A pdb=" N LEU R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS R 34 " --> pdb=" O ILE R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 45 through 61 removed outlier: 4.320A pdb=" N LEU R 59 " --> pdb=" O ILE R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 61 through 78 Processing helix chain 'S' and resid 6 through 42 removed outlier: 3.763A pdb=" N TYR S 10 " --> pdb=" O MET S 6 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA S 21 " --> pdb=" O MET S 17 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU S 31 " --> pdb=" O GLY S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 45 through 61 removed outlier: 3.932A pdb=" N LEU S 59 " --> pdb=" O ILE S 55 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP S 61 " --> pdb=" O MET S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 61 through 76 Processing helix chain 'Y' and resid 2 through 25 removed outlier: 3.844A pdb=" N LYS Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 140 removed outlier: 3.844A pdb=" N LEU Y 29 " --> pdb=" O VAL Y 25 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA Y 47 " --> pdb=" O GLY Y 43 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP Y 55 " --> pdb=" O HIS Y 51 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER Y 60 " --> pdb=" O LEU Y 56 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU Y 65 " --> pdb=" O ALA Y 61 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS Y 66 " --> pdb=" O THR Y 62 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE Y 76 " --> pdb=" O ALA Y 72 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS Y 81 " --> pdb=" O GLU Y 77 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS Y 91 " --> pdb=" O LEU Y 87 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG Y 98 " --> pdb=" O ALA Y 94 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLN Y 123 " --> pdb=" O GLU Y 119 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG Y 138 " --> pdb=" O LYS Y 134 " (cutoff:3.500A) Processing helix chain 'Y' and resid 141 through 156 Processing helix chain 'a' and resid 7 through 15 removed outlier: 5.144A pdb=" N GLY a 13 " --> pdb=" O GLN a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 65 removed outlier: 3.722A pdb=" N LEU a 55 " --> pdb=" O VAL a 51 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 73 through 92 removed outlier: 4.031A pdb=" N ALA a 78 " --> pdb=" O LYS a 74 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE a 79 " --> pdb=" O PHE a 75 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER a 89 " --> pdb=" O PHE a 85 " (cutoff:3.500A) Processing helix chain 'a' and resid 100 through 118 removed outlier: 3.638A pdb=" N LEU a 104 " --> pdb=" O LEU a 100 " (cutoff:3.500A) Processing helix chain 'a' and resid 119 through 121 No H-bonds generated for 'chain 'a' and resid 119 through 121' Processing helix chain 'a' and resid 124 through 133 Processing helix chain 'a' and resid 142 through 145 Processing helix chain 'a' and resid 146 through 181 removed outlier: 3.762A pdb=" N THR a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER a 152 " --> pdb=" O ASN a 148 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE a 166 " --> pdb=" O LEU a 162 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N ILE a 171 " --> pdb=" O LYS a 167 " (cutoff:3.500A) removed outlier: 9.412A pdb=" N GLY a 172 " --> pdb=" O MET a 168 " (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 229 removed outlier: 3.626A pdb=" N LYS a 203 " --> pdb=" O SER a 199 " (cutoff:3.500A) Proline residue: a 204 - end of helix removed outlier: 3.770A pdb=" N LEU a 211 " --> pdb=" O LEU a 207 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE a 222 " --> pdb=" O GLY a 218 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU a 229 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing helix chain 'a' and resid 230 through 233 Processing helix chain 'a' and resid 234 through 269 Proline residue: a 240 - end of helix removed outlier: 3.503A pdb=" N ILE a 246 " --> pdb=" O ALA a 242 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU a 247 " --> pdb=" O ILE a 243 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE a 248 " --> pdb=" O PHE a 244 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA a 253 " --> pdb=" O ILE a 249 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 135 through 142 removed outlier: 6.970A pdb=" N ALA W 106 " --> pdb=" O LYS W 137 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ASN W 139 " --> pdb=" O ALA W 106 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL W 108 " --> pdb=" O ASN W 139 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N LYS W 141 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N VAL W 110 " --> pdb=" O LYS W 141 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG C 40 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL C 34 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL C 38 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY C 72 " --> pdb=" O LEU C 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 25 through 35 removed outlier: 13.413A pdb=" N ALA C 25 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N GLY C 92 " --> pdb=" O ALA C 25 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ASN C 27 " --> pdb=" O CYS C 90 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR C 91 " --> pdb=" O MET C 52 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N MET C 52 " --> pdb=" O THR C 91 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLU C 51 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP D 14 " --> pdb=" O VAL D 6 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N VAL D 8 " --> pdb=" O VAL D 12 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE D 50 " --> pdb=" O GLN D 45 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN D 45 " --> pdb=" O ILE D 50 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG D 52 " --> pdb=" O GLN D 43 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP D 27 " --> pdb=" O VAL D 42 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ALA D 28 " --> pdb=" O LEU D 71 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLN D 32 " --> pdb=" O ASP D 67 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ASP D 67 " --> pdb=" O GLN D 32 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 107 through 109 removed outlier: 3.580A pdb=" N ILE C 198 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 329 through 331 removed outlier: 7.983A pdb=" N ILE C 330 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE C 167 " --> pdb=" O ILE C 330 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU C 166 " --> pdb=" O ILE C 353 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N LEU C 355 " --> pdb=" O LEU C 166 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE C 168 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 59 through 66 removed outlier: 4.547A pdb=" N ARG B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU B 51 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N MET B 52 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ARG B 40 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 38 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N GLY B 72 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARG F 52 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N VAL F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL F 8 " --> pdb=" O VAL F 12 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ASP F 14 " --> pdb=" O VAL F 6 " (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 109 Processing sheet with id=AA9, first strand: chain 'B' and resid 145 through 146 removed outlier: 4.546A 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: 6.380A pdb=" N ILE B 167 " --> pdb=" O ILE B 330 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N LEU B 166 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N LEU B 355 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 6.616A 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: 3.790A pdb=" N ARG A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLU A 51 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N MET A 52 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG A 40 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 34 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 38 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N VAL A 74 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N ALA A 63 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ASP E 67 " --> pdb=" O GLN E 32 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLN E 32 " --> pdb=" O ASP E 67 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ARG E 52 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 8 " --> pdb=" O VAL E 12 " (cutoff:3.500A) removed outlier: 6.600A 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 108 removed outlier: 3.811A pdb=" N ILE A 198 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 329 through 331 removed outlier: 6.677A pdb=" N ILE A 167 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU A 166 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N LEU A 355 " --> pdb=" O LEU A 166 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE A 168 " --> pdb=" O LEU A 355 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.220A pdb=" N VAL H 8 " --> pdb=" O MET H 15 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N VAL H 53 " --> pdb=" O GLU H 21 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ILE H 23 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARG H 51 " --> pdb=" O ILE H 23 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N VAL H 25 " --> pdb=" O MET H 49 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N MET H 49 " --> pdb=" O VAL H 25 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 32 through 34 removed outlier: 6.132A pdb=" N HIS H 5 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N VAL H 78 " --> pdb=" O HIS H 5 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP H 7 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ILE H 68 " --> pdb=" O LEU H 79 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLY H 67 " --> pdb=" O ILE H 45 " (cutoff:3.500A) removed outlier: 4.578A 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: 7.634A pdb=" N VAL G 133 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU G 114 " --> pdb=" O VAL G 133 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLN G 135 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N MET G 116 " --> pdb=" O GLN G 135 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL G 75 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ALA G 115 " --> pdb=" O VAL G 75 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR G 77 " --> pdb=" O ALA G 115 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE G 117 " --> pdb=" O TYR G 77 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL G 79 " --> pdb=" O ILE G 117 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ARG G 74 " --> pdb=" O LYS G 166 " (cutoff:3.500A) removed outlier: 8.690A pdb=" N TYR G 168 " --> pdb=" O ARG G 74 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N GLY G 76 " --> pdb=" O TYR G 168 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N VAL G 170 " --> pdb=" O GLY G 76 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU G 78 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N ASN G 172 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.896A pdb=" N VAL G 80 " --> pdb=" O ASN G 172 " (cutoff:3.500A) removed outlier: 11.624A pdb=" N PHE G 174 " --> pdb=" O VAL G 80 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU G 167 " --> pdb=" O LEU G 187 " (cutoff:3.500A) removed outlier: 6.563A 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: 4.677A 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: 6.425A pdb=" N MET F 88 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N VAL F 237 " --> pdb=" O THR F 291 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL F 293 " --> pdb=" O VAL F 237 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU F 239 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N ALA F 295 " --> pdb=" O LEU F 239 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N VAL F 241 " --> pdb=" O ALA F 295 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N TYR F 297 " --> pdb=" O VAL F 241 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL F 145 " --> pdb=" O GLN F 294 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL F 296 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N LEU F 147 " --> pdb=" O VAL F 296 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N LYS F 144 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N VAL F 319 " --> pdb=" O LYS F 144 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N GLY F 146 " --> pdb=" O VAL F 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 125 through 126 removed outlier: 4.725A 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: 6.213A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 87 through 88 removed outlier: 6.213A pdb=" N MET E 88 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N VAL E 237 " --> pdb=" O THR E 291 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL E 293 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 239 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ALA E 295 " --> pdb=" O LEU E 239 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL E 241 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VAL E 145 " --> pdb=" O GLN E 294 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LYS E 144 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL E 319 " --> pdb=" O LYS E 144 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N GLY E 146 " --> pdb=" O VAL E 319 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 76 through 79 removed outlier: 4.673A pdb=" N GLU D 105 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 87 through 88 removed outlier: 6.369A pdb=" N MET D 88 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N GLN D 208 " --> pdb=" O MET D 88 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N VAL D 145 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL D 296 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU D 147 " --> pdb=" O VAL D 296 " (cutoff:3.500A) 2252 hydrogen bonds defined for protein. 6513 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.47 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 6336 1.30 - 1.43: 8776 1.43 - 1.56: 22032 1.56 - 1.69: 24 1.69 - 1.81: 360 Bond restraints: 37528 Sorted by residual: bond pdb=" C MET Y 30 " pdb=" N ALA Y 31 " ideal model delta sigma weight residual 1.334 1.464 -0.130 1.43e-02 4.89e+03 8.21e+01 bond pdb=" C4 ATP A 600 " pdb=" C5 ATP A 600 " ideal model delta sigma weight residual 1.388 1.457 -0.069 1.00e-02 1.00e+04 4.71e+01 bond pdb=" C4 ATP B 600 " pdb=" C5 ATP B 600 " ideal model delta sigma weight residual 1.388 1.456 -0.068 1.00e-02 1.00e+04 4.65e+01 bond pdb=" C4 ATP C 600 " pdb=" C5 ATP C 600 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.40e+01 bond pdb=" C5 ATP B 600 " pdb=" C6 ATP B 600 " ideal model delta sigma weight residual 1.409 1.472 -0.063 1.00e-02 1.00e+04 3.99e+01 ... (remaining 37523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.29: 50691 5.29 - 10.58: 99 10.58 - 15.87: 1 15.87 - 21.16: 3 21.16 - 26.45: 3 Bond angle restraints: 50797 Sorted by residual: angle pdb=" PB ATP A 600 " pdb=" O3B ATP A 600 " pdb=" PG ATP A 600 " ideal model delta sigma weight residual 139.87 113.42 26.45 1.00e+00 1.00e+00 7.00e+02 angle pdb=" PB ATP B 600 " pdb=" O3B ATP B 600 " pdb=" PG ATP B 600 " ideal model delta sigma weight residual 139.87 114.55 25.32 1.00e+00 1.00e+00 6.41e+02 angle pdb=" PB ATP C 600 " pdb=" O3B ATP C 600 " pdb=" PG ATP C 600 " ideal model delta sigma weight residual 139.87 115.68 24.19 1.00e+00 1.00e+00 5.85e+02 angle pdb=" PA ATP A 600 " pdb=" O3A ATP A 600 " pdb=" PB ATP A 600 " ideal model delta sigma weight residual 136.83 116.13 20.70 1.00e+00 1.00e+00 4.29e+02 angle pdb=" PA ATP C 600 " pdb=" O3A ATP C 600 " pdb=" PB ATP C 600 " ideal model delta sigma weight residual 136.83 117.54 19.29 1.00e+00 1.00e+00 3.72e+02 ... (remaining 50792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.84: 22278 34.84 - 69.68: 459 69.68 - 104.52: 52 104.52 - 139.36: 2 139.36 - 174.20: 3 Dihedral angle restraints: 22794 sinusoidal: 9010 harmonic: 13784 Sorted by residual: dihedral pdb=" O2A ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PA ADP E 500 " pdb=" PB ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 114.20 -174.20 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' ADP F 500 " pdb=" O5' ADP F 500 " pdb=" PA ADP F 500 " pdb=" O2A ADP F 500 " ideal model delta sinusoidal sigma weight residual 300.00 152.32 147.69 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O1B ADP E 500 " pdb=" O3A ADP E 500 " pdb=" PB ADP E 500 " pdb=" PA ADP E 500 " ideal model delta sinusoidal sigma weight residual -60.00 82.47 -142.47 1 2.00e+01 2.50e-03 4.30e+01 ... (remaining 22791 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 5462 0.092 - 0.184: 427 0.184 - 0.276: 23 0.276 - 0.369: 5 0.369 - 0.461: 3 Chirality restraints: 5920 Sorted by residual: chirality pdb=" CA LEU a 178 " pdb=" N LEU a 178 " pdb=" C LEU a 178 " pdb=" CB LEU a 178 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.31e+00 chirality pdb=" CA GLU X 48 " pdb=" N GLU X 48 " pdb=" C GLU X 48 " pdb=" CB GLU X 48 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.84e+00 chirality pdb=" CA ASP B 261 " pdb=" N ASP B 261 " pdb=" C ASP B 261 " pdb=" CB ASP B 261 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 ... (remaining 5917 not shown) Planarity restraints: 6550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET Y 30 " -0.025 2.00e-02 2.50e+03 4.78e-02 2.28e+01 pdb=" C MET Y 30 " 0.083 2.00e-02 2.50e+03 pdb=" O MET Y 30 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA Y 31 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY F 207 " -0.020 2.00e-02 2.50e+03 4.05e-02 1.64e+01 pdb=" C GLY F 207 " 0.070 2.00e-02 2.50e+03 pdb=" O GLY F 207 " -0.026 2.00e-02 2.50e+03 pdb=" N GLN F 208 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 264 " 0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C ALA D 264 " -0.065 2.00e-02 2.50e+03 pdb=" O ALA D 264 " 0.024 2.00e-02 2.50e+03 pdb=" N VAL D 265 " 0.023 2.00e-02 2.50e+03 ... (remaining 6547 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 47 2.37 - 3.00: 23498 3.00 - 3.64: 53446 3.64 - 4.27: 84149 4.27 - 4.90: 141748 Nonbonded interactions: 302888 Sorted by model distance: nonbonded pdb=" O2G ATP B 600 " pdb="MG MG B 601 " model vdw 1.740 2.170 nonbonded pdb=" O2B ATP B 600 " pdb="MG MG B 601 " model vdw 1.793 2.170 nonbonded pdb=" OG1 THR D 156 " pdb="MG MG D 502 " model vdw 1.817 2.170 nonbonded pdb=" O2B ATP A 600 " pdb="MG MG A 601 " model vdw 1.821 2.170 nonbonded pdb=" O1 PO4 D 501 " pdb="MG MG D 502 " model vdw 1.850 2.170 ... (remaining 302883 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 31.620 Find NCS groups from input model: 0.840 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: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.010 0.130 37528 Z= 0.483 Angle : 0.937 26.453 50797 Z= 0.610 Chirality : 0.053 0.461 5920 Planarity : 0.005 0.048 6550 Dihedral : 14.887 174.200 13976 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.95 % Allowed : 8.32 % Favored : 88.74 % 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: -2.77 (0.10), residues: 4807 helix: -1.86 (0.08), residues: 2588 sheet: -1.04 (0.20), residues: 516 loop : -1.74 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG X 117 TYR 0.022 0.002 TYR Y 24 PHE 0.023 0.002 PHE Y 20 TRP 0.025 0.002 TRP Y 26 HIS 0.007 0.002 HIS a 95 Details of bonding type rmsd covalent geometry : bond 0.00971 (37528) covalent geometry : angle 0.93698 (50797) hydrogen bonds : bond 0.16344 ( 2242) hydrogen bonds : angle 7.29100 ( 6513) *********************** 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 876 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 763 time to evaluate : 1.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 70 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7671 (mt-10) REVERT: W 90 ASP cc_start: 0.9275 (m-30) cc_final: 0.8994 (m-30) REVERT: W 143 ASP cc_start: 0.8289 (t0) cc_final: 0.8035 (t0) REVERT: W 156 ASP cc_start: 0.8563 (p0) cc_final: 0.8091 (p0) REVERT: C 86 MET cc_start: 0.8721 (mtt) cc_final: 0.8488 (mtt) REVERT: C 161 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8561 (mtt-85) REVERT: C 187 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7779 (ptt90) REVERT: B 7 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7902 (mp0) REVERT: A 236 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.8576 (t80) REVERT: A 426 LYS cc_start: 0.8599 (mmtt) cc_final: 0.8333 (mmtp) REVERT: A 429 GLU cc_start: 0.8967 (tp30) cc_final: 0.8687 (tp30) REVERT: A 463 LYS cc_start: 0.7877 (tttt) cc_final: 0.7512 (ttpp) REVERT: X 106 GLN cc_start: 0.9192 (tm-30) cc_final: 0.8985 (tm-30) REVERT: X 123 GLN cc_start: 0.8206 (mm110) cc_final: 0.7804 (mm-40) REVERT: H 13 GLN cc_start: 0.7791 (pt0) cc_final: 0.7580 (pm20) REVERT: H 22 LYS cc_start: 0.8408 (ptpp) cc_final: 0.8062 (pttt) REVERT: H 49 MET cc_start: 0.8837 (mmt) cc_final: 0.8587 (mmm) REVERT: H 51 ARG cc_start: 0.8322 (mtp-110) cc_final: 0.7940 (ttp80) REVERT: H 65 SER cc_start: 0.9139 (m) cc_final: 0.8407 (t) REVERT: G 116 MET cc_start: 0.9238 (mmm) cc_final: 0.8582 (mmm) REVERT: F 226 MET cc_start: 0.8793 (mtt) cc_final: 0.8546 (mtt) REVERT: E 136 MET cc_start: 0.9115 (mmm) cc_final: 0.8798 (mmm) REVERT: E 242 ASP cc_start: 0.7988 (t70) cc_final: 0.7730 (t0) REVERT: E 249 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8384 (mp) REVERT: E 381 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8481 (tm-30) REVERT: D 88 MET cc_start: 0.8987 (mtm) cc_final: 0.8547 (mtm) REVERT: D 301 ASP cc_start: 0.8538 (t0) cc_final: 0.8216 (t0) REVERT: D 386 ASP cc_start: 0.8443 (m-30) cc_final: 0.8049 (m-30) REVERT: I 10 TYR cc_start: 0.8807 (m-80) cc_final: 0.8586 (m-80) REVERT: I 57 MET cc_start: 0.9238 (tmm) cc_final: 0.8821 (tmm) REVERT: I 63 ILE cc_start: 0.9400 (mm) cc_final: 0.9171 (mt) REVERT: I 73 TYR cc_start: 0.8656 (t80) cc_final: 0.8277 (t80) REVERT: J 68 VAL cc_start: 0.9029 (t) cc_final: 0.8735 (p) REVERT: J 75 MET cc_start: 0.9067 (ttp) cc_final: 0.8610 (ttm) REVERT: L 10 TYR cc_start: 0.9002 (m-80) cc_final: 0.8508 (m-80) REVERT: L 11 MET cc_start: 0.8883 (tpt) cc_final: 0.8477 (tpt) REVERT: L 37 GLU cc_start: 0.8576 (pt0) cc_final: 0.8282 (mm-30) REVERT: L 57 MET cc_start: 0.8508 (tmm) cc_final: 0.8213 (tmm) REVERT: L 61 ASP cc_start: 0.8991 (m-30) cc_final: 0.8694 (m-30) REVERT: M 30 ILE cc_start: 0.8918 (mt) cc_final: 0.8620 (mt) REVERT: M 34 LYS cc_start: 0.9323 (mmtm) cc_final: 0.9050 (mmmt) REVERT: M 42 GLN cc_start: 0.9130 (pt0) cc_final: 0.8707 (pp30) REVERT: M 73 TYR cc_start: 0.8751 (t80) cc_final: 0.8475 (t80) REVERT: N 10 TYR cc_start: 0.8677 (m-80) cc_final: 0.8326 (m-10) REVERT: N 42 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8632 (mm-40) REVERT: N 55 ILE cc_start: 0.8974 (mm) cc_final: 0.8740 (mt) REVERT: N 65 MET cc_start: 0.9285 (mtt) cc_final: 0.9066 (mtm) REVERT: O 6 MET cc_start: 0.7516 (ttm) cc_final: 0.7201 (tmm) REVERT: P 8 LEU cc_start: 0.9081 (mt) cc_final: 0.8819 (tp) REVERT: P 17 MET cc_start: 0.8923 (mtm) cc_final: 0.8707 (mtp) REVERT: P 53 PHE cc_start: 0.9303 (t80) cc_final: 0.9061 (t80) REVERT: P 73 TYR cc_start: 0.8437 (t80) cc_final: 0.8090 (t80) REVERT: Q 17 MET cc_start: 0.8317 (mtm) cc_final: 0.7564 (mtm) REVERT: R 44 ASP cc_start: 0.7892 (m-30) cc_final: 0.7625 (m-30) REVERT: S 11 MET cc_start: 0.9116 (tpp) cc_final: 0.8722 (tpt) REVERT: S 17 MET cc_start: 0.8495 (mtp) cc_final: 0.8186 (mmm) REVERT: S 73 TYR cc_start: 0.8551 (t80) cc_final: 0.8051 (t80) REVERT: Y 37 GLN cc_start: 0.8548 (mt0) cc_final: 0.8284 (mm-40) REVERT: Y 83 ARG cc_start: 0.7442 (ttm110) cc_final: 0.7204 (ttp80) REVERT: Y 98 ARG cc_start: 0.8754 (ttp80) cc_final: 0.8547 (ttp80) REVERT: a 24 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6786 (mmt180) REVERT: a 26 PHE cc_start: 0.6216 (OUTLIER) cc_final: 0.5075 (m-80) REVERT: a 94 TYR cc_start: 0.6962 (t80) cc_final: 0.6404 (t80) REVERT: a 115 MET cc_start: 0.8096 (mtm) cc_final: 0.7874 (mtp) REVERT: a 119 ASP cc_start: 0.8261 (t0) cc_final: 0.7892 (t0) REVERT: a 155 LEU cc_start: 0.9245 (mt) cc_final: 0.8920 (mt) REVERT: a 167 LYS cc_start: 0.8969 (tttt) cc_final: 0.8333 (mtpp) REVERT: a 210 ARG cc_start: 0.8870 (ttm110) cc_final: 0.8555 (ttp-170) REVERT: a 231 TRP cc_start: 0.7521 (p-90) cc_final: 0.7006 (p-90) REVERT: a 263 TYR cc_start: 0.9094 (m-10) cc_final: 0.8848 (m-10) outliers start: 113 outliers final: 57 residues processed: 850 average time/residue: 0.2413 time to fit residues: 324.0176 Evaluate side-chains 642 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 577 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 187 ARG Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 374 VAL Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain B residue 513 TRP Chi-restraints excluded: chain A residue 20 ASN Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 172 GLN Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain A residue 462 SER Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 66 LYS Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 78 GLN Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain X residue 147 ASP Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 210 ASP 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 95 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 423 THR Chi-restraints excluded: chain E residue 15 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 319 VAL Chi-restraints excluded: chain E residue 360 VAL Chi-restraints excluded: chain E residue 389 VAL Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain Y residue 88 ASP Chi-restraints excluded: chain Y residue 141 ASP Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 26 PHE Chi-restraints excluded: chain a residue 147 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 0.9980 chunk 388 optimal weight: 1.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 W 82 ASN ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 369 ASN C 479 HIS C 488 GLN C 511 GLN B 4 ASN B 58 ASN B 186 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 ASN A 147 GLN A 344 ASN A 479 HIS A 484 GLN X 64 GLN X 80 ASN H 87 GLN G 59 ASN G 111 GLN D 170 HIS D 243 ASN D 279 GLN I 42 GLN L 5 ASN L 52 GLN P 5 ASN Q 3 ASN R 5 ASN R 52 GLN S 52 GLN Y 10 GLN Y 64 GLN Y 85 GLN a 14 HIS a 252 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.090572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.062306 restraints weight = 87479.222| |-----------------------------------------------------------------------------| r_work (start): 0.2838 rms_B_bonded: 2.32 r_work: 0.2710 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 37528 Z= 0.144 Angle : 0.655 9.457 50797 Z= 0.340 Chirality : 0.045 0.207 5920 Planarity : 0.004 0.042 6550 Dihedral : 8.943 173.526 5455 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.21 % Allowed : 12.54 % Favored : 84.25 % 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: -0.39 (0.12), residues: 4807 helix: 0.31 (0.10), residues: 2559 sheet: -0.58 (0.21), residues: 508 loop : -0.84 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG X 117 TYR 0.018 0.001 TYR A 236 PHE 0.036 0.001 PHE L 54 TRP 0.013 0.001 TRP a 186 HIS 0.007 0.001 HIS C 479 Details of bonding type rmsd covalent geometry : bond 0.00306 (37528) covalent geometry : angle 0.65453 (50797) hydrogen bonds : bond 0.05171 ( 2242) hydrogen bonds : angle 4.99224 ( 6513) *********************** 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 787 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 664 time to evaluate : 1.381 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 39 LYS cc_start: 0.9380 (mttt) cc_final: 0.9080 (mttm) REVERT: W 109 ASP cc_start: 0.8294 (m-30) cc_final: 0.7787 (t0) REVERT: W 141 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7438 (mtmm) REVERT: W 143 ASP cc_start: 0.8277 (t0) cc_final: 0.8037 (t0) REVERT: W 147 MET cc_start: 0.8162 (pmm) cc_final: 0.7744 (pmm) REVERT: W 156 ASP cc_start: 0.8717 (p0) cc_final: 0.8228 (p0) REVERT: W 164 ARG cc_start: 0.8376 (ttm170) cc_final: 0.8174 (ttm170) REVERT: B 7 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 488 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8960 (mm110) REVERT: A 230 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: A 488 GLN cc_start: 0.8996 (mm-40) cc_final: 0.8744 (mm-40) REVERT: X 73 GLN cc_start: 0.8565 (tp-100) cc_final: 0.8246 (tp-100) REVERT: X 83 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.8316 (tmm-80) REVERT: X 96 GLN cc_start: 0.8269 (pp30) cc_final: 0.8057 (pp30) REVERT: X 106 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8656 (pp30) REVERT: X 123 GLN cc_start: 0.8247 (mm110) cc_final: 0.7514 (mm-40) REVERT: X 145 ASN cc_start: 0.7786 (t0) cc_final: 0.7306 (m-40) REVERT: H 51 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.8575 (ttp80) REVERT: H 65 SER cc_start: 0.9251 (m) cc_final: 0.8707 (t) REVERT: H 98 LYS cc_start: 0.9086 (mtmt) cc_final: 0.8419 (mtmm) REVERT: H 127 GLN cc_start: 0.8160 (tm-30) cc_final: 0.7918 (tm-30) REVERT: H 132 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8396 (pt0) REVERT: G 246 MET cc_start: 0.9106 (mmp) cc_final: 0.8868 (mmm) REVERT: F 193 MET cc_start: 0.9073 (mmp) cc_final: 0.8847 (mmp) REVERT: F 345 ASP cc_start: 0.9018 (t0) cc_final: 0.8803 (t0) REVERT: E 192 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8410 (tp30) REVERT: E 249 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.8998 (mp) REVERT: E 365 GLN cc_start: 0.9150 (pt0) cc_final: 0.8645 (tp40) REVERT: D 301 ASP cc_start: 0.8977 (t0) cc_final: 0.8607 (t70) REVERT: I 42 GLN cc_start: 0.8084 (mm110) cc_final: 0.7865 (mm110) REVERT: I 54 PHE cc_start: 0.8815 (m-80) cc_final: 0.8478 (m-80) REVERT: I 57 MET cc_start: 0.9361 (tmm) cc_final: 0.9018 (tmm) REVERT: I 73 TYR cc_start: 0.8854 (t80) cc_final: 0.8410 (t80) REVERT: J 6 MET cc_start: 0.7689 (mtm) cc_final: 0.7394 (ptt) REVERT: J 10 TYR cc_start: 0.8866 (m-80) cc_final: 0.8265 (m-80) REVERT: J 11 MET cc_start: 0.8008 (tpp) cc_final: 0.7677 (tpp) REVERT: L 11 MET cc_start: 0.8998 (tpt) cc_final: 0.8586 (tpt) REVERT: L 50 ARG cc_start: 0.8735 (mtm110) cc_final: 0.8466 (mtm-85) REVERT: L 76 PHE cc_start: 0.8145 (m-80) cc_final: 0.7781 (m-10) REVERT: M 26 ILE cc_start: 0.9402 (mt) cc_final: 0.9102 (mm) REVERT: M 30 ILE cc_start: 0.9331 (mt) cc_final: 0.8971 (mt) REVERT: M 75 MET cc_start: 0.8749 (ttp) cc_final: 0.8390 (tmm) REVERT: N 11 MET cc_start: 0.8013 (OUTLIER) cc_final: 0.7797 (tpp) REVERT: N 16 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8534 (ttm) REVERT: N 55 ILE cc_start: 0.9075 (mm) cc_final: 0.8787 (mt) REVERT: N 57 MET cc_start: 0.8962 (tmm) cc_final: 0.8566 (ppp) REVERT: N 61 ASP cc_start: 0.8001 (p0) cc_final: 0.7668 (p0) REVERT: N 63 ILE cc_start: 0.9055 (mm) cc_final: 0.8510 (mt) REVERT: O 50 ARG cc_start: 0.8849 (ttp80) cc_final: 0.8631 (ttp-170) REVERT: O 57 MET cc_start: 0.9176 (tmm) cc_final: 0.8883 (tmm) REVERT: P 10 TYR cc_start: 0.8699 (m-80) cc_final: 0.8206 (m-80) REVERT: P 17 MET cc_start: 0.8948 (mtm) cc_final: 0.8693 (mtp) REVERT: P 73 TYR cc_start: 0.8206 (t80) cc_final: 0.7862 (t80) REVERT: Q 7 ASP cc_start: 0.8478 (t0) cc_final: 0.7452 (m-30) REVERT: Q 52 GLN cc_start: 0.8766 (mm-40) cc_final: 0.8519 (mm-40) REVERT: S 6 MET cc_start: 0.8106 (mpp) cc_final: 0.7584 (pmm) REVERT: S 11 MET cc_start: 0.8988 (tpp) cc_final: 0.8524 (tpt) REVERT: S 17 MET cc_start: 0.8744 (mtp) cc_final: 0.8364 (mmm) REVERT: S 49 LEU cc_start: 0.9302 (mt) cc_final: 0.9056 (mt) REVERT: S 73 TYR cc_start: 0.8443 (t80) cc_final: 0.7988 (t80) REVERT: Y 64 GLN cc_start: 0.7994 (OUTLIER) cc_final: 0.7688 (mm110) REVERT: Y 65 LEU cc_start: 0.7148 (OUTLIER) cc_final: 0.6917 (tp) REVERT: Y 83 ARG cc_start: 0.7627 (ttm110) cc_final: 0.7329 (ttp80) REVERT: Y 91 LYS cc_start: 0.9096 (OUTLIER) cc_final: 0.8883 (mmtm) REVERT: Y 98 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8368 (ttt90) REVERT: Y 119 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7684 (tm-30) REVERT: Y 147 ASP cc_start: 0.9211 (t70) cc_final: 0.8995 (t0) REVERT: a 24 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.6494 (mmt180) REVERT: a 91 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8446 (mmmt) REVERT: a 155 LEU cc_start: 0.9125 (mt) cc_final: 0.8876 (mt) REVERT: a 164 TYR cc_start: 0.8029 (m-80) cc_final: 0.7695 (m-80) REVERT: a 167 LYS cc_start: 0.8810 (tttt) cc_final: 0.8249 (mtpp) REVERT: a 169 LYS cc_start: 0.6374 (mttt) cc_final: 0.5898 (mmtp) REVERT: a 219 GLU cc_start: 0.8924 (tt0) cc_final: 0.8605 (pp20) REVERT: a 231 TRP cc_start: 0.7520 (p-90) cc_final: 0.7202 (p-90) outliers start: 123 outliers final: 52 residues processed: 744 average time/residue: 0.2249 time to fit residues: 271.0974 Evaluate side-chains 645 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 580 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 141 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 411 SER Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 230 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 132 GLU Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 170 VAL Chi-restraints excluded: chain G residue 180 GLN 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 E residue 104 GLU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 360 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 D residue 219 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 26 ILE Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain M residue 28 ILE Chi-restraints excluded: chain N residue 11 MET Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 22 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 52 GLN Chi-restraints excluded: chain Y residue 53 ASP Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 65 LEU Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 91 LYS Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 147 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 389 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 344 optimal weight: 0.9980 chunk 431 optimal weight: 7.9990 chunk 167 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 307 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 GLN B 4 ASN B 147 GLN ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN H 24 GLN H 104 HIS G 64 HIS E 351 GLN L 52 GLN P 52 GLN Q 42 GLN R 52 GLN S 52 GLN Y 85 GLN a 76 GLN a 132 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.088672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.059934 restraints weight = 87749.355| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.28 r_work: 0.2668 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 37528 Z= 0.229 Angle : 0.653 10.711 50797 Z= 0.338 Chirality : 0.045 0.205 5920 Planarity : 0.004 0.043 6550 Dihedral : 8.018 157.166 5382 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.15 % Allowed : 13.97 % Favored : 82.87 % 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: 0.21 (0.12), residues: 4807 helix: 0.88 (0.10), residues: 2581 sheet: -0.53 (0.21), residues: 522 loop : -0.65 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Y 49 TYR 0.018 0.002 TYR A 236 PHE 0.040 0.002 PHE L 54 TRP 0.011 0.001 TRP a 186 HIS 0.015 0.001 HIS a 132 Details of bonding type rmsd covalent geometry : bond 0.00541 (37528) covalent geometry : angle 0.65280 (50797) hydrogen bonds : bond 0.05050 ( 2242) hydrogen bonds : angle 4.79276 ( 6513) *********************** 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 730 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 609 time to evaluate : 1.429 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 109 ASP cc_start: 0.8332 (m-30) cc_final: 0.7852 (t0) REVERT: W 141 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7785 (mtmm) REVERT: W 156 ASP cc_start: 0.8775 (p0) cc_final: 0.8323 (p0) REVERT: B 7 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7862 (mp0) REVERT: B 488 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8963 (mm110) REVERT: A 262 ASP cc_start: 0.8354 (p0) cc_final: 0.8009 (p0) REVERT: A 488 GLN cc_start: 0.8965 (mm-40) cc_final: 0.8752 (tm-30) REVERT: X 73 GLN cc_start: 0.8548 (tp-100) cc_final: 0.8154 (tp-100) REVERT: X 83 ARG cc_start: 0.8472 (OUTLIER) cc_final: 0.7998 (ttm-80) REVERT: X 85 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8493 (mt0) REVERT: X 106 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8784 (pp30) REVERT: X 123 GLN cc_start: 0.8232 (mm110) cc_final: 0.7375 (mm-40) REVERT: X 145 ASN cc_start: 0.7779 (t0) cc_final: 0.7296 (m-40) REVERT: H 51 ARG cc_start: 0.9022 (mtp-110) cc_final: 0.8770 (ttp80) REVERT: H 65 SER cc_start: 0.9318 (OUTLIER) cc_final: 0.8714 (t) REVERT: H 98 LYS cc_start: 0.9136 (mtmt) cc_final: 0.8575 (mtmm) REVERT: G 246 MET cc_start: 0.9111 (mmp) cc_final: 0.8868 (mmm) REVERT: E 125 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9282 (mp) REVERT: E 192 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8519 (tp30) REVERT: E 232 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8698 (m-30) REVERT: E 249 LEU cc_start: 0.9405 (OUTLIER) cc_final: 0.8957 (mp) REVERT: E 365 GLN cc_start: 0.9161 (pt0) cc_final: 0.8593 (tp-100) REVERT: D 301 ASP cc_start: 0.9058 (t0) cc_final: 0.8712 (t0) REVERT: D 366 ARG cc_start: 0.8666 (tpt170) cc_final: 0.8146 (tpt170) REVERT: D 370 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8473 (mp) REVERT: D 386 ASP cc_start: 0.8702 (m-30) cc_final: 0.8341 (m-30) REVERT: I 57 MET cc_start: 0.9338 (tmm) cc_final: 0.9004 (tmm) REVERT: L 11 MET cc_start: 0.8842 (tpt) cc_final: 0.8477 (tpt) REVERT: L 37 GLU cc_start: 0.9043 (tt0) cc_final: 0.8497 (tp30) REVERT: L 52 GLN cc_start: 0.9398 (mm110) cc_final: 0.9144 (mm110) REVERT: M 30 ILE cc_start: 0.9319 (mt) cc_final: 0.8995 (mt) REVERT: M 61 ASP cc_start: 0.8920 (m-30) cc_final: 0.8414 (m-30) REVERT: M 75 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: N 16 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8543 (ttm) REVERT: N 55 ILE cc_start: 0.9092 (mm) cc_final: 0.8771 (mt) REVERT: N 57 MET cc_start: 0.8683 (tmm) cc_final: 0.8375 (ppp) REVERT: N 61 ASP cc_start: 0.8140 (p0) cc_final: 0.7595 (p0) REVERT: N 66 ILE cc_start: 0.9078 (tt) cc_final: 0.8635 (tp) REVERT: N 70 LEU cc_start: 0.9102 (mt) cc_final: 0.8893 (mp) REVERT: O 6 MET cc_start: 0.6630 (OUTLIER) cc_final: 0.6056 (mpp) REVERT: O 57 MET cc_start: 0.9151 (tmm) cc_final: 0.8881 (tmm) REVERT: O 61 ASP cc_start: 0.8127 (p0) cc_final: 0.7906 (p0) REVERT: O 75 MET cc_start: 0.8576 (mtp) cc_final: 0.8262 (tpp) REVERT: P 10 TYR cc_start: 0.8792 (m-80) cc_final: 0.8338 (m-80) REVERT: P 17 MET cc_start: 0.8823 (mtm) cc_final: 0.8594 (mtp) REVERT: P 50 ARG cc_start: 0.8297 (ttp-170) cc_final: 0.7928 (ttp-170) REVERT: P 73 TYR cc_start: 0.8290 (t80) cc_final: 0.7870 (t80) REVERT: Q 37 GLU cc_start: 0.8821 (tt0) cc_final: 0.8398 (tt0) REVERT: S 6 MET cc_start: 0.7979 (mpp) cc_final: 0.7480 (pmm) REVERT: S 11 MET cc_start: 0.8899 (tpp) cc_final: 0.8422 (tpt) REVERT: S 17 MET cc_start: 0.8816 (mtp) cc_final: 0.8430 (mmm) REVERT: S 49 LEU cc_start: 0.9305 (mt) cc_final: 0.9065 (mt) REVERT: S 57 MET cc_start: 0.9136 (tmm) cc_final: 0.8784 (tmm) REVERT: S 73 TYR cc_start: 0.8450 (t80) cc_final: 0.8073 (t80) REVERT: Y 63 ASP cc_start: 0.8326 (t70) cc_final: 0.8107 (p0) REVERT: Y 64 GLN cc_start: 0.8232 (mp10) cc_final: 0.7751 (mm110) REVERT: Y 98 ARG cc_start: 0.8889 (ttp80) cc_final: 0.8442 (ttt90) REVERT: Y 119 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7747 (tm-30) REVERT: Y 147 ASP cc_start: 0.9208 (t70) cc_final: 0.8992 (t0) REVERT: a 24 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6220 (mmt180) REVERT: a 91 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8445 (mmmt) REVERT: a 94 TYR cc_start: 0.7318 (t80) cc_final: 0.6695 (t80) REVERT: a 115 MET cc_start: 0.7935 (mtp) cc_final: 0.7719 (mtm) REVERT: a 119 ASP cc_start: 0.7845 (t0) cc_final: 0.7572 (t0) REVERT: a 164 TYR cc_start: 0.7955 (m-80) cc_final: 0.7224 (m-80) REVERT: a 169 LYS cc_start: 0.6348 (mttt) cc_final: 0.5910 (mmtt) REVERT: a 219 GLU cc_start: 0.8919 (tt0) cc_final: 0.8668 (pp20) REVERT: a 224 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9220 (mp) REVERT: a 231 TRP cc_start: 0.7567 (p-90) cc_final: 0.7215 (p-90) outliers start: 121 outliers final: 69 residues processed: 693 average time/residue: 0.2182 time to fit residues: 247.0843 Evaluate side-chains 655 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 572 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 38 THR Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 108 VAL Chi-restraints excluded: chain W residue 141 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 27 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 225 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 83 ARG Chi-restraints excluded: chain X residue 124 VAL Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 180 GLN 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 83 THR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 349 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 D residue 219 VAL Chi-restraints excluded: chain D residue 277 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain M residue 75 MET Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain O residue 6 MET Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 15 VAL Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 5 ASN Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 52 GLN Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 119 GLU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 224 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 267 optimal weight: 8.9990 chunk 362 optimal weight: 10.0000 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.9980 chunk 331 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 235 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 chunk 394 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 379 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN B 425 GLN X 51 HIS X 80 ASN F 324 GLN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN S 52 GLN Y 85 GLN a 76 GLN a 252 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.062505 restraints weight = 87571.408| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.30 r_work: 0.2716 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37528 Z= 0.133 Angle : 0.592 10.467 50797 Z= 0.303 Chirality : 0.043 0.191 5920 Planarity : 0.004 0.047 6550 Dihedral : 7.603 141.624 5381 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.69 % Allowed : 15.20 % Favored : 82.12 % 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: 1.29 (0.10), residues: 2575 sheet: -0.40 (0.22), residues: 527 loop : -0.49 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 117 TYR 0.036 0.001 TYR O 10 PHE 0.018 0.001 PHE L 35 TRP 0.013 0.001 TRP a 186 HIS 0.004 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00299 (37528) covalent geometry : angle 0.59208 (50797) hydrogen bonds : bond 0.04425 ( 2242) hydrogen bonds : angle 4.53087 ( 6513) *********************** 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 722 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 619 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 109 ASP cc_start: 0.8316 (m-30) cc_final: 0.7834 (t0) REVERT: W 141 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7814 (mtmm) REVERT: W 143 ASP cc_start: 0.8014 (t0) cc_final: 0.7719 (t0) REVERT: W 156 ASP cc_start: 0.8718 (p0) cc_final: 0.8245 (p0) REVERT: B 7 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.7911 (mp0) REVERT: A 262 ASP cc_start: 0.8184 (p0) cc_final: 0.7768 (p0) REVERT: X 73 GLN cc_start: 0.8434 (tp-100) cc_final: 0.8106 (tp-100) REVERT: X 117 ARG cc_start: 0.7809 (ttp80) cc_final: 0.7144 (ttp80) REVERT: X 123 GLN cc_start: 0.8223 (mm110) cc_final: 0.7587 (mm-40) REVERT: X 145 ASN cc_start: 0.7661 (t0) cc_final: 0.7168 (m110) REVERT: H 65 SER cc_start: 0.9231 (m) cc_final: 0.8666 (t) REVERT: H 98 LYS cc_start: 0.9137 (mtmt) cc_final: 0.8572 (mtmm) REVERT: G 101 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: F 193 MET cc_start: 0.9026 (mmp) cc_final: 0.8682 (mmp) REVERT: E 125 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9308 (mp) REVERT: E 192 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8449 (tp30) REVERT: E 232 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8632 (m-30) REVERT: E 249 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.8987 (mp) REVERT: E 323 ARG cc_start: 0.8838 (tpp80) cc_final: 0.8580 (ttp80) REVERT: E 365 GLN cc_start: 0.9090 (pt0) cc_final: 0.8579 (tp-100) REVERT: D 301 ASP cc_start: 0.9038 (t0) cc_final: 0.8686 (t0) REVERT: D 366 ARG cc_start: 0.8723 (tpt170) cc_final: 0.8482 (tpt170) REVERT: D 370 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8492 (mp) REVERT: I 17 MET cc_start: 0.8441 (mmt) cc_final: 0.8228 (mmt) REVERT: I 57 MET cc_start: 0.9176 (tmm) cc_final: 0.8864 (tmm) REVERT: J 51 THR cc_start: 0.9049 (m) cc_final: 0.8730 (p) REVERT: L 5 ASN cc_start: 0.7069 (p0) cc_final: 0.6695 (m110) REVERT: L 11 MET cc_start: 0.8844 (tpt) cc_final: 0.8500 (tpt) REVERT: L 16 MET cc_start: 0.8841 (ttm) cc_final: 0.8399 (tmm) REVERT: L 34 LYS cc_start: 0.9301 (tptt) cc_final: 0.9026 (tppt) REVERT: L 37 GLU cc_start: 0.8988 (tt0) cc_final: 0.8517 (tp30) REVERT: L 61 ASP cc_start: 0.8807 (m-30) cc_final: 0.8418 (m-30) REVERT: L 74 VAL cc_start: 0.8890 (t) cc_final: 0.8644 (p) REVERT: L 76 PHE cc_start: 0.7861 (m-80) cc_final: 0.7558 (m-10) REVERT: M 17 MET cc_start: 0.8857 (mmt) cc_final: 0.8627 (mmt) REVERT: M 30 ILE cc_start: 0.9292 (mt) cc_final: 0.8948 (mt) REVERT: M 75 MET cc_start: 0.8751 (ttp) cc_final: 0.8518 (tmm) REVERT: N 16 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8553 (ttm) REVERT: N 55 ILE cc_start: 0.9016 (mm) cc_final: 0.8671 (mt) REVERT: N 57 MET cc_start: 0.8573 (tmm) cc_final: 0.8202 (ppp) REVERT: N 61 ASP cc_start: 0.8106 (p0) cc_final: 0.7350 (p0) REVERT: N 66 ILE cc_start: 0.9006 (tt) cc_final: 0.8630 (tp) REVERT: N 70 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8822 (mp) REVERT: O 53 PHE cc_start: 0.9485 (t80) cc_final: 0.9147 (t80) REVERT: O 57 MET cc_start: 0.9153 (tmm) cc_final: 0.8889 (tmm) REVERT: O 61 ASP cc_start: 0.8144 (p0) cc_final: 0.7898 (p0) REVERT: O 75 MET cc_start: 0.8543 (mtp) cc_final: 0.8162 (tpt) REVERT: P 6 MET cc_start: 0.8359 (ptp) cc_final: 0.7807 (ptp) REVERT: P 10 TYR cc_start: 0.8734 (m-80) cc_final: 0.8298 (m-80) REVERT: P 17 MET cc_start: 0.8915 (mtm) cc_final: 0.8714 (mtp) REVERT: P 52 GLN cc_start: 0.9013 (mm110) cc_final: 0.8799 (tp40) REVERT: P 73 TYR cc_start: 0.8225 (t80) cc_final: 0.7877 (t80) REVERT: Q 37 GLU cc_start: 0.8834 (tt0) cc_final: 0.8442 (tt0) REVERT: Q 42 GLN cc_start: 0.8734 (mm110) cc_final: 0.8183 (mp10) REVERT: S 6 MET cc_start: 0.7808 (mpp) cc_final: 0.7446 (pmm) REVERT: S 17 MET cc_start: 0.8837 (mtp) cc_final: 0.8429 (mmm) REVERT: S 73 TYR cc_start: 0.8458 (t80) cc_final: 0.8072 (t80) REVERT: Y 64 GLN cc_start: 0.8167 (mp10) cc_final: 0.7714 (mm-40) REVERT: Y 98 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8425 (tpt90) REVERT: Y 147 ASP cc_start: 0.9210 (t70) cc_final: 0.8988 (t0) REVERT: a 24 ARG cc_start: 0.7630 (OUTLIER) cc_final: 0.6195 (mmt180) REVERT: a 91 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8457 (mmmt) REVERT: a 106 LEU cc_start: 0.9118 (tp) cc_final: 0.8896 (pp) REVERT: a 164 TYR cc_start: 0.7896 (m-80) cc_final: 0.7652 (m-80) REVERT: a 169 LYS cc_start: 0.6445 (mttt) cc_final: 0.5933 (mmtt) REVERT: a 216 TYR cc_start: 0.8858 (t80) cc_final: 0.8649 (t80) REVERT: a 219 GLU cc_start: 0.8829 (tt0) cc_final: 0.8609 (pp20) REVERT: a 224 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9208 (mp) REVERT: a 231 TRP cc_start: 0.7568 (p-90) cc_final: 0.7278 (p-90) outliers start: 103 outliers final: 59 residues processed: 694 average time/residue: 0.2138 time to fit residues: 243.8731 Evaluate side-chains 634 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 564 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 141 LYS Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain B residue 7 GLU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 180 GLN 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 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 366 ARG 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 D residue 219 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 5 ASN Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain R residue 75 MET Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 224 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 404 optimal weight: 2.9990 chunk 445 optimal weight: 5.9990 chunk 374 optimal weight: 20.0000 chunk 443 optimal weight: 0.8980 chunk 278 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 201 optimal weight: 0.9990 chunk 362 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN O 52 GLN P 52 GLN R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN a 76 GLN a 245 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.061993 restraints weight = 87409.549| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.30 r_work: 0.2703 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 37528 Z= 0.156 Angle : 0.599 11.259 50797 Z= 0.304 Chirality : 0.043 0.193 5920 Planarity : 0.004 0.047 6550 Dihedral : 7.301 139.932 5375 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.87 % Allowed : 16.16 % Favored : 80.97 % 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: 0.86 (0.12), residues: 4807 helix: 1.46 (0.10), residues: 2584 sheet: -0.36 (0.22), residues: 533 loop : -0.41 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG X 113 TYR 0.029 0.001 TYR O 10 PHE 0.018 0.001 PHE L 35 TRP 0.014 0.001 TRP a 186 HIS 0.004 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00365 (37528) covalent geometry : angle 0.59938 (50797) hydrogen bonds : bond 0.04343 ( 2242) hydrogen bonds : angle 4.46023 ( 6513) *********************** 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 694 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 584 time to evaluate : 1.334 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: W 143 ASP cc_start: 0.8111 (t0) cc_final: 0.7816 (t0) REVERT: W 156 ASP cc_start: 0.8738 (p0) cc_final: 0.8285 (p0) REVERT: B 67 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8876 (mm-30) REVERT: A 262 ASP cc_start: 0.8281 (p0) cc_final: 0.7851 (p0) REVERT: A 356 GLU cc_start: 0.8430 (tp30) cc_final: 0.7972 (tt0) REVERT: A 484 GLN cc_start: 0.8953 (tp40) cc_final: 0.8726 (tm-30) REVERT: X 73 GLN cc_start: 0.8440 (tp-100) cc_final: 0.8112 (tp-100) REVERT: X 117 ARG cc_start: 0.7737 (ttp80) cc_final: 0.7406 (ttp80) REVERT: X 123 GLN cc_start: 0.8153 (mm110) cc_final: 0.7191 (mm-40) REVERT: X 145 ASN cc_start: 0.7762 (t0) cc_final: 0.7269 (m-40) REVERT: H 51 ARG cc_start: 0.8777 (mtp-110) cc_final: 0.8549 (ttp80) REVERT: H 65 SER cc_start: 0.9260 (m) cc_final: 0.8654 (t) REVERT: H 98 LYS cc_start: 0.9115 (mtmt) cc_final: 0.8547 (mtmm) REVERT: G 101 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: E 125 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9311 (mp) REVERT: E 192 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8462 (tp30) REVERT: E 232 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8617 (m-30) REVERT: E 249 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9017 (mp) REVERT: E 365 GLN cc_start: 0.9079 (pt0) cc_final: 0.8594 (tp-100) REVERT: D 121 ASN cc_start: 0.7259 (m110) cc_final: 0.7025 (m110) REVERT: D 301 ASP cc_start: 0.8991 (t0) cc_final: 0.8621 (t0) REVERT: D 370 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8535 (mp) REVERT: I 17 MET cc_start: 0.8538 (mmt) cc_final: 0.8286 (mmt) REVERT: I 57 MET cc_start: 0.9131 (tmm) cc_final: 0.8890 (tmm) REVERT: J 17 MET cc_start: 0.9369 (mmp) cc_final: 0.9027 (mmt) REVERT: L 5 ASN cc_start: 0.7041 (p0) cc_final: 0.6488 (m-40) REVERT: L 11 MET cc_start: 0.8825 (tpt) cc_final: 0.8523 (tpt) REVERT: L 16 MET cc_start: 0.8808 (ttm) cc_final: 0.8401 (tmm) REVERT: L 17 MET cc_start: 0.9246 (mmt) cc_final: 0.8930 (mmm) REVERT: L 34 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.9032 (tppt) REVERT: L 35 PHE cc_start: 0.8979 (t80) cc_final: 0.8722 (t80) REVERT: L 37 GLU cc_start: 0.8996 (tt0) cc_final: 0.8588 (tp30) REVERT: L 74 VAL cc_start: 0.8903 (t) cc_final: 0.8700 (p) REVERT: L 76 PHE cc_start: 0.7864 (m-80) cc_final: 0.7598 (m-10) REVERT: M 30 ILE cc_start: 0.9289 (mt) cc_final: 0.8943 (mt) REVERT: M 75 MET cc_start: 0.8754 (ttp) cc_final: 0.8489 (tmm) REVERT: N 16 MET cc_start: 0.8879 (OUTLIER) cc_final: 0.8590 (ttm) REVERT: N 55 ILE cc_start: 0.9066 (mm) cc_final: 0.8748 (mt) REVERT: N 57 MET cc_start: 0.8341 (tmm) cc_final: 0.7793 (tmm) REVERT: N 61 ASP cc_start: 0.8092 (p0) cc_final: 0.6643 (p0) REVERT: N 64 PRO cc_start: 0.9124 (Cg_exo) cc_final: 0.8902 (Cg_endo) REVERT: N 66 ILE cc_start: 0.9037 (tt) cc_final: 0.8680 (tp) REVERT: N 70 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8810 (mp) REVERT: O 6 MET cc_start: 0.7160 (mpp) cc_final: 0.6920 (mpp) REVERT: O 11 MET cc_start: 0.9133 (mmm) cc_final: 0.8928 (mmm) REVERT: O 57 MET cc_start: 0.9150 (tmm) cc_final: 0.8905 (tmm) REVERT: O 61 ASP cc_start: 0.8128 (p0) cc_final: 0.7833 (p0) REVERT: O 75 MET cc_start: 0.8476 (mtp) cc_final: 0.8051 (tpt) REVERT: P 6 MET cc_start: 0.8420 (ptp) cc_final: 0.7994 (ptp) REVERT: P 10 TYR cc_start: 0.8763 (m-80) cc_final: 0.8511 (m-80) REVERT: P 11 MET cc_start: 0.8878 (tpp) cc_final: 0.8432 (tpp) REVERT: P 16 MET cc_start: 0.8989 (mmt) cc_final: 0.8328 (mmm) REVERT: P 50 ARG cc_start: 0.8158 (ttp80) cc_final: 0.7928 (mtm180) REVERT: P 73 TYR cc_start: 0.8230 (t80) cc_final: 0.7833 (t80) REVERT: Q 34 LYS cc_start: 0.9188 (tppt) cc_final: 0.8977 (mmtt) REVERT: Q 37 GLU cc_start: 0.8846 (tt0) cc_final: 0.8456 (tt0) REVERT: Q 42 GLN cc_start: 0.8791 (mm110) cc_final: 0.8217 (mp10) REVERT: R 6 MET cc_start: 0.7796 (ptp) cc_final: 0.7582 (ptp) REVERT: S 11 MET cc_start: 0.8678 (tpp) cc_final: 0.8198 (tpt) REVERT: S 17 MET cc_start: 0.8853 (mtp) cc_final: 0.8329 (mmm) REVERT: S 73 TYR cc_start: 0.8425 (t80) cc_final: 0.7985 (t80) REVERT: Y 22 MET cc_start: 0.8493 (ptm) cc_final: 0.7548 (tpp) REVERT: Y 98 ARG cc_start: 0.8857 (ttp80) cc_final: 0.8422 (tpt90) REVERT: Y 147 ASP cc_start: 0.9192 (t70) cc_final: 0.8967 (t0) REVERT: a 24 ARG cc_start: 0.7621 (OUTLIER) cc_final: 0.6208 (mmt180) REVERT: a 56 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7518 (t80) REVERT: a 91 LYS cc_start: 0.9041 (mmmt) cc_final: 0.8540 (mmmt) REVERT: a 94 TYR cc_start: 0.7462 (t80) cc_final: 0.6913 (t80) REVERT: a 164 TYR cc_start: 0.8144 (m-80) cc_final: 0.7465 (m-80) REVERT: a 169 LYS cc_start: 0.6449 (mttt) cc_final: 0.5915 (mmtt) REVERT: a 219 GLU cc_start: 0.8785 (tt0) cc_final: 0.8582 (pp20) REVERT: a 224 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9221 (mp) REVERT: a 231 TRP cc_start: 0.7586 (p-90) cc_final: 0.7295 (p-90) outliers start: 110 outliers final: 70 residues processed: 662 average time/residue: 0.2172 time to fit residues: 236.6060 Evaluate side-chains 639 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 558 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 150 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 366 ARG 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 219 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 224 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 326 optimal weight: 1.9990 chunk 395 optimal weight: 3.9990 chunk 425 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 416 optimal weight: 10.0000 chunk 422 optimal weight: 9.9990 chunk 225 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 456 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN ** J 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN a 76 GLN a 245 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.089800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.061714 restraints weight = 87842.806| |-----------------------------------------------------------------------------| r_work (start): 0.2824 rms_B_bonded: 2.30 r_work: 0.2697 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 37528 Z= 0.177 Angle : 0.616 11.764 50797 Z= 0.311 Chirality : 0.044 0.191 5920 Planarity : 0.004 0.048 6550 Dihedral : 7.124 140.334 5370 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.05 % Allowed : 16.50 % Favored : 80.45 % 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: 0.94 (0.12), residues: 4807 helix: 1.55 (0.10), residues: 2584 sheet: -0.37 (0.22), residues: 536 loop : -0.40 (0.15), residues: 1687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG X 113 TYR 0.019 0.001 TYR L 73 PHE 0.028 0.001 PHE Q 53 TRP 0.014 0.001 TRP a 186 HIS 0.004 0.001 HIS Y 51 Details of bonding type rmsd covalent geometry : bond 0.00421 (37528) covalent geometry : angle 0.61611 (50797) hydrogen bonds : bond 0.04360 ( 2242) hydrogen bonds : angle 4.45190 ( 6513) *********************** 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 694 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 577 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 143 ASP cc_start: 0.8148 (t0) cc_final: 0.7897 (t0) REVERT: W 156 ASP cc_start: 0.8732 (p0) cc_final: 0.8369 (p0) REVERT: C 132 ILE cc_start: 0.9388 (pt) cc_final: 0.9054 (mm) REVERT: B 67 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8888 (mm-30) REVERT: A 262 ASP cc_start: 0.8283 (p0) cc_final: 0.7832 (p0) REVERT: A 386 MET cc_start: 0.9212 (mmt) cc_final: 0.8956 (mmt) REVERT: A 484 GLN cc_start: 0.8913 (tp40) cc_final: 0.8698 (tm-30) REVERT: X 73 GLN cc_start: 0.8448 (tp-100) cc_final: 0.8113 (tp-100) REVERT: X 117 ARG cc_start: 0.7683 (ttp80) cc_final: 0.7181 (ttp80) REVERT: X 118 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8230 (mp0) REVERT: X 123 GLN cc_start: 0.8184 (mm110) cc_final: 0.7228 (mm-40) REVERT: X 145 ASN cc_start: 0.7744 (t0) cc_final: 0.7251 (m-40) REVERT: H 65 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8664 (t) REVERT: E 125 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9362 (mp) REVERT: E 192 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8478 (tp30) REVERT: E 232 ASP cc_start: 0.8828 (OUTLIER) cc_final: 0.8599 (m-30) REVERT: E 249 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9016 (mp) REVERT: E 365 GLN cc_start: 0.9072 (pt0) cc_final: 0.8616 (tp40) REVERT: D 301 ASP cc_start: 0.9007 (t0) cc_final: 0.8661 (t0) REVERT: D 370 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8563 (mp) REVERT: I 42 GLN cc_start: 0.7941 (mm110) cc_final: 0.7734 (mm-40) REVERT: I 56 VAL cc_start: 0.9598 (t) cc_final: 0.9323 (p) REVERT: I 57 MET cc_start: 0.9080 (tmm) cc_final: 0.8823 (tmm) REVERT: I 75 MET cc_start: 0.8951 (mmm) cc_final: 0.8736 (tpt) REVERT: J 17 MET cc_start: 0.9402 (mmp) cc_final: 0.9042 (mmt) REVERT: J 75 MET cc_start: 0.8880 (tpp) cc_final: 0.8402 (tpp) REVERT: L 5 ASN cc_start: 0.7013 (p0) cc_final: 0.6465 (m-40) REVERT: L 11 MET cc_start: 0.8801 (tpt) cc_final: 0.8476 (tpt) REVERT: L 34 LYS cc_start: 0.9337 (OUTLIER) cc_final: 0.9015 (tppt) REVERT: L 37 GLU cc_start: 0.8965 (tt0) cc_final: 0.8611 (tp30) REVERT: L 74 VAL cc_start: 0.8905 (t) cc_final: 0.8674 (p) REVERT: L 76 PHE cc_start: 0.7979 (m-80) cc_final: 0.7671 (m-10) REVERT: M 30 ILE cc_start: 0.9271 (mt) cc_final: 0.8916 (mt) REVERT: M 57 MET cc_start: 0.9178 (tmm) cc_final: 0.8713 (tmm) REVERT: M 61 ASP cc_start: 0.8700 (m-30) cc_final: 0.8361 (m-30) REVERT: M 75 MET cc_start: 0.8717 (ttp) cc_final: 0.8470 (tmm) REVERT: N 16 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8665 (ttm) REVERT: N 55 ILE cc_start: 0.9068 (mm) cc_final: 0.8744 (mt) REVERT: N 57 MET cc_start: 0.8323 (tmm) cc_final: 0.7737 (tmm) REVERT: N 61 ASP cc_start: 0.8123 (p0) cc_final: 0.6969 (p0) REVERT: N 64 PRO cc_start: 0.9133 (Cg_exo) cc_final: 0.8925 (Cg_endo) REVERT: N 66 ILE cc_start: 0.9070 (tt) cc_final: 0.8715 (tp) REVERT: N 70 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8802 (mp) REVERT: O 57 MET cc_start: 0.9139 (tmm) cc_final: 0.8876 (tmm) REVERT: O 61 ASP cc_start: 0.8097 (p0) cc_final: 0.7756 (p0) REVERT: O 75 MET cc_start: 0.8513 (mtp) cc_final: 0.8124 (tpp) REVERT: P 6 MET cc_start: 0.8448 (ptp) cc_final: 0.7980 (ptp) REVERT: P 42 GLN cc_start: 0.7883 (mm-40) cc_final: 0.7278 (mt0) REVERT: P 73 TYR cc_start: 0.8219 (t80) cc_final: 0.7870 (t80) REVERT: Q 34 LYS cc_start: 0.9142 (tppt) cc_final: 0.8887 (mmtt) REVERT: Q 37 GLU cc_start: 0.8877 (tt0) cc_final: 0.8470 (tt0) REVERT: Q 42 GLN cc_start: 0.8837 (mm110) cc_final: 0.8612 (mp10) REVERT: R 59 LEU cc_start: 0.9161 (mt) cc_final: 0.8892 (mp) REVERT: S 6 MET cc_start: 0.7824 (mpp) cc_final: 0.7487 (pmm) REVERT: S 11 MET cc_start: 0.8679 (tpp) cc_final: 0.8184 (tpt) REVERT: S 17 MET cc_start: 0.8820 (mtp) cc_final: 0.8226 (mmm) REVERT: S 73 TYR cc_start: 0.8548 (t80) cc_final: 0.8009 (t80) REVERT: Y 64 GLN cc_start: 0.7878 (mm110) cc_final: 0.7665 (mm-40) REVERT: Y 71 GLU cc_start: 0.8416 (mm-30) cc_final: 0.8119 (tp30) REVERT: Y 98 ARG cc_start: 0.8867 (ttp80) cc_final: 0.8417 (tpt90) REVERT: Y 147 ASP cc_start: 0.9193 (t70) cc_final: 0.8950 (t0) REVERT: a 24 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.6271 (mmt180) REVERT: a 56 PHE cc_start: 0.8144 (OUTLIER) cc_final: 0.7575 (t80) REVERT: a 94 TYR cc_start: 0.7530 (t80) cc_final: 0.6867 (t80) REVERT: a 106 LEU cc_start: 0.9107 (tp) cc_final: 0.8899 (pp) REVERT: a 164 TYR cc_start: 0.8011 (m-80) cc_final: 0.7606 (m-80) REVERT: a 169 LYS cc_start: 0.6413 (mttt) cc_final: 0.5758 (mmtt) REVERT: a 231 TRP cc_start: 0.7590 (p-90) cc_final: 0.7304 (p-90) outliers start: 117 outliers final: 85 residues processed: 656 average time/residue: 0.2126 time to fit residues: 230.4549 Evaluate side-chains 651 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 555 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain B residue 504 LEU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 389 VAL 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 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 22 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 55 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 51 HIS Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 127 LEU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 252 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 141 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 435 optimal weight: 5.9990 chunk 376 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 82 optimal weight: 0.0980 chunk 342 optimal weight: 3.9990 chunk 293 optimal weight: 0.6980 chunk 323 optimal weight: 3.9990 chunk 311 optimal weight: 7.9990 chunk 389 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN X 104 GLN D 243 ASN D 437 HIS ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN ** S 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN a 76 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.090225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.061486 restraints weight = 87157.502| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.37 r_work: 0.2701 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2570 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 37528 Z= 0.145 Angle : 0.611 12.344 50797 Z= 0.306 Chirality : 0.043 0.186 5920 Planarity : 0.004 0.047 6550 Dihedral : 6.960 140.826 5369 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.97 % Allowed : 16.84 % Favored : 80.19 % 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: 1.06 (0.12), residues: 4807 helix: 1.64 (0.10), residues: 2582 sheet: -0.27 (0.22), residues: 541 loop : -0.34 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 113 TYR 0.020 0.001 TYR F 116 PHE 0.021 0.001 PHE L 35 TRP 0.015 0.001 TRP a 186 HIS 0.004 0.001 HIS W 21 Details of bonding type rmsd covalent geometry : bond 0.00336 (37528) covalent geometry : angle 0.61130 (50797) hydrogen bonds : bond 0.04188 ( 2242) hydrogen bonds : angle 4.39736 ( 6513) *********************** 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 698 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 584 time to evaluate : 1.306 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 143 ASP cc_start: 0.8393 (t0) cc_final: 0.7987 (t0) REVERT: W 156 ASP cc_start: 0.8745 (p0) cc_final: 0.8376 (p0) REVERT: C 132 ILE cc_start: 0.9388 (pt) cc_final: 0.9075 (mm) REVERT: B 67 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8926 (mm-30) REVERT: A 262 ASP cc_start: 0.8299 (p0) cc_final: 0.7887 (p0) REVERT: A 356 GLU cc_start: 0.8385 (tp30) cc_final: 0.7977 (tt0) REVERT: A 386 MET cc_start: 0.9235 (mmt) cc_final: 0.8980 (mmt) REVERT: A 484 GLN cc_start: 0.8927 (tp40) cc_final: 0.8704 (tm-30) REVERT: X 117 ARG cc_start: 0.7599 (ttp80) cc_final: 0.7126 (ttp80) REVERT: X 118 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: X 123 GLN cc_start: 0.8199 (mm110) cc_final: 0.7208 (mm-40) REVERT: X 145 ASN cc_start: 0.7763 (t0) cc_final: 0.7264 (m-40) REVERT: H 65 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8611 (t) REVERT: E 125 LEU cc_start: 0.9625 (OUTLIER) cc_final: 0.9375 (mp) REVERT: E 192 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8425 (tp30) REVERT: E 232 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8639 (m-30) REVERT: E 249 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9011 (mp) REVERT: E 365 GLN cc_start: 0.9034 (pt0) cc_final: 0.8612 (tp40) REVERT: D 243 ASN cc_start: 0.8856 (OUTLIER) cc_final: 0.8361 (m110) REVERT: D 301 ASP cc_start: 0.9018 (t0) cc_final: 0.8681 (t0) REVERT: D 370 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8527 (mp) REVERT: I 42 GLN cc_start: 0.7968 (mm110) cc_final: 0.7726 (mm-40) REVERT: I 56 VAL cc_start: 0.9575 (t) cc_final: 0.9262 (p) REVERT: I 57 MET cc_start: 0.9000 (tmm) cc_final: 0.8740 (tmm) REVERT: J 17 MET cc_start: 0.9428 (mmp) cc_final: 0.8881 (mmt) REVERT: L 5 ASN cc_start: 0.6973 (p0) cc_final: 0.6399 (m110) REVERT: L 11 MET cc_start: 0.8829 (tpt) cc_final: 0.8498 (tpt) REVERT: L 34 LYS cc_start: 0.9323 (OUTLIER) cc_final: 0.8972 (tppt) REVERT: L 35 PHE cc_start: 0.8971 (t80) cc_final: 0.8671 (t80) REVERT: L 37 GLU cc_start: 0.9002 (tt0) cc_final: 0.8594 (tp30) REVERT: L 42 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8179 (tm-30) REVERT: L 44 ASP cc_start: 0.9186 (m-30) cc_final: 0.8883 (p0) REVERT: L 76 PHE cc_start: 0.7933 (m-80) cc_final: 0.7664 (m-10) REVERT: M 30 ILE cc_start: 0.9247 (mt) cc_final: 0.8880 (mt) REVERT: M 55 ILE cc_start: 0.8745 (mm) cc_final: 0.8519 (mt) REVERT: N 16 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8686 (ttm) REVERT: N 55 ILE cc_start: 0.9050 (mm) cc_final: 0.8723 (mt) REVERT: N 57 MET cc_start: 0.8290 (tmm) cc_final: 0.7684 (tmm) REVERT: N 61 ASP cc_start: 0.8135 (p0) cc_final: 0.6486 (p0) REVERT: N 66 ILE cc_start: 0.9071 (tt) cc_final: 0.8705 (tp) REVERT: N 70 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8756 (mp) REVERT: O 57 MET cc_start: 0.9159 (tmm) cc_final: 0.8895 (tmm) REVERT: O 61 ASP cc_start: 0.8096 (p0) cc_final: 0.7797 (p0) REVERT: O 75 MET cc_start: 0.8466 (mtp) cc_final: 0.8141 (tpp) REVERT: P 73 TYR cc_start: 0.8104 (t80) cc_final: 0.7769 (t80) REVERT: Q 34 LYS cc_start: 0.9130 (tppt) cc_final: 0.8872 (tppt) REVERT: Q 37 GLU cc_start: 0.8842 (tt0) cc_final: 0.8533 (tt0) REVERT: Q 42 GLN cc_start: 0.8838 (mm110) cc_final: 0.8574 (mp10) REVERT: R 57 MET cc_start: 0.9122 (ttt) cc_final: 0.8839 (ttt) REVERT: R 63 ILE cc_start: 0.9217 (mm) cc_final: 0.9007 (mt) REVERT: S 11 MET cc_start: 0.8628 (tpp) cc_final: 0.8125 (tpt) REVERT: S 17 MET cc_start: 0.8841 (mtp) cc_final: 0.8191 (mmm) REVERT: S 73 TYR cc_start: 0.8595 (t80) cc_final: 0.8082 (t80) REVERT: Y 64 GLN cc_start: 0.7983 (mm110) cc_final: 0.7781 (mm-40) REVERT: Y 71 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8152 (tp30) REVERT: Y 98 ARG cc_start: 0.8862 (ttp80) cc_final: 0.8412 (tpt90) REVERT: Y 147 ASP cc_start: 0.9243 (t70) cc_final: 0.9029 (t0) REVERT: a 24 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.6259 (mmt180) REVERT: a 56 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7522 (t80) REVERT: a 91 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8742 (mmmt) REVERT: a 94 TYR cc_start: 0.7545 (t80) cc_final: 0.6895 (t80) REVERT: a 106 LEU cc_start: 0.9110 (tp) cc_final: 0.8904 (pp) REVERT: a 119 ASP cc_start: 0.8051 (t0) cc_final: 0.7722 (t0) REVERT: a 164 TYR cc_start: 0.7984 (m-80) cc_final: 0.7499 (m-80) REVERT: a 169 LYS cc_start: 0.6399 (mttt) cc_final: 0.5816 (mmtt) REVERT: a 231 TRP cc_start: 0.7539 (p-90) cc_final: 0.7262 (p-90) REVERT: a 259 LEU cc_start: 0.9508 (OUTLIER) cc_final: 0.9276 (mm) outliers start: 114 outliers final: 83 residues processed: 658 average time/residue: 0.2129 time to fit residues: 232.0969 Evaluate side-chains 652 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 556 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 262 ASP Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain X residue 139 SER Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain E residue 54 ILE Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 232 ASP Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 389 VAL 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 198 VAL Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 61 ASP Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain P residue 30 ILE Chi-restraints excluded: chain P residue 46 ILE Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain Q residue 74 VAL Chi-restraints excluded: chain R residue 52 GLN Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 127 LEU Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 252 GLN Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 40 optimal weight: 0.9990 chunk 110 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 chunk 332 optimal weight: 0.8980 chunk 317 optimal weight: 0.3980 chunk 434 optimal weight: 9.9990 chunk 132 optimal weight: 0.0970 chunk 92 optimal weight: 1.9990 chunk 351 optimal weight: 1.9990 chunk 330 optimal weight: 0.8980 chunk 249 optimal weight: 0.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 80 ASN X 104 GLN D 243 ASN J 52 GLN O 52 GLN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 GLN Y 85 GLN a 76 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.091753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.063256 restraints weight = 86645.600| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.31 r_work: 0.2743 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2614 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 37528 Z= 0.119 Angle : 0.600 11.911 50797 Z= 0.299 Chirality : 0.042 0.199 5920 Planarity : 0.004 0.049 6550 Dihedral : 6.711 139.220 5367 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.55 % Allowed : 17.52 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.12), residues: 4807 helix: 1.76 (0.10), residues: 2582 sheet: -0.15 (0.22), residues: 533 loop : -0.24 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG X 113 TYR 0.021 0.001 TYR F 116 PHE 0.019 0.001 PHE Q 53 TRP 0.013 0.001 TRP a 186 HIS 0.004 0.000 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00264 (37528) covalent geometry : angle 0.60019 (50797) hydrogen bonds : bond 0.03935 ( 2242) hydrogen bonds : angle 4.30547 ( 6513) *********************** 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 693 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 595 time to evaluate : 1.503 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 105 THR cc_start: 0.9315 (m) cc_final: 0.9017 (p) REVERT: W 143 ASP cc_start: 0.8284 (t0) cc_final: 0.8014 (t0) REVERT: W 144 LYS cc_start: 0.9269 (mmtm) cc_final: 0.9036 (mmtt) REVERT: W 156 ASP cc_start: 0.8652 (p0) cc_final: 0.8308 (p0) REVERT: C 132 ILE cc_start: 0.9375 (pt) cc_final: 0.9120 (mm) REVERT: B 448 LEU cc_start: 0.9220 (mt) cc_final: 0.8968 (mp) REVERT: A 356 GLU cc_start: 0.8348 (tp30) cc_final: 0.7944 (tt0) REVERT: A 484 GLN cc_start: 0.8901 (tp40) cc_final: 0.8687 (tm-30) REVERT: X 117 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7056 (ttp80) REVERT: X 118 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8138 (mp0) REVERT: X 123 GLN cc_start: 0.8205 (mm110) cc_final: 0.7594 (mm-40) REVERT: X 145 ASN cc_start: 0.7597 (t0) cc_final: 0.7077 (m-40) REVERT: H 65 SER cc_start: 0.9110 (m) cc_final: 0.8583 (t) REVERT: G 15 ASN cc_start: 0.8662 (t0) cc_final: 0.8454 (t0) REVERT: E 125 LEU cc_start: 0.9569 (OUTLIER) cc_final: 0.9361 (mp) REVERT: E 192 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8418 (tp30) REVERT: E 365 GLN cc_start: 0.8967 (pt0) cc_final: 0.8642 (tp40) REVERT: D 243 ASN cc_start: 0.8839 (OUTLIER) cc_final: 0.8481 (m110) REVERT: D 301 ASP cc_start: 0.8973 (t0) cc_final: 0.8630 (t0) REVERT: D 370 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8489 (mp) REVERT: I 17 MET cc_start: 0.8586 (mmt) cc_final: 0.8301 (mmt) REVERT: I 41 ARG cc_start: 0.8618 (mtm110) cc_final: 0.8391 (tpp-160) REVERT: I 56 VAL cc_start: 0.9502 (t) cc_final: 0.9182 (p) REVERT: I 57 MET cc_start: 0.8957 (tmm) cc_final: 0.8728 (tmm) REVERT: J 17 MET cc_start: 0.9289 (mmp) cc_final: 0.8996 (mmt) REVERT: J 75 MET cc_start: 0.8915 (tpp) cc_final: 0.8438 (tpp) REVERT: L 5 ASN cc_start: 0.6638 (p0) cc_final: 0.6041 (m-40) REVERT: L 11 MET cc_start: 0.8880 (tpt) cc_final: 0.8559 (tpt) REVERT: L 34 LYS cc_start: 0.9276 (OUTLIER) cc_final: 0.8976 (tppt) REVERT: L 37 GLU cc_start: 0.8955 (tt0) cc_final: 0.8610 (tp30) REVERT: L 42 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8305 (tm-30) REVERT: L 50 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8339 (mtp180) REVERT: L 76 PHE cc_start: 0.7867 (m-80) cc_final: 0.7620 (m-10) REVERT: M 30 ILE cc_start: 0.9250 (mt) cc_final: 0.8879 (mt) REVERT: M 55 ILE cc_start: 0.8758 (mm) cc_final: 0.8522 (mt) REVERT: M 57 MET cc_start: 0.9117 (tmm) cc_final: 0.8832 (tmm) REVERT: N 16 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8648 (ttm) REVERT: N 51 THR cc_start: 0.8931 (m) cc_final: 0.8664 (p) REVERT: N 55 ILE cc_start: 0.9056 (mm) cc_final: 0.8741 (mt) REVERT: N 57 MET cc_start: 0.8161 (tmm) cc_final: 0.7542 (tmm) REVERT: N 61 ASP cc_start: 0.8230 (p0) cc_final: 0.6674 (p0) REVERT: N 66 ILE cc_start: 0.9069 (tt) cc_final: 0.8707 (tp) REVERT: N 70 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8754 (mp) REVERT: O 53 PHE cc_start: 0.9415 (t80) cc_final: 0.9135 (t80) REVERT: O 57 MET cc_start: 0.9140 (tmm) cc_final: 0.8876 (tmm) REVERT: O 61 ASP cc_start: 0.8152 (p0) cc_final: 0.7808 (p0) REVERT: O 75 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.8187 (tpp) REVERT: P 42 GLN cc_start: 0.7797 (mm-40) cc_final: 0.7165 (mt0) REVERT: P 73 TYR cc_start: 0.8029 (t80) cc_final: 0.7712 (t80) REVERT: P 75 MET cc_start: 0.8660 (tpp) cc_final: 0.8438 (tpp) REVERT: Q 34 LYS cc_start: 0.9194 (tppt) cc_final: 0.8982 (tppt) REVERT: Q 37 GLU cc_start: 0.8811 (tt0) cc_final: 0.8406 (tt0) REVERT: Q 42 GLN cc_start: 0.8762 (mm110) cc_final: 0.8520 (mp10) REVERT: R 6 MET cc_start: 0.7716 (ptp) cc_final: 0.7407 (pmm) REVERT: R 63 ILE cc_start: 0.9237 (mm) cc_final: 0.9030 (mt) REVERT: S 6 MET cc_start: 0.7927 (mpp) cc_final: 0.7527 (pmm) REVERT: S 11 MET cc_start: 0.8763 (tpp) cc_final: 0.8203 (tpt) REVERT: S 17 MET cc_start: 0.8822 (mtp) cc_final: 0.8131 (mmm) REVERT: S 73 TYR cc_start: 0.8579 (t80) cc_final: 0.8032 (t80) REVERT: Y 22 MET cc_start: 0.8638 (ptt) cc_final: 0.8347 (ppp) REVERT: Y 71 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8256 (tp30) REVERT: Y 98 ARG cc_start: 0.8859 (ttp80) cc_final: 0.8579 (tpp-160) REVERT: Y 147 ASP cc_start: 0.9214 (t70) cc_final: 0.9000 (t0) REVERT: a 24 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.6239 (mmt180) REVERT: a 56 PHE cc_start: 0.8100 (OUTLIER) cc_final: 0.7481 (t80) REVERT: a 91 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8712 (mmmt) REVERT: a 94 TYR cc_start: 0.7512 (t80) cc_final: 0.6849 (t80) REVERT: a 106 LEU cc_start: 0.9100 (tp) cc_final: 0.8896 (pp) REVERT: a 119 ASP cc_start: 0.7922 (t0) cc_final: 0.7584 (t0) REVERT: a 164 TYR cc_start: 0.7955 (m-80) cc_final: 0.7639 (m-80) REVERT: a 169 LYS cc_start: 0.6564 (mttt) cc_final: 0.5963 (mmtt) REVERT: a 201 LEU cc_start: 0.9072 (tp) cc_final: 0.8694 (pp) REVERT: a 231 TRP cc_start: 0.7478 (p-90) cc_final: 0.7276 (p-90) REVERT: a 259 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9268 (mm) outliers start: 98 outliers final: 68 residues processed: 656 average time/residue: 0.2178 time to fit residues: 235.4668 Evaluate side-chains 640 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 561 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 236 TYR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 366 ARG 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 88 MET Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 243 ASN Chi-restraints excluded: chain D residue 296 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain I residue 44 ASP Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 LEU Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 24 ARG Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 252 GLN Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 179 optimal weight: 9.9990 chunk 4 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 352 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 349 optimal weight: 7.9990 chunk 219 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 317 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 73 GLN X 104 GLN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN a 76 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.091265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.062575 restraints weight = 87660.574| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.32 r_work: 0.2721 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 37528 Z= 0.142 Angle : 0.621 12.647 50797 Z= 0.310 Chirality : 0.043 0.238 5920 Planarity : 0.004 0.054 6550 Dihedral : 6.594 137.056 5365 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.27 % Allowed : 17.86 % Favored : 79.87 % 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: 1.25 (0.12), residues: 4807 helix: 1.77 (0.10), residues: 2583 sheet: -0.17 (0.22), residues: 547 loop : -0.23 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 113 TYR 0.025 0.001 TYR O 10 PHE 0.022 0.001 PHE N 53 TRP 0.014 0.001 TRP a 186 HIS 0.004 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00333 (37528) covalent geometry : angle 0.62109 (50797) hydrogen bonds : bond 0.04020 ( 2242) hydrogen bonds : angle 4.33074 ( 6513) *********************** 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 653 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 566 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 105 THR cc_start: 0.9328 (m) cc_final: 0.9030 (p) REVERT: W 116 LEU cc_start: 0.8482 (mp) cc_final: 0.8225 (mp) REVERT: W 143 ASP cc_start: 0.8195 (t0) cc_final: 0.7934 (t0) REVERT: W 144 LYS cc_start: 0.9249 (mmtm) cc_final: 0.9026 (mmtt) REVERT: W 156 ASP cc_start: 0.8662 (p0) cc_final: 0.8321 (p0) REVERT: C 132 ILE cc_start: 0.9356 (pt) cc_final: 0.9065 (mm) REVERT: B 448 LEU cc_start: 0.9221 (mt) cc_final: 0.8964 (mp) REVERT: A 356 GLU cc_start: 0.8372 (tp30) cc_final: 0.7980 (tt0) REVERT: A 484 GLN cc_start: 0.8935 (tp40) cc_final: 0.8713 (tm-30) REVERT: X 123 GLN cc_start: 0.8217 (mm110) cc_final: 0.7626 (mm-40) REVERT: H 46 LYS cc_start: 0.9417 (mptt) cc_final: 0.9183 (mptt) REVERT: H 65 SER cc_start: 0.9155 (m) cc_final: 0.8594 (t) REVERT: H 72 GLN cc_start: 0.8413 (mm-40) cc_final: 0.8116 (mm-40) REVERT: F 123 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8869 (mm110) REVERT: E 125 LEU cc_start: 0.9587 (OUTLIER) cc_final: 0.9362 (mp) REVERT: E 192 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8447 (tp30) REVERT: E 365 GLN cc_start: 0.8979 (pt0) cc_final: 0.8612 (tp40) REVERT: D 301 ASP cc_start: 0.8984 (t0) cc_final: 0.8660 (t0) REVERT: D 370 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8472 (mp) REVERT: I 17 MET cc_start: 0.8585 (mmt) cc_final: 0.8256 (mmt) REVERT: I 41 ARG cc_start: 0.8596 (mtm110) cc_final: 0.8170 (ttp-110) REVERT: I 42 GLN cc_start: 0.8149 (mm-40) cc_final: 0.7665 (mm-40) REVERT: I 56 VAL cc_start: 0.9569 (t) cc_final: 0.9293 (p) REVERT: I 57 MET cc_start: 0.8954 (tmm) cc_final: 0.8648 (tmm) REVERT: J 16 MET cc_start: 0.9214 (mmt) cc_final: 0.8987 (mmm) REVERT: J 75 MET cc_start: 0.8902 (tpp) cc_final: 0.8343 (tpp) REVERT: L 5 ASN cc_start: 0.7141 (p0) cc_final: 0.6416 (m-40) REVERT: L 10 TYR cc_start: 0.8785 (m-80) cc_final: 0.7870 (m-80) REVERT: L 11 MET cc_start: 0.8883 (tpt) cc_final: 0.8592 (tpt) REVERT: L 34 LYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8998 (tppt) REVERT: L 37 GLU cc_start: 0.8979 (tt0) cc_final: 0.8469 (tp30) REVERT: L 41 ARG cc_start: 0.7980 (mtt90) cc_final: 0.7730 (mtp85) REVERT: L 42 GLN cc_start: 0.8672 (tm-30) cc_final: 0.8456 (tm-30) REVERT: L 50 ARG cc_start: 0.8545 (mtm-85) cc_final: 0.8328 (mtp180) REVERT: L 74 VAL cc_start: 0.8867 (t) cc_final: 0.8586 (p) REVERT: L 76 PHE cc_start: 0.7909 (m-80) cc_final: 0.7592 (m-10) REVERT: M 11 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.7682 (tmm) REVERT: M 30 ILE cc_start: 0.9231 (mt) cc_final: 0.8866 (mt) REVERT: M 57 MET cc_start: 0.9128 (tmm) cc_final: 0.8885 (tmm) REVERT: N 16 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8682 (ttm) REVERT: N 42 GLN cc_start: 0.8945 (mm-40) cc_final: 0.8706 (mm-40) REVERT: N 55 ILE cc_start: 0.8986 (mm) cc_final: 0.8662 (mt) REVERT: N 57 MET cc_start: 0.8211 (tmm) cc_final: 0.7648 (tmm) REVERT: N 61 ASP cc_start: 0.8127 (p0) cc_final: 0.6805 (p0) REVERT: N 66 ILE cc_start: 0.9091 (tt) cc_final: 0.8863 (pt) REVERT: N 70 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8803 (mp) REVERT: O 50 ARG cc_start: 0.8886 (ttp-170) cc_final: 0.8646 (ttp-170) REVERT: O 53 PHE cc_start: 0.9430 (t80) cc_final: 0.9162 (t80) REVERT: O 57 MET cc_start: 0.9146 (tmm) cc_final: 0.8890 (tmm) REVERT: O 61 ASP cc_start: 0.8158 (p0) cc_final: 0.7801 (p0) REVERT: O 75 MET cc_start: 0.8399 (OUTLIER) cc_final: 0.8168 (tpp) REVERT: P 17 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8620 (mmt) REVERT: P 42 GLN cc_start: 0.7872 (mm-40) cc_final: 0.7251 (mt0) REVERT: P 73 TYR cc_start: 0.8048 (t80) cc_final: 0.7727 (t80) REVERT: R 6 MET cc_start: 0.7775 (ptp) cc_final: 0.7474 (pmm) REVERT: S 6 MET cc_start: 0.7905 (mpp) cc_final: 0.7502 (pmm) REVERT: S 11 MET cc_start: 0.8635 (tpp) cc_final: 0.8098 (tpt) REVERT: S 17 MET cc_start: 0.8845 (mtp) cc_final: 0.8142 (mmm) REVERT: S 73 TYR cc_start: 0.8580 (t80) cc_final: 0.8002 (t80) REVERT: Y 22 MET cc_start: 0.8584 (ptt) cc_final: 0.8312 (ppp) REVERT: Y 71 GLU cc_start: 0.8567 (mm-30) cc_final: 0.8268 (tp30) REVERT: Y 98 ARG cc_start: 0.8874 (ttp80) cc_final: 0.8581 (tpp-160) REVERT: Y 147 ASP cc_start: 0.9228 (t70) cc_final: 0.9010 (t0) REVERT: a 56 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7400 (t80) REVERT: a 62 SER cc_start: 0.6990 (OUTLIER) cc_final: 0.6621 (m) REVERT: a 91 LYS cc_start: 0.8899 (mmmt) cc_final: 0.8678 (mmmt) REVERT: a 94 TYR cc_start: 0.7541 (t80) cc_final: 0.6855 (t80) REVERT: a 119 ASP cc_start: 0.8006 (t0) cc_final: 0.7676 (t0) REVERT: a 164 TYR cc_start: 0.8035 (m-80) cc_final: 0.7494 (m-80) REVERT: a 169 LYS cc_start: 0.6520 (mttt) cc_final: 0.5973 (mmtt) REVERT: a 201 LEU cc_start: 0.9111 (tp) cc_final: 0.8722 (pp) REVERT: a 219 GLU cc_start: 0.8653 (pp20) cc_final: 0.8424 (pp20) REVERT: a 231 TRP cc_start: 0.7641 (p-90) cc_final: 0.7187 (p-90) REVERT: a 259 LEU cc_start: 0.9500 (OUTLIER) cc_final: 0.9274 (mm) outliers start: 87 outliers final: 62 residues processed: 625 average time/residue: 0.2123 time to fit residues: 218.2884 Evaluate side-chains 628 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 555 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain X residue 118 GLU Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 74 VAL Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 16 MET Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 114 LEU Chi-restraints excluded: chain a residue 252 GLN Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 317 optimal weight: 0.6980 chunk 283 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 289 optimal weight: 5.9990 chunk 281 optimal weight: 3.9990 chunk 258 optimal weight: 0.0670 chunk 191 optimal weight: 3.9990 chunk 395 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 432 optimal weight: 4.9990 overall best weight: 2.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 104 GLN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.061351 restraints weight = 87020.178| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.35 r_work: 0.2694 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 37528 Z= 0.177 Angle : 0.646 13.011 50797 Z= 0.323 Chirality : 0.044 0.222 5920 Planarity : 0.004 0.051 6550 Dihedral : 6.629 137.218 5361 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.22 % Allowed : 17.91 % Favored : 79.87 % 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: 1.19 (0.12), residues: 4807 helix: 1.73 (0.10), residues: 2571 sheet: -0.24 (0.21), residues: 554 loop : -0.24 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG X 117 TYR 0.021 0.001 TYR F 116 PHE 0.022 0.001 PHE L 35 TRP 0.023 0.002 TRP X 26 HIS 0.006 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00423 (37528) covalent geometry : angle 0.64625 (50797) hydrogen bonds : bond 0.04189 ( 2242) hydrogen bonds : angle 4.40022 ( 6513) ********************** 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 659 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 574 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: W 43 MET cc_start: 0.9214 (tpp) cc_final: 0.8955 (tpt) REVERT: W 105 THR cc_start: 0.9332 (m) cc_final: 0.9051 (p) REVERT: W 116 LEU cc_start: 0.8530 (mp) cc_final: 0.8254 (mp) REVERT: W 143 ASP cc_start: 0.8286 (t0) cc_final: 0.8024 (t0) REVERT: W 144 LYS cc_start: 0.9271 (mmtm) cc_final: 0.9052 (mmtt) REVERT: W 156 ASP cc_start: 0.8725 (p0) cc_final: 0.8358 (p0) REVERT: C 132 ILE cc_start: 0.9362 (pt) cc_final: 0.9095 (mm) REVERT: B 448 LEU cc_start: 0.9232 (mt) cc_final: 0.8974 (mp) REVERT: A 262 ASP cc_start: 0.8328 (p0) cc_final: 0.7898 (p0) REVERT: A 356 GLU cc_start: 0.8380 (tp30) cc_final: 0.7967 (tt0) REVERT: A 484 GLN cc_start: 0.8966 (tp40) cc_final: 0.8729 (tm-30) REVERT: X 123 GLN cc_start: 0.8215 (mm110) cc_final: 0.7604 (mm-40) REVERT: H 46 LYS cc_start: 0.9444 (mptt) cc_final: 0.9233 (mptt) REVERT: H 51 ARG cc_start: 0.8843 (mtp-110) cc_final: 0.8622 (mtp-110) REVERT: H 65 SER cc_start: 0.9175 (m) cc_final: 0.8570 (t) REVERT: H 72 GLN cc_start: 0.8366 (mm-40) cc_final: 0.8105 (mm-40) REVERT: G 102 MET cc_start: 0.8638 (mtp) cc_final: 0.8430 (mtp) REVERT: F 123 GLN cc_start: 0.9104 (mm-40) cc_final: 0.8871 (mm110) REVERT: E 123 GLN cc_start: 0.8714 (tt0) cc_final: 0.8474 (tm-30) REVERT: E 125 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9343 (mp) REVERT: E 192 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8458 (tp30) REVERT: E 365 GLN cc_start: 0.9003 (pt0) cc_final: 0.8621 (tp40) REVERT: D 301 ASP cc_start: 0.9008 (t0) cc_final: 0.8671 (t0) REVERT: D 370 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8517 (mp) REVERT: I 17 MET cc_start: 0.8624 (mmt) cc_final: 0.8327 (mmt) REVERT: I 28 ILE cc_start: 0.9364 (mm) cc_final: 0.9107 (mt) REVERT: I 41 ARG cc_start: 0.8532 (mtm110) cc_final: 0.8237 (ttp-110) REVERT: I 42 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7578 (mm-40) REVERT: I 56 VAL cc_start: 0.9587 (t) cc_final: 0.9307 (p) REVERT: I 57 MET cc_start: 0.9007 (tmm) cc_final: 0.8684 (tmm) REVERT: J 16 MET cc_start: 0.9216 (mmt) cc_final: 0.8878 (mmt) REVERT: J 75 MET cc_start: 0.8916 (tpp) cc_final: 0.8362 (tpp) REVERT: L 5 ASN cc_start: 0.7233 (p0) cc_final: 0.6344 (m110) REVERT: L 10 TYR cc_start: 0.8774 (m-80) cc_final: 0.7736 (m-80) REVERT: L 11 MET cc_start: 0.8933 (tpt) cc_final: 0.8717 (tpt) REVERT: L 34 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8992 (tppt) REVERT: L 37 GLU cc_start: 0.8991 (tt0) cc_final: 0.8491 (tp30) REVERT: L 42 GLN cc_start: 0.8586 (tm-30) cc_final: 0.8154 (tm-30) REVERT: L 74 VAL cc_start: 0.8884 (t) cc_final: 0.8603 (p) REVERT: M 11 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.7645 (tmm) REVERT: M 30 ILE cc_start: 0.9209 (mt) cc_final: 0.8839 (mt) REVERT: M 57 MET cc_start: 0.9150 (tmm) cc_final: 0.8898 (tmm) REVERT: N 55 ILE cc_start: 0.8989 (mm) cc_final: 0.8672 (mt) REVERT: N 57 MET cc_start: 0.8160 (tmm) cc_final: 0.7572 (tmm) REVERT: N 61 ASP cc_start: 0.8134 (p0) cc_final: 0.6771 (p0) REVERT: N 65 MET cc_start: 0.9239 (mtt) cc_final: 0.8745 (mtm) REVERT: N 66 ILE cc_start: 0.9113 (tt) cc_final: 0.8796 (tp) REVERT: N 70 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8739 (mp) REVERT: O 50 ARG cc_start: 0.8884 (ttp-170) cc_final: 0.8639 (ttp-170) REVERT: O 53 PHE cc_start: 0.9442 (t80) cc_final: 0.9165 (t80) REVERT: O 57 MET cc_start: 0.9143 (tmm) cc_final: 0.8855 (tmm) REVERT: O 61 ASP cc_start: 0.8085 (p0) cc_final: 0.7779 (p0) REVERT: O 75 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8146 (tpp) REVERT: P 17 MET cc_start: 0.8931 (OUTLIER) cc_final: 0.8604 (mmt) REVERT: P 42 GLN cc_start: 0.7885 (mm-40) cc_final: 0.7287 (mt0) REVERT: P 73 TYR cc_start: 0.8105 (t80) cc_final: 0.7824 (t80) REVERT: Q 42 GLN cc_start: 0.8706 (mm110) cc_final: 0.8469 (mp10) REVERT: R 6 MET cc_start: 0.7817 (ptp) cc_final: 0.7453 (pmm) REVERT: R 16 MET cc_start: 0.9320 (mmm) cc_final: 0.8796 (mmm) REVERT: R 34 LYS cc_start: 0.9055 (mttm) cc_final: 0.8565 (mtpt) REVERT: S 6 MET cc_start: 0.7982 (mpp) cc_final: 0.7601 (pmm) REVERT: S 17 MET cc_start: 0.8896 (mtp) cc_final: 0.8118 (mmm) REVERT: S 73 TYR cc_start: 0.8592 (t80) cc_final: 0.8012 (t80) REVERT: Y 22 MET cc_start: 0.8619 (ptt) cc_final: 0.8329 (ppp) REVERT: Y 71 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8267 (tp30) REVERT: Y 98 ARG cc_start: 0.8881 (ttp80) cc_final: 0.8428 (tpt90) REVERT: Y 147 ASP cc_start: 0.9257 (t70) cc_final: 0.9009 (t0) REVERT: a 56 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7491 (t80) REVERT: a 62 SER cc_start: 0.7127 (OUTLIER) cc_final: 0.6661 (m) REVERT: a 91 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8667 (mmmt) REVERT: a 94 TYR cc_start: 0.7459 (t80) cc_final: 0.6814 (t80) REVERT: a 119 ASP cc_start: 0.8041 (t0) cc_final: 0.7757 (t0) REVERT: a 164 TYR cc_start: 0.7982 (m-80) cc_final: 0.7667 (m-80) REVERT: a 169 LYS cc_start: 0.6475 (mttt) cc_final: 0.5928 (mmtt) REVERT: a 201 LEU cc_start: 0.9127 (tp) cc_final: 0.8734 (pp) REVERT: a 219 GLU cc_start: 0.8682 (pp20) cc_final: 0.8416 (pp20) REVERT: a 259 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9287 (mm) outliers start: 85 outliers final: 66 residues processed: 632 average time/residue: 0.2178 time to fit residues: 227.8899 Evaluate side-chains 640 residues out of total 3849 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 564 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain W residue 30 MET Chi-restraints excluded: chain W residue 48 SER Chi-restraints excluded: chain W residue 146 VAL Chi-restraints excluded: chain W residue 157 MET Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 99 VAL Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 227 THR Chi-restraints excluded: chain C residue 236 TYR Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 441 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 121 LEU Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 395 THR Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 26 HIS Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 173 THR Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 511 GLN Chi-restraints excluded: chain H residue 75 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain G residue 69 ASP Chi-restraints excluded: chain G residue 180 GLN Chi-restraints excluded: chain G residue 243 MET Chi-restraints excluded: chain F residue 42 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 340 THR Chi-restraints excluded: chain E residue 366 ARG Chi-restraints excluded: chain E residue 431 MET Chi-restraints excluded: chain E residue 438 LEU Chi-restraints excluded: chain D residue 116 TYR Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 348 VAL Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain I residue 31 LEU Chi-restraints excluded: chain J residue 15 VAL Chi-restraints excluded: chain J residue 60 VAL Chi-restraints excluded: chain L residue 34 LYS Chi-restraints excluded: chain M residue 11 MET Chi-restraints excluded: chain M residue 78 VAL Chi-restraints excluded: chain N residue 63 ILE Chi-restraints excluded: chain N residue 70 LEU Chi-restraints excluded: chain O residue 56 VAL Chi-restraints excluded: chain O residue 75 MET Chi-restraints excluded: chain P residue 17 MET Chi-restraints excluded: chain P residue 68 VAL Chi-restraints excluded: chain Q residue 63 ILE Chi-restraints excluded: chain R residue 61 ASP Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 22 ILE Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain Y residue 15 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Y residue 140 VAL Chi-restraints excluded: chain Y residue 152 LEU Chi-restraints excluded: chain a residue 56 PHE Chi-restraints excluded: chain a residue 62 SER Chi-restraints excluded: chain a residue 79 ILE Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain a residue 252 GLN Chi-restraints excluded: chain a residue 259 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 389 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 225 optimal weight: 3.9990 chunk 402 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 188 optimal weight: 5.9990 chunk 238 optimal weight: 5.9990 chunk 422 optimal weight: 4.9990 chunk 303 optimal weight: 0.0870 chunk 216 optimal weight: 0.9990 chunk 237 optimal weight: 0.6980 overall best weight: 0.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 73 GLN X 104 GLN D 243 ASN ** P 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 64 GLN Y 85 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.091618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.062909 restraints weight = 86983.678| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.38 r_work: 0.2737 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 37528 Z= 0.128 Angle : 0.632 13.004 50797 Z= 0.314 Chirality : 0.043 0.254 5920 Planarity : 0.004 0.053 6550 Dihedral : 6.523 136.227 5361 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.90 % Allowed : 18.40 % Favored : 79.69 % 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: 1.29 (0.12), residues: 4807 helix: 1.80 (0.10), residues: 2583 sheet: -0.12 (0.22), residues: 533 loop : -0.22 (0.15), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG X 117 TYR 0.026 0.001 TYR O 10 PHE 0.022 0.001 PHE L 35 TRP 0.027 0.002 TRP a 231 HIS 0.007 0.001 HIS G 200 Details of bonding type rmsd covalent geometry : bond 0.00293 (37528) covalent geometry : angle 0.63198 (50797) hydrogen bonds : bond 0.03933 ( 2242) hydrogen bonds : angle 4.34799 ( 6513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11752.28 seconds wall clock time: 200 minutes 23.47 seconds (12023.47 seconds total)