Starting phenix.real_space_refine on Fri Jan 24 12:29:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9gct_51236/01_2025/9gct_51236.cif Found real_map, /net/cci-nas-00/data/ceres_data/9gct_51236/01_2025/9gct_51236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9gct_51236/01_2025/9gct_51236.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9gct_51236/01_2025/9gct_51236.map" model { file = "/net/cci-nas-00/data/ceres_data/9gct_51236/01_2025/9gct_51236.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9gct_51236/01_2025/9gct_51236.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.011 sd= 0.053 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 45 5.49 5 Mg 15 5.21 5 S 342 5.16 5 C 46088 2.51 5 N 13357 2.21 5 O 14093 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 73940 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "B" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "C" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "D" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "E" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "F" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "G" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 401} Chain: "H" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "J" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "K" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "L" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "M" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "N" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "O" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "P" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "Y" Number of atoms: 3298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3298 Classifications: {'peptide': 419} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 400} Chain: "a" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "b" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "c" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "d" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "e" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "f" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "g" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "h" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "i" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "j" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "k" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "l" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "o" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "p" Number of atoms: 1478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1478 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 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: "E" 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: 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: "G" 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: "H" 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: "J" 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: "K" 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: "L" 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: "M" 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: "N" 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: "O" 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: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 33.49, per 1000 atoms: 0.45 Number of scatterers: 73940 At special positions: 0 Unit cell: (180.999, 213.759, 272.727, 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 342 16.00 P 45 15.00 Mg 15 11.99 O 14093 8.00 N 13357 7.00 C 46088 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: 14.73 Conformation dependent library (CDL) restraints added in 7.5 seconds 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17520 Finding SS restraints... Secondary structure from input PDB file: 388 helices and 66 sheets defined 58.9% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.04 Creating SS restraints... Processing helix chain 'A' and resid 2 through 9 removed outlier: 4.698A pdb=" N LEU A 6 " --> pdb=" O ASN A 2 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR A 9 " --> pdb=" O GLU A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 21 removed outlier: 4.322A pdb=" N LEU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 21 " --> pdb=" O LEU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 82 through 89 Processing helix chain 'A' and resid 153 through 166 Processing helix chain 'A' and resid 183 through 199 removed outlier: 3.621A pdb=" N LEU A 187 " --> pdb=" O GLY A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.545A pdb=" N VAL A 216 " --> pdb=" O ARG A 212 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLN A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 255 removed outlier: 3.527A pdb=" N HIS A 239 " --> pdb=" O PRO A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 290 through 293 removed outlier: 3.501A pdb=" N ALA A 293 " --> pdb=" O ASP A 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 293' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.994A pdb=" N GLU A 329 " --> pdb=" O SER A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.704A pdb=" N ALA A 350 " --> pdb=" O SER A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.525A pdb=" N LEU A 371 " --> pdb=" O LYS A 367 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 372' Processing helix chain 'A' and resid 374 through 388 Processing helix chain 'A' and resid 391 through 405 removed outlier: 3.774A pdb=" N MET A 405 " --> pdb=" O ASN A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 417 Processing helix chain 'B' and resid 2 through 9 removed outlier: 4.346A pdb=" N LEU B 6 " --> pdb=" O ASN B 2 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR B 9 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 22 removed outlier: 3.963A pdb=" N LEU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 removed outlier: 3.675A pdb=" N ILE B 34 " --> pdb=" O ARG B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 89 removed outlier: 3.635A pdb=" N ILE B 86 " --> pdb=" O SER B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 128 removed outlier: 3.642A pdb=" N ARG B 128 " --> pdb=" O GLU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 166 Processing helix chain 'B' and resid 183 through 199 removed outlier: 4.004A pdb=" N LEU B 187 " --> pdb=" O GLY B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 220 removed outlier: 4.506A pdb=" N GLN B 220 " --> pdb=" O VAL B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 235 through 255 removed outlier: 3.820A pdb=" N HIS B 239 " --> pdb=" O PRO B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 292 through 294 No H-bonds generated for 'chain 'B' and resid 292 through 294' Processing helix chain 'B' and resid 295 through 302 removed outlier: 4.340A pdb=" N ARG B 299 " --> pdb=" O HIS B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 335 removed outlier: 3.953A pdb=" N GLU B 329 " --> pdb=" O SER B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'B' and resid 367 through 372 removed outlier: 3.917A pdb=" N LEU B 371 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 388 removed outlier: 3.651A pdb=" N LEU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 404 Processing helix chain 'B' and resid 408 through 418 removed outlier: 3.889A pdb=" N ARG B 418 " --> pdb=" O GLU B 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 Processing helix chain 'C' and resid 11 through 21 removed outlier: 3.975A pdb=" N ILE C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET C 21 " --> pdb=" O LEU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 155 through 166 removed outlier: 3.989A pdb=" N ALA C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 Processing helix chain 'C' and resid 212 through 220 removed outlier: 3.723A pdb=" N VAL C 216 " --> pdb=" O ARG C 212 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN C 220 " --> pdb=" O VAL C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 255 removed outlier: 3.822A pdb=" N HIS C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 278 Processing helix chain 'C' and resid 290 through 302 Proline residue: C 297 - end of helix removed outlier: 3.924A pdb=" N PHE C 300 " --> pdb=" O ARG C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 336 removed outlier: 3.839A pdb=" N GLU C 329 " --> pdb=" O SER C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 339 No H-bonds generated for 'chain 'C' and resid 337 through 339' Processing helix chain 'C' and resid 346 through 353 removed outlier: 3.559A pdb=" N ALA C 350 " --> pdb=" O SER C 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 388 Processing helix chain 'C' and resid 391 through 403 Processing helix chain 'C' and resid 408 through 418 Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.957A pdb=" N LEU D 6 " --> pdb=" O ASN D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 22 removed outlier: 4.011A pdb=" N LEU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 46 Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.743A pdb=" N ILE D 86 " --> pdb=" O SER D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 removed outlier: 4.099A pdb=" N ASN D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 155 through 166 removed outlier: 4.226A pdb=" N ALA D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 235 through 256 removed outlier: 3.677A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 266 through 278 Processing helix chain 'D' and resid 294 through 303 removed outlier: 3.611A pdb=" N LYS D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 335 removed outlier: 3.925A pdb=" N GLU D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 353 removed outlier: 3.660A pdb=" N ALA D 350 " --> pdb=" O SER D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 373 through 388 Processing helix chain 'D' and resid 391 through 402 Processing helix chain 'D' and resid 408 through 418 Processing helix chain 'E' and resid 2 through 9 removed outlier: 3.762A pdb=" N LEU E 6 " --> pdb=" O ASN E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 22 removed outlier: 3.597A pdb=" N GLU E 19 " --> pdb=" O ILE E 15 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ASN E 20 " --> pdb=" O THR E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 45 removed outlier: 3.504A pdb=" N SER E 45 " --> pdb=" O GLN E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 89 Processing helix chain 'E' and resid 123 through 129 removed outlier: 4.033A pdb=" N ASN E 129 " --> pdb=" O GLU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 156 through 166 Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'E' and resid 212 through 221 Processing helix chain 'E' and resid 235 through 256 removed outlier: 3.732A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N HIS E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 278 Processing helix chain 'E' and resid 285 through 289 removed outlier: 3.922A pdb=" N VAL E 289 " --> pdb=" O THR E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 303 Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.636A pdb=" N ALA E 350 " --> pdb=" O SER E 346 " (cutoff:3.500A) Processing helix chain 'E' and resid 367 through 371 removed outlier: 3.903A pdb=" N LEU E 370 " --> pdb=" O LYS E 367 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU E 371 " --> pdb=" O GLU E 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 367 through 371' Processing helix chain 'E' and resid 373 through 388 removed outlier: 3.714A pdb=" N LEU E 377 " --> pdb=" O THR E 373 " (cutoff:3.500A) Processing helix chain 'E' and resid 391 through 405 removed outlier: 4.115A pdb=" N MET E 405 " --> pdb=" O ASN E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 419 Processing helix chain 'F' and resid 3 through 8 Processing helix chain 'F' and resid 10 through 22 removed outlier: 3.608A pdb=" N LEU F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 45 removed outlier: 3.516A pdb=" N ILE F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 89 Processing helix chain 'F' and resid 123 through 129 removed outlier: 4.082A pdb=" N ASN F 129 " --> pdb=" O GLU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 166 Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'F' and resid 212 through 222 removed outlier: 3.696A pdb=" N VAL F 216 " --> pdb=" O ARG F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 235 through 255 Processing helix chain 'F' and resid 266 through 278 Processing helix chain 'F' and resid 291 through 293 No H-bonds generated for 'chain 'F' and resid 291 through 293' Processing helix chain 'F' and resid 294 through 302 removed outlier: 3.730A pdb=" N LYS F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 334 removed outlier: 3.756A pdb=" N GLU F 329 " --> pdb=" O SER F 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 353 removed outlier: 3.814A pdb=" N ALA F 350 " --> pdb=" O SER F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 373 through 386 Processing helix chain 'F' and resid 391 through 402 Processing helix chain 'F' and resid 408 through 417 Processing helix chain 'G' and resid 3 through 8 removed outlier: 3.534A pdb=" N LYS G 7 " --> pdb=" O LEU G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 20 removed outlier: 4.310A pdb=" N LEU G 14 " --> pdb=" O PRO G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 45 Processing helix chain 'G' and resid 82 through 90 removed outlier: 3.751A pdb=" N PHE G 89 " --> pdb=" O GLN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 129 removed outlier: 3.640A pdb=" N ASN G 129 " --> pdb=" O GLU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 166 Processing helix chain 'G' and resid 183 through 199 Processing helix chain 'G' and resid 212 through 223 Processing helix chain 'G' and resid 235 through 256 Processing helix chain 'G' and resid 267 through 278 Processing helix chain 'G' and resid 290 through 302 removed outlier: 4.497A pdb=" N ARG G 296 " --> pdb=" O ASN G 292 " (cutoff:3.500A) Proline residue: G 297 - end of helix Processing helix chain 'G' and resid 326 through 336 Processing helix chain 'G' and resid 346 through 353 Processing helix chain 'G' and resid 367 through 372 removed outlier: 3.960A pdb=" N LEU G 371 " --> pdb=" O LYS G 367 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 367 through 372' Processing helix chain 'G' and resid 373 through 388 Processing helix chain 'G' and resid 391 through 405 removed outlier: 4.159A pdb=" N MET G 405 " --> pdb=" O ASN G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 418 Processing helix chain 'H' and resid 2 through 9 Processing helix chain 'H' and resid 10 through 20 removed outlier: 3.951A pdb=" N LEU H 14 " --> pdb=" O PRO H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 45 Processing helix chain 'H' and resid 82 through 89 removed outlier: 3.546A pdb=" N PHE H 89 " --> pdb=" O GLN H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 123 through 129 removed outlier: 3.735A pdb=" N ASN H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 136 Processing helix chain 'H' and resid 153 through 166 removed outlier: 3.550A pdb=" N SER H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 199 Processing helix chain 'H' and resid 212 through 223 removed outlier: 3.525A pdb=" N VAL H 216 " --> pdb=" O ARG H 212 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL H 223 " --> pdb=" O MET H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 256 removed outlier: 3.867A pdb=" N HIS H 239 " --> pdb=" O PRO H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 278 removed outlier: 3.569A pdb=" N LEU H 270 " --> pdb=" O SER H 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 294 through 303 Processing helix chain 'H' and resid 325 through 336 removed outlier: 4.308A pdb=" N GLU H 329 " --> pdb=" O SER H 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 352 removed outlier: 4.071A pdb=" N ALA H 350 " --> pdb=" O SER H 346 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 372 removed outlier: 3.614A pdb=" N LEU H 371 " --> pdb=" O LYS H 367 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR H 372 " --> pdb=" O GLU H 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 367 through 372' Processing helix chain 'H' and resid 373 through 388 removed outlier: 3.758A pdb=" N LEU H 377 " --> pdb=" O THR H 373 " (cutoff:3.500A) Processing helix chain 'H' and resid 392 through 404 Processing helix chain 'H' and resid 408 through 418 removed outlier: 3.602A pdb=" N ARG H 418 " --> pdb=" O GLU H 414 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 9 removed outlier: 4.300A pdb=" N LEU J 6 " --> pdb=" O ASN J 2 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR J 9 " --> pdb=" O GLU J 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 21 Processing helix chain 'J' and resid 30 through 45 Processing helix chain 'J' and resid 82 through 90 removed outlier: 4.016A pdb=" N ILE J 86 " --> pdb=" O SER J 82 " (cutoff:3.500A) Processing helix chain 'J' and resid 155 through 166 removed outlier: 4.079A pdb=" N ALA J 159 " --> pdb=" O GLU J 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 199 Processing helix chain 'J' and resid 212 through 222 Processing helix chain 'J' and resid 235 through 255 removed outlier: 3.547A pdb=" N HIS J 239 " --> pdb=" O PRO J 235 " (cutoff:3.500A) Processing helix chain 'J' and resid 266 through 278 Processing helix chain 'J' and resid 294 through 302 Processing helix chain 'J' and resid 326 through 333 Processing helix chain 'J' and resid 346 through 351 removed outlier: 4.220A pdb=" N ALA J 350 " --> pdb=" O SER J 346 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU J 351 " --> pdb=" O ARG J 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 346 through 351' Processing helix chain 'J' and resid 374 through 388 removed outlier: 3.638A pdb=" N GLN J 378 " --> pdb=" O GLN J 374 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 405 removed outlier: 4.433A pdb=" N MET J 405 " --> pdb=" O ASN J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 418 removed outlier: 4.280A pdb=" N ARG J 418 " --> pdb=" O GLU J 414 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 9 removed outlier: 3.852A pdb=" N LEU K 6 " --> pdb=" O ASN K 2 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR K 9 " --> pdb=" O GLU K 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 22 removed outlier: 3.690A pdb=" N LEU K 14 " --> pdb=" O PRO K 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 46 Processing helix chain 'K' and resid 82 through 90 removed outlier: 3.508A pdb=" N ILE K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 123 through 129 removed outlier: 3.772A pdb=" N ASN K 129 " --> pdb=" O GLU K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 132 through 136 Processing helix chain 'K' and resid 155 through 166 removed outlier: 4.551A pdb=" N ALA K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 199 Processing helix chain 'K' and resid 212 through 223 removed outlier: 4.159A pdb=" N VAL K 216 " --> pdb=" O ARG K 212 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR K 217 " --> pdb=" O PRO K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 235 through 255 removed outlier: 3.696A pdb=" N HIS K 239 " --> pdb=" O PRO K 235 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 278 Processing helix chain 'K' and resid 294 through 302 Processing helix chain 'K' and resid 325 through 335 Processing helix chain 'K' and resid 346 through 351 removed outlier: 4.148A pdb=" N ALA K 350 " --> pdb=" O SER K 346 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU K 351 " --> pdb=" O ARG K 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 346 through 351' Processing helix chain 'K' and resid 368 through 372 removed outlier: 3.808A pdb=" N THR K 372 " --> pdb=" O GLU K 369 " (cutoff:3.500A) Processing helix chain 'K' and resid 374 through 388 Processing helix chain 'K' and resid 391 through 402 removed outlier: 3.510A pdb=" N LYS K 402 " --> pdb=" O PHE K 398 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 419 removed outlier: 3.884A pdb=" N SER K 419 " --> pdb=" O MET K 415 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 8 Processing helix chain 'L' and resid 10 through 21 removed outlier: 3.643A pdb=" N LEU L 14 " --> pdb=" O PRO L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 46 Processing helix chain 'L' and resid 82 through 90 removed outlier: 3.688A pdb=" N ILE L 86 " --> pdb=" O SER L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 136 Processing helix chain 'L' and resid 156 through 166 Processing helix chain 'L' and resid 183 through 199 Processing helix chain 'L' and resid 212 through 223 Processing helix chain 'L' and resid 235 through 255 removed outlier: 3.678A pdb=" N HIS L 239 " --> pdb=" O PRO L 235 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU L 255 " --> pdb=" O LYS L 251 " (cutoff:3.500A) Processing helix chain 'L' and resid 266 through 278 Processing helix chain 'L' and resid 294 through 302 removed outlier: 3.631A pdb=" N LYS L 298 " --> pdb=" O LEU L 294 " (cutoff:3.500A) Processing helix chain 'L' and resid 326 through 335 removed outlier: 3.692A pdb=" N VAL L 330 " --> pdb=" O LYS L 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 351 Processing helix chain 'L' and resid 367 through 372 removed outlier: 3.573A pdb=" N LEU L 371 " --> pdb=" O LYS L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 388 removed outlier: 3.538A pdb=" N LEU L 377 " --> pdb=" O THR L 373 " (cutoff:3.500A) Processing helix chain 'L' and resid 391 through 403 removed outlier: 3.682A pdb=" N ALA L 395 " --> pdb=" O GLY L 391 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 414 removed outlier: 3.618A pdb=" N PHE L 412 " --> pdb=" O THR L 408 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 9 Processing helix chain 'M' and resid 10 through 22 removed outlier: 3.535A pdb=" N LEU M 14 " --> pdb=" O PRO M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 30 through 45 removed outlier: 3.865A pdb=" N SER M 45 " --> pdb=" O GLN M 41 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 123 through 128 removed outlier: 3.651A pdb=" N ALA M 127 " --> pdb=" O LYS M 123 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG M 128 " --> pdb=" O PRO M 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 123 through 128' Processing helix chain 'M' and resid 155 through 166 removed outlier: 4.439A pdb=" N ALA M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 199 Processing helix chain 'M' and resid 212 through 223 Processing helix chain 'M' and resid 235 through 255 removed outlier: 3.671A pdb=" N HIS M 239 " --> pdb=" O PRO M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 266 through 278 Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'M' and resid 325 through 334 removed outlier: 3.599A pdb=" N GLU M 329 " --> pdb=" O SER M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 350 removed outlier: 3.635A pdb=" N ILE M 349 " --> pdb=" O SER M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 374 through 388 Processing helix chain 'M' and resid 391 through 405 removed outlier: 3.580A pdb=" N ALA M 395 " --> pdb=" O GLY M 391 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N MET M 405 " --> pdb=" O ASN M 401 " (cutoff:3.500A) Processing helix chain 'M' and resid 408 through 419 Processing helix chain 'N' and resid 3 through 8 removed outlier: 3.790A pdb=" N ASN N 8 " --> pdb=" O THR N 4 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 22 removed outlier: 3.671A pdb=" N LEU N 14 " --> pdb=" O PRO N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 29 removed outlier: 4.196A pdb=" N ARG N 28 " --> pdb=" O ASN N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 46 Processing helix chain 'N' and resid 82 through 90 removed outlier: 3.622A pdb=" N PHE N 89 " --> pdb=" O GLN N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 123 through 129 removed outlier: 3.840A pdb=" N ASN N 129 " --> pdb=" O GLU N 125 " (cutoff:3.500A) Processing helix chain 'N' and resid 156 through 166 removed outlier: 3.716A pdb=" N LEU N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 199 Processing helix chain 'N' and resid 212 through 223 Processing helix chain 'N' and resid 235 through 255 removed outlier: 3.697A pdb=" N HIS N 239 " --> pdb=" O PRO N 235 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 278 Processing helix chain 'N' and resid 294 through 302 Processing helix chain 'N' and resid 325 through 335 removed outlier: 4.734A pdb=" N GLU N 329 " --> pdb=" O SER N 325 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL N 330 " --> pdb=" O LYS N 326 " (cutoff:3.500A) Processing helix chain 'N' and resid 367 through 371 removed outlier: 3.817A pdb=" N LEU N 370 " --> pdb=" O LYS N 367 " (cutoff:3.500A) Processing helix chain 'N' and resid 373 through 388 Processing helix chain 'N' and resid 391 through 404 Processing helix chain 'N' and resid 408 through 419 removed outlier: 3.503A pdb=" N PHE N 412 " --> pdb=" O THR N 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 7 Processing helix chain 'O' and resid 10 through 22 Processing helix chain 'O' and resid 30 through 46 removed outlier: 3.505A pdb=" N ILE O 34 " --> pdb=" O ARG O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 71 Processing helix chain 'O' and resid 82 through 90 Processing helix chain 'O' and resid 123 through 129 removed outlier: 3.837A pdb=" N ASN O 129 " --> pdb=" O GLU O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 153 through 166 removed outlier: 3.598A pdb=" N LEU O 157 " --> pdb=" O SER O 153 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N THR O 158 " --> pdb=" O THR O 154 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 199 Processing helix chain 'O' and resid 212 through 223 removed outlier: 3.620A pdb=" N GLN O 220 " --> pdb=" O VAL O 216 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG O 221 " --> pdb=" O THR O 217 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL O 223 " --> pdb=" O MET O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 235 through 256 removed outlier: 3.618A pdb=" N HIS O 239 " --> pdb=" O PRO O 235 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS O 256 " --> pdb=" O ARG O 252 " (cutoff:3.500A) Processing helix chain 'O' and resid 266 through 278 Processing helix chain 'O' and resid 290 through 302 Proline residue: O 297 - end of helix Processing helix chain 'O' and resid 325 through 335 removed outlier: 3.947A pdb=" N GLU O 329 " --> pdb=" O SER O 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 347 through 352 removed outlier: 3.637A pdb=" N GLU O 351 " --> pdb=" O LYS O 348 " (cutoff:3.500A) Processing helix chain 'O' and resid 373 through 388 Processing helix chain 'O' and resid 391 through 404 Processing helix chain 'O' and resid 408 through 418 Processing helix chain 'P' and resid 2 through 9 removed outlier: 4.606A pdb=" N LEU P 6 " --> pdb=" O ASN P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 22 removed outlier: 4.249A pdb=" N LEU P 14 " --> pdb=" O PRO P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 30 through 44 Processing helix chain 'P' and resid 82 through 90 Processing helix chain 'P' and resid 123 through 128 Processing helix chain 'P' and resid 156 through 166 Processing helix chain 'P' and resid 183 through 199 removed outlier: 3.519A pdb=" N HIS P 199 " --> pdb=" O ILE P 195 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 223 removed outlier: 3.616A pdb=" N VAL P 216 " --> pdb=" O ARG P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 235 through 256 removed outlier: 3.698A pdb=" N HIS P 256 " --> pdb=" O ARG P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 266 through 278 Processing helix chain 'P' and resid 291 through 293 No H-bonds generated for 'chain 'P' and resid 291 through 293' Processing helix chain 'P' and resid 294 through 300 removed outlier: 3.831A pdb=" N LYS P 298 " --> pdb=" O LEU P 294 " (cutoff:3.500A) Processing helix chain 'P' and resid 328 through 335 removed outlier: 3.535A pdb=" N TYR P 332 " --> pdb=" O ASP P 328 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 353 removed outlier: 3.776A pdb=" N ALA P 350 " --> pdb=" O SER P 346 " (cutoff:3.500A) Processing helix chain 'P' and resid 367 through 372 removed outlier: 3.784A pdb=" N LEU P 370 " --> pdb=" O LYS P 367 " (cutoff:3.500A) Processing helix chain 'P' and resid 374 through 388 Processing helix chain 'P' and resid 391 through 405 removed outlier: 3.696A pdb=" N ALA P 395 " --> pdb=" O GLY P 391 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N MET P 396 " --> pdb=" O GLU P 392 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N MET P 405 " --> pdb=" O ASN P 401 " (cutoff:3.500A) Processing helix chain 'P' and resid 408 through 417 removed outlier: 3.622A pdb=" N PHE P 412 " --> pdb=" O THR P 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 9 Processing helix chain 'Y' and resid 10 through 22 removed outlier: 3.885A pdb=" N LEU Y 14 " --> pdb=" O PRO Y 10 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR Y 16 " --> pdb=" O SER Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 30 through 44 removed outlier: 3.787A pdb=" N ILE Y 34 " --> pdb=" O ARG Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 90 removed outlier: 3.713A pdb=" N ILE Y 86 " --> pdb=" O SER Y 82 " (cutoff:3.500A) Processing helix chain 'Y' and resid 123 through 128 Processing helix chain 'Y' and resid 156 through 166 Processing helix chain 'Y' and resid 183 through 199 Processing helix chain 'Y' and resid 212 through 223 removed outlier: 3.792A pdb=" N VAL Y 216 " --> pdb=" O ARG Y 212 " (cutoff:3.500A) Processing helix chain 'Y' and resid 235 through 255 removed outlier: 3.894A pdb=" N HIS Y 239 " --> pdb=" O PRO Y 235 " (cutoff:3.500A) Processing helix chain 'Y' and resid 266 through 278 removed outlier: 3.915A pdb=" N LEU Y 270 " --> pdb=" O SER Y 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 290 through 299 removed outlier: 3.825A pdb=" N LEU Y 294 " --> pdb=" O ALA Y 291 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N HIS Y 295 " --> pdb=" O ASN Y 292 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ARG Y 296 " --> pdb=" O ALA Y 293 " (cutoff:3.500A) Proline residue: Y 297 - end of helix Processing helix chain 'Y' and resid 325 through 333 removed outlier: 4.350A pdb=" N GLU Y 329 " --> pdb=" O SER Y 325 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 351 removed outlier: 3.578A pdb=" N ALA Y 350 " --> pdb=" O SER Y 346 " (cutoff:3.500A) Processing helix chain 'Y' and resid 374 through 388 Processing helix chain 'Y' and resid 391 through 404 removed outlier: 3.817A pdb=" N ALA Y 395 " --> pdb=" O GLY Y 391 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU Y 397 " --> pdb=" O ILE Y 393 " (cutoff:3.500A) Processing helix chain 'Y' and resid 408 through 419 Processing helix chain 'a' and resid 5 through 40 Processing helix chain 'a' and resid 45 through 92 Processing helix chain 'a' and resid 92 through 100 Processing helix chain 'a' and resid 100 through 110 removed outlier: 3.864A pdb=" N SER a 108 " --> pdb=" O LEU a 104 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU a 109 " --> pdb=" O MET a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 111 through 130 Processing helix chain 'a' and resid 130 through 137 removed outlier: 3.972A pdb=" N LEU a 134 " --> pdb=" O LEU a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 154 removed outlier: 3.617A pdb=" N LEU a 150 " --> pdb=" O ASP a 146 " (cutoff:3.500A) Processing helix chain 'a' and resid 158 through 165 removed outlier: 3.901A pdb=" N VAL a 162 " --> pdb=" O ASP a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 190 Processing helix chain 'b' and resid 5 through 40 removed outlier: 4.201A pdb=" N GLY b 40 " --> pdb=" O ARG b 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 92 Processing helix chain 'b' and resid 92 through 100 removed outlier: 3.934A pdb=" N LEU b 96 " --> pdb=" O HIS b 92 " (cutoff:3.500A) Processing helix chain 'b' and resid 100 through 110 removed outlier: 4.056A pdb=" N GLU b 109 " --> pdb=" O MET b 105 " (cutoff:3.500A) Processing helix chain 'b' and resid 111 through 134 Processing helix chain 'b' and resid 146 through 153 removed outlier: 3.580A pdb=" N LEU b 150 " --> pdb=" O ASP b 146 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE b 153 " --> pdb=" O ILE b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 158 through 162 Processing helix chain 'b' and resid 170 through 190 Processing helix chain 'c' and resid 5 through 41 Processing helix chain 'c' and resid 45 through 92 Processing helix chain 'c' and resid 92 through 100 Processing helix chain 'c' and resid 100 through 109 removed outlier: 4.122A pdb=" N GLU c 109 " --> pdb=" O MET c 105 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 137 Processing helix chain 'c' and resid 143 through 145 No H-bonds generated for 'chain 'c' and resid 143 through 145' Processing helix chain 'c' and resid 146 through 154 Processing helix chain 'c' and resid 158 through 165 Processing helix chain 'c' and resid 170 through 190 Processing helix chain 'd' and resid 5 through 40 Processing helix chain 'd' and resid 44 through 92 Processing helix chain 'd' and resid 92 through 100 Processing helix chain 'd' and resid 100 through 109 removed outlier: 4.403A pdb=" N GLU d 109 " --> pdb=" O MET d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 111 through 137 removed outlier: 4.031A pdb=" N GLY d 137 " --> pdb=" O TRP d 133 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 154 Processing helix chain 'd' and resid 159 through 164 removed outlier: 4.222A pdb=" N ASP d 164 " --> pdb=" O ALA d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 190 Processing helix chain 'e' and resid 5 through 40 Processing helix chain 'e' and resid 44 through 101 removed outlier: 6.690A pdb=" N THR e 94 " --> pdb=" O GLN e 90 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA e 95 " --> pdb=" O GLN e 91 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA e 99 " --> pdb=" O ALA e 95 " (cutoff:3.500A) Processing helix chain 'e' and resid 102 through 104 No H-bonds generated for 'chain 'e' and resid 102 through 104' Processing helix chain 'e' and resid 111 through 137 removed outlier: 3.709A pdb=" N TRP e 133 " --> pdb=" O ALA e 129 " (cutoff:3.500A) Processing helix chain 'e' and resid 146 through 154 Processing helix chain 'e' and resid 158 through 166 removed outlier: 4.169A pdb=" N ASP e 164 " --> pdb=" O ALA e 160 " (cutoff:3.500A) Processing helix chain 'e' and resid 170 through 190 Processing helix chain 'f' and resid 5 through 40 Processing helix chain 'f' and resid 44 through 91 removed outlier: 3.905A pdb=" N GLN f 90 " --> pdb=" O ASN f 86 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLN f 91 " --> pdb=" O ASP f 87 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 100 Processing helix chain 'f' and resid 101 through 104 Processing helix chain 'f' and resid 111 through 137 Processing helix chain 'f' and resid 146 through 154 removed outlier: 3.725A pdb=" N LEU f 150 " --> pdb=" O ASP f 146 " (cutoff:3.500A) Processing helix chain 'f' and resid 158 through 165 Processing helix chain 'f' and resid 170 through 190 removed outlier: 3.510A pdb=" N VAL f 190 " --> pdb=" O SER f 186 " (cutoff:3.500A) Processing helix chain 'g' and resid 5 through 40 Processing helix chain 'g' and resid 44 through 101 removed outlier: 6.328A pdb=" N THR g 94 " --> pdb=" O GLN g 90 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALA g 95 " --> pdb=" O GLN g 91 " (cutoff:3.500A) Processing helix chain 'g' and resid 102 through 104 No H-bonds generated for 'chain 'g' and resid 102 through 104' Processing helix chain 'g' and resid 111 through 137 Processing helix chain 'g' and resid 146 through 154 removed outlier: 3.601A pdb=" N LEU g 150 " --> pdb=" O ASP g 146 " (cutoff:3.500A) Processing helix chain 'g' and resid 158 through 164 removed outlier: 3.594A pdb=" N ASP g 164 " --> pdb=" O ALA g 160 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 190 Processing helix chain 'h' and resid 5 through 40 Processing helix chain 'h' and resid 44 through 92 Processing helix chain 'h' and resid 92 through 105 Proline residue: h 102 - end of helix Processing helix chain 'h' and resid 109 through 111 No H-bonds generated for 'chain 'h' and resid 109 through 111' Processing helix chain 'h' and resid 112 through 137 removed outlier: 3.689A pdb=" N CYS h 117 " --> pdb=" O ILE h 113 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA h 125 " --> pdb=" O ARG h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 146 through 154 removed outlier: 3.905A pdb=" N LEU h 150 " --> pdb=" O ASP h 146 " (cutoff:3.500A) Processing helix chain 'h' and resid 158 through 165 Processing helix chain 'h' and resid 170 through 190 Processing helix chain 'i' and resid 5 through 40 Processing helix chain 'i' and resid 44 through 92 removed outlier: 3.569A pdb=" N LEU i 48 " --> pdb=" O ASN i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 101 removed outlier: 4.362A pdb=" N ALA i 99 " --> pdb=" O ALA i 95 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU i 100 " --> pdb=" O LEU i 96 " (cutoff:3.500A) Processing helix chain 'i' and resid 102 through 105 removed outlier: 3.897A pdb=" N MET i 105 " --> pdb=" O PRO i 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 102 through 105' Processing helix chain 'i' and resid 106 through 110 removed outlier: 3.574A pdb=" N GLU i 109 " --> pdb=" O GLY i 106 " (cutoff:3.500A) Processing helix chain 'i' and resid 111 through 137 Processing helix chain 'i' and resid 146 through 154 Processing helix chain 'i' and resid 158 through 167 removed outlier: 3.934A pdb=" N VAL i 162 " --> pdb=" O ASP i 158 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU i 167 " --> pdb=" O ASP i 163 " (cutoff:3.500A) Processing helix chain 'i' and resid 170 through 190 removed outlier: 3.564A pdb=" N VAL i 190 " --> pdb=" O SER i 186 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 39 Processing helix chain 'j' and resid 44 through 92 Processing helix chain 'j' and resid 92 through 100 removed outlier: 3.531A pdb=" N LEU j 100 " --> pdb=" O LEU j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 100 through 107 Processing helix chain 'j' and resid 111 through 137 Processing helix chain 'j' and resid 146 through 154 Processing helix chain 'j' and resid 158 through 164 removed outlier: 3.605A pdb=" N VAL j 162 " --> pdb=" O ASP j 158 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP j 164 " --> pdb=" O ALA j 160 " (cutoff:3.500A) Processing helix chain 'j' and resid 170 through 190 removed outlier: 3.539A pdb=" N VAL j 190 " --> pdb=" O SER j 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 5 through 40 Processing helix chain 'k' and resid 45 through 89 Processing helix chain 'k' and resid 92 through 100 removed outlier: 4.202A pdb=" N LEU k 96 " --> pdb=" O HIS k 92 " (cutoff:3.500A) Processing helix chain 'k' and resid 101 through 106 removed outlier: 4.417A pdb=" N GLY k 106 " --> pdb=" O PRO k 102 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 136 Processing helix chain 'k' and resid 146 through 154 removed outlier: 4.360A pdb=" N THR k 152 " --> pdb=" O ASP k 148 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE k 153 " --> pdb=" O ILE k 149 " (cutoff:3.500A) Processing helix chain 'k' and resid 158 through 165 Processing helix chain 'k' and resid 170 through 190 Processing helix chain 'l' and resid 5 through 40 Processing helix chain 'l' and resid 45 through 92 Processing helix chain 'l' and resid 92 through 100 removed outlier: 3.918A pdb=" N LEU l 96 " --> pdb=" O HIS l 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 100 through 109 removed outlier: 3.839A pdb=" N GLU l 109 " --> pdb=" O MET l 105 " (cutoff:3.500A) Processing helix chain 'l' and resid 111 through 133 removed outlier: 4.189A pdb=" N TRP l 133 " --> pdb=" O ALA l 129 " (cutoff:3.500A) Processing helix chain 'l' and resid 143 through 145 No H-bonds generated for 'chain 'l' and resid 143 through 145' Processing helix chain 'l' and resid 146 through 154 removed outlier: 3.511A pdb=" N ILE l 153 " --> pdb=" O ILE l 149 " (cutoff:3.500A) Processing helix chain 'l' and resid 158 through 166 Processing helix chain 'l' and resid 170 through 190 Processing helix chain 'o' and resid 5 through 40 Processing helix chain 'o' and resid 45 through 93 Processing helix chain 'o' and resid 93 through 100 Processing helix chain 'o' and resid 100 through 108 removed outlier: 3.825A pdb=" N LEU o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) Processing helix chain 'o' and resid 111 through 135 Processing helix chain 'o' and resid 146 through 154 Processing helix chain 'o' and resid 158 through 167 removed outlier: 3.714A pdb=" N VAL o 162 " --> pdb=" O ASP o 158 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP o 163 " --> pdb=" O VAL o 159 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU o 167 " --> pdb=" O ASP o 163 " (cutoff:3.500A) Processing helix chain 'o' and resid 170 through 190 removed outlier: 3.589A pdb=" N VAL o 190 " --> pdb=" O SER o 186 " (cutoff:3.500A) Processing helix chain 'p' and resid 5 through 40 Processing helix chain 'p' and resid 45 through 100 removed outlier: 6.918A pdb=" N THR p 94 " --> pdb=" O GLN p 90 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA p 95 " --> pdb=" O GLN p 91 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU p 96 " --> pdb=" O HIS p 92 " (cutoff:3.500A) Processing helix chain 'p' and resid 100 through 109 removed outlier: 3.574A pdb=" N LEU p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU p 109 " --> pdb=" O MET p 105 " (cutoff:3.500A) Processing helix chain 'p' and resid 111 through 135 removed outlier: 3.871A pdb=" N TRP p 133 " --> pdb=" O ALA p 129 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA p 135 " --> pdb=" O LEU p 131 " (cutoff:3.500A) Processing helix chain 'p' and resid 146 through 154 removed outlier: 3.627A pdb=" N ILE p 153 " --> pdb=" O ILE p 149 " (cutoff:3.500A) Processing helix chain 'p' and resid 158 through 164 removed outlier: 3.793A pdb=" N VAL p 162 " --> pdb=" O ASP p 158 " (cutoff:3.500A) Processing helix chain 'p' and resid 170 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 57 removed outlier: 3.740A pdb=" N LEU A 113 " --> pdb=" O TYR A 80 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 112 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS A 100 " --> pdb=" O LEU A 114 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N VAL A 116 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N SER A 98 " --> pdb=" O VAL A 116 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU A 118 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N THR A 96 " --> pdb=" O GLU A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.571A pdb=" N VAL A 203 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 261 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 316 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE A 262 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR A 318 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 264 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N LEU A 320 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 203 through 208 removed outlier: 3.571A pdb=" N VAL A 203 " --> pdb=" O ASP A 259 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 261 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 260 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE A 316 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N ILE A 262 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR A 318 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 264 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N LEU A 320 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLY A 174 " --> pdb=" O ALA A 317 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ALA A 319 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 176 " --> pdb=" O ALA A 319 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG A 173 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N LEU A 343 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 175 " --> pdb=" O LEU A 343 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU A 342 " --> pdb=" O GLY A 364 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 364 " --> pdb=" O GLU A 342 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.159A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 49 through 51 removed outlier: 4.159A pdb=" N ILE B 49 " --> pdb=" O ILE B 101 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.560A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL B 260 " --> pdb=" O THR B 314 " (cutoff:3.500A) removed outlier: 7.923A pdb=" N ILE B 316 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE B 262 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR B 318 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU B 264 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N LEU B 320 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 203 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ILE B 261 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET B 205 " --> pdb=" O ILE B 261 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 204 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N VAL B 228 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 206 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N SER B 230 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 208 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 138 through 139 removed outlier: 3.560A pdb=" N ASN B 306 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLY B 174 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N ALA B 319 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 176 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 284 through 285 removed outlier: 3.869A pdb=" N VAL B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 79 through 81 Processing sheet with id=AB2, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.970A pdb=" N GLU C 118 " --> pdb=" O SER C 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 138 through 139 removed outlier: 6.404A pdb=" N VAL C 260 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ILE C 316 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 262 " --> pdb=" O ILE C 316 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N THR C 318 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU C 264 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE C 261 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASP C 265 " --> pdb=" O LEU C 207 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N VAL C 228 " --> pdb=" O LEU C 204 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL C 206 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 138 through 139 removed outlier: 5.865A pdb=" N GLY C 174 " --> pdb=" O ALA C 317 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N ALA C 319 " --> pdb=" O GLY C 174 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE C 176 " --> pdb=" O ALA C 319 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG C 173 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 8.062A pdb=" N LEU C 343 " --> pdb=" O ARG C 173 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU C 175 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N LEU C 345 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL C 177 " --> pdb=" O LEU C 345 " (cutoff:3.500A) removed outlier: 10.459A pdb=" N GLU C 342 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N ASN C 361 " --> pdb=" O GLU C 342 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N HIS C 344 " --> pdb=" O ASP C 359 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 144 through 145 removed outlier: 4.540A pdb=" N ILE C 168 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 111 through 112 removed outlier: 5.980A pdb=" N LYS D 100 " --> pdb=" O VAL D 116 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL D 116 " --> pdb=" O LYS D 100 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.955A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR D 318 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N VAL D 228 " --> pdb=" O LEU D 204 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL D 206 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N SER D 230 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N LEU D 208 " --> pdb=" O SER D 230 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 138 through 139 removed outlier: 3.955A pdb=" N ASN D 306 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLY D 174 " --> pdb=" O ALA D 317 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ALA D 319 " --> pdb=" O GLY D 174 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE D 176 " --> pdb=" O ALA D 319 " (cutoff:3.500A) removed outlier: 10.223A pdb=" N GLU D 342 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N ASN D 361 " --> pdb=" O GLU D 342 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N HIS D 344 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 144 through 145 removed outlier: 4.147A pdb=" N ILE D 168 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 81 Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 81 removed outlier: 3.591A pdb=" N GLU E 118 " --> pdb=" O SER E 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.694A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL E 260 " --> pdb=" O THR E 314 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ILE E 316 " --> pdb=" O VAL E 260 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE E 262 " --> pdb=" O ILE E 316 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N THR E 318 " --> pdb=" O ILE E 262 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LEU E 264 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N VAL E 228 " --> pdb=" O LEU E 204 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N VAL E 206 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N SER E 230 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N LEU E 208 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 138 through 139 removed outlier: 3.694A pdb=" N ASN E 306 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLY E 174 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA E 319 " --> pdb=" O GLY E 174 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE E 176 " --> pdb=" O ALA E 319 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG E 173 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N LEU E 343 " --> pdb=" O ARG E 173 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU E 175 " --> pdb=" O LEU E 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 144 through 145 removed outlier: 4.211A pdb=" N ILE E 168 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AC7, first strand: chain 'F' and resid 63 through 66 Processing sheet with id=AC8, first strand: chain 'F' and resid 227 through 231 removed outlier: 6.989A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 227 through 231 removed outlier: 6.989A pdb=" N VAL F 228 " --> pdb=" O LEU F 204 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL F 206 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N SER F 230 " --> pdb=" O VAL F 206 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU F 208 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N VAL F 260 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE F 316 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ILE F 262 " --> pdb=" O ILE F 316 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N THR F 318 " --> pdb=" O ILE F 262 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LEU F 264 " --> pdb=" O THR F 318 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N LEU F 320 " --> pdb=" O LEU F 264 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLY F 174 " --> pdb=" O ALA F 317 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ALA F 319 " --> pdb=" O GLY F 174 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE F 176 " --> pdb=" O ALA F 319 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY F 364 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 79 through 81 Processing sheet with id=AD2, first strand: chain 'G' and resid 229 through 231 removed outlier: 7.876A pdb=" N SER G 230 " --> pdb=" O VAL G 206 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU G 208 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL G 203 " --> pdb=" O ILE G 261 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU G 263 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N MET G 205 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N ASP G 265 " --> pdb=" O MET G 205 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LEU G 207 " --> pdb=" O ASP G 265 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N ILE G 316 " --> pdb=" O VAL G 260 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE G 262 " --> pdb=" O ILE G 316 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N THR G 318 " --> pdb=" O ILE G 262 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N LEU G 264 " --> pdb=" O THR G 318 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N LEU G 320 " --> pdb=" O LEU G 264 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N SER G 266 " --> pdb=" O LEU G 320 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N GLY G 174 " --> pdb=" O ALA G 317 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N ALA G 319 " --> pdb=" O GLY G 174 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ILE G 176 " --> pdb=" O ALA G 319 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU G 345 " --> pdb=" O VAL G 177 " (cutoff:3.500A) removed outlier: 11.097A pdb=" N GLU G 342 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N ASN G 361 " --> pdb=" O GLU G 342 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N HIS G 344 " --> pdb=" O ASP G 359 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 49 through 57 removed outlier: 3.742A pdb=" N ILE H 79 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N TYR H 80 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 9.824A pdb=" N LYS H 115 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N LEU H 113 " --> pdb=" O ARG H 102 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ARG H 102 " --> pdb=" O LEU H 113 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS H 115 " --> pdb=" O LYS H 100 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N SER H 98 " --> pdb=" O ASN H 117 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL H 119 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N THR H 96 " --> pdb=" O VAL H 119 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 227 through 231 removed outlier: 8.512A pdb=" N VAL H 228 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL H 206 " --> pdb=" O VAL H 228 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N SER H 230 " --> pdb=" O VAL H 206 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU H 208 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL H 203 " --> pdb=" O ASP H 259 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU H 263 " --> pdb=" O MET H 205 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP H 265 " --> pdb=" O LEU H 207 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE H 209 " --> pdb=" O ASP H 265 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL H 260 " --> pdb=" O THR H 314 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE H 316 " --> pdb=" O VAL H 260 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ILE H 262 " --> pdb=" O ILE H 316 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR H 318 " --> pdb=" O ILE H 262 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU H 264 " --> pdb=" O THR H 318 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N GLY H 174 " --> pdb=" O ALA H 317 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ALA H 319 " --> pdb=" O GLY H 174 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE H 176 " --> pdb=" O ALA H 319 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 63 through 66 removed outlier: 6.317A pdb=" N THR J 96 " --> pdb=" O GLU J 118 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU J 118 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N SER J 98 " --> pdb=" O VAL J 116 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N VAL J 116 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LYS J 100 " --> pdb=" O LEU J 114 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU J 113 " --> pdb=" O TYR J 80 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 138 through 139 removed outlier: 3.790A pdb=" N ASN J 306 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL J 260 " --> pdb=" O THR J 314 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ILE J 316 " --> pdb=" O VAL J 260 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE J 262 " --> pdb=" O ILE J 316 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N THR J 318 " --> pdb=" O ILE J 262 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N LEU J 264 " --> pdb=" O THR J 318 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N LEU J 320 " --> pdb=" O LEU J 264 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE J 261 " --> pdb=" O VAL J 203 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET J 205 " --> pdb=" O ILE J 261 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP J 265 " --> pdb=" O LEU J 207 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE J 209 " --> pdb=" O ASP J 265 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL J 228 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL J 206 " --> pdb=" O VAL J 228 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER J 230 " --> pdb=" O VAL J 206 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU J 208 " --> pdb=" O SER J 230 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 138 through 139 removed outlier: 3.790A pdb=" N ASN J 306 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY J 174 " --> pdb=" O ALA J 317 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ALA J 319 " --> pdb=" O GLY J 174 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE J 176 " --> pdb=" O ALA J 319 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 144 through 145 removed outlier: 4.151A pdb=" N ILE J 168 " --> pdb=" O LEU J 145 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 79 through 81 removed outlier: 6.396A pdb=" N THR K 96 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL K 119 " --> pdb=" O THR K 96 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER K 98 " --> pdb=" O ASN K 117 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ARG K 102 " --> pdb=" O LEU K 113 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU K 113 " --> pdb=" O ARG K 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 138 through 139 Processing sheet with id=AE2, first strand: chain 'K' and resid 138 through 139 removed outlier: 6.421A pdb=" N GLY K 174 " --> pdb=" O ALA K 317 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ALA K 319 " --> pdb=" O GLY K 174 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ILE K 176 " --> pdb=" O ALA K 319 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ARG K 173 " --> pdb=" O MET K 341 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N LEU K 343 " --> pdb=" O ARG K 173 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU K 175 " --> pdb=" O LEU K 343 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU K 345 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N VAL K 177 " --> pdb=" O LEU K 345 " (cutoff:3.500A) removed outlier: 10.159A pdb=" N GLU K 342 " --> pdb=" O ASN K 361 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N ASN K 361 " --> pdb=" O GLU K 342 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS K 344 " --> pdb=" O ASP K 359 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'K' and resid 144 through 145 removed outlier: 4.429A pdb=" N ILE K 168 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'K' and resid 206 through 209 removed outlier: 6.295A pdb=" N VAL K 206 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N SER K 230 " --> pdb=" O VAL K 206 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU K 208 " --> pdb=" O SER K 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'K' and resid 284 through 285 Processing sheet with id=AE6, first strand: chain 'L' and resid 79 through 81 removed outlier: 6.415A pdb=" N THR L 96 " --> pdb=" O VAL L 119 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N VAL L 119 " --> pdb=" O THR L 96 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N SER L 98 " --> pdb=" O ASN L 117 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ARG L 102 " --> pdb=" O LEU L 113 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N LEU L 113 " --> pdb=" O ARG L 102 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.798A pdb=" N ASN L 306 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL L 260 " --> pdb=" O THR L 314 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE L 316 " --> pdb=" O VAL L 260 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE L 262 " --> pdb=" O ILE L 316 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N THR L 318 " --> pdb=" O ILE L 262 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU L 264 " --> pdb=" O THR L 318 " (cutoff:3.500A) removed outlier: 8.488A pdb=" N LEU L 320 " --> pdb=" O LEU L 264 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL L 228 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N VAL L 206 " --> pdb=" O VAL L 228 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N SER L 230 " --> pdb=" O VAL L 206 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU L 208 " --> pdb=" O SER L 230 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.798A pdb=" N ASN L 306 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N GLY L 174 " --> pdb=" O ALA L 317 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N ALA L 319 " --> pdb=" O GLY L 174 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ILE L 176 " --> pdb=" O ALA L 319 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'L' and resid 144 through 145 removed outlier: 4.205A pdb=" N ILE L 168 " --> pdb=" O LEU L 145 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 64 through 66 removed outlier: 6.218A pdb=" N LYS M 100 " --> pdb=" O VAL M 116 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL M 116 " --> pdb=" O LYS M 100 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ARG M 102 " --> pdb=" O LEU M 114 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N LEU M 114 " --> pdb=" O ARG M 102 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 138 through 139 removed outlier: 3.684A pdb=" N ASN M 306 " --> pdb=" O LEU M 139 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 144 through 145 removed outlier: 4.242A pdb=" N ILE M 168 " --> pdb=" O LEU M 145 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 226 through 231 removed outlier: 6.140A pdb=" N LEU M 204 " --> pdb=" O GLU M 226 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL M 228 " --> pdb=" O LEU M 204 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N VAL M 206 " --> pdb=" O VAL M 228 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N SER M 230 " --> pdb=" O VAL M 206 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LEU M 208 " --> pdb=" O SER M 230 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY M 174 " --> pdb=" O ALA M 317 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA M 319 " --> pdb=" O GLY M 174 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N ILE M 176 " --> pdb=" O ALA M 319 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 284 through 285 removed outlier: 3.528A pdb=" N VAL M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 49 through 55 removed outlier: 3.596A pdb=" N ILE N 49 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP N 95 " --> pdb=" O LEU N 55 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG N 102 " --> pdb=" O ALA N 112 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 49 through 55 removed outlier: 3.596A pdb=" N ILE N 49 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASP N 95 " --> pdb=" O LEU N 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 63 through 65 Processing sheet with id=AF9, first strand: chain 'N' and resid 138 through 139 removed outlier: 6.712A pdb=" N VAL N 260 " --> pdb=" O THR N 314 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N ILE N 316 " --> pdb=" O VAL N 260 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ILE N 262 " --> pdb=" O ILE N 316 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N THR N 318 " --> pdb=" O ILE N 262 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LEU N 264 " --> pdb=" O THR N 318 " (cutoff:3.500A) removed outlier: 9.041A pdb=" N LEU N 320 " --> pdb=" O LEU N 264 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE N 261 " --> pdb=" O VAL N 203 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET N 205 " --> pdb=" O ILE N 261 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP N 265 " --> pdb=" O LEU N 207 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE N 209 " --> pdb=" O ASP N 265 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU N 226 " --> pdb=" O LEU N 204 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N VAL N 206 " --> pdb=" O GLU N 226 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'N' and resid 138 through 139 removed outlier: 5.930A pdb=" N GLY N 174 " --> pdb=" O ALA N 317 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA N 319 " --> pdb=" O GLY N 174 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE N 176 " --> pdb=" O ALA N 319 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'N' and resid 144 through 145 removed outlier: 4.193A pdb=" N ILE N 168 " --> pdb=" O LEU N 145 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 64 through 66 removed outlier: 6.371A pdb=" N THR O 96 " --> pdb=" O GLU O 118 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N GLU O 118 " --> pdb=" O THR O 96 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N SER O 98 " --> pdb=" O VAL O 116 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N VAL O 116 " --> pdb=" O SER O 98 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS O 100 " --> pdb=" O LEU O 114 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 138 through 139 removed outlier: 3.562A pdb=" N ASN O 306 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N VAL O 260 " --> pdb=" O THR O 314 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ILE O 316 " --> pdb=" O VAL O 260 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE O 262 " --> pdb=" O ILE O 316 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR O 318 " --> pdb=" O ILE O 262 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU O 264 " --> pdb=" O THR O 318 " (cutoff:3.500A) removed outlier: 8.804A pdb=" N LEU O 320 " --> pdb=" O LEU O 264 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP O 265 " --> pdb=" O LEU O 207 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL O 228 " --> pdb=" O LEU O 204 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N VAL O 206 " --> pdb=" O VAL O 228 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N SER O 230 " --> pdb=" O VAL O 206 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LEU O 208 " --> pdb=" O SER O 230 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 138 through 139 removed outlier: 3.562A pdb=" N ASN O 306 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N GLY O 174 " --> pdb=" O ALA O 317 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ALA O 319 " --> pdb=" O GLY O 174 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ILE O 176 " --> pdb=" O ALA O 319 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'P' and resid 79 through 81 removed outlier: 3.597A pdb=" N ASP P 95 " --> pdb=" O LEU P 55 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'P' and resid 79 through 81 removed outlier: 3.597A pdb=" N ASP P 95 " --> pdb=" O LEU P 55 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'P' and resid 144 through 145 removed outlier: 4.442A pdb=" N ILE P 168 " --> pdb=" O LEU P 145 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'P' and resid 203 through 204 removed outlier: 3.507A pdb=" N ILE P 261 " --> pdb=" O VAL P 203 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'P' and resid 207 through 208 removed outlier: 3.551A pdb=" N ASP P 265 " --> pdb=" O LEU P 207 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLY P 174 " --> pdb=" O ALA P 317 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N ALA P 319 " --> pdb=" O GLY P 174 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE P 176 " --> pdb=" O ALA P 319 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG P 173 " --> pdb=" O MET P 341 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU P 343 " --> pdb=" O ARG P 173 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU P 175 " --> pdb=" O LEU P 343 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Y' and resid 118 through 119 removed outlier: 3.565A pdb=" N SER Y 98 " --> pdb=" O GLU Y 118 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG Y 102 " --> pdb=" O ALA Y 112 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA Y 112 " --> pdb=" O ARG Y 102 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP Y 95 " --> pdb=" O LEU Y 55 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Y' and resid 203 through 208 removed outlier: 3.937A pdb=" N VAL Y 203 " --> pdb=" O ASP Y 259 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE Y 261 " --> pdb=" O VAL Y 203 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N MET Y 205 " --> pdb=" O ILE Y 261 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP Y 265 " --> pdb=" O LEU Y 207 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLY Y 174 " --> pdb=" O ALA Y 317 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N ALA Y 319 " --> pdb=" O GLY Y 174 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE Y 176 " --> pdb=" O ALA Y 319 " (cutoff:3.500A) removed outlier: 10.810A pdb=" N GLU Y 342 " --> pdb=" O ASN Y 361 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N ASN Y 361 " --> pdb=" O GLU Y 342 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N HIS Y 344 " --> pdb=" O ASP Y 359 " (cutoff:3.500A) 4232 hydrogen bonds defined for protein. 12330 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: 36.81 Time building geometry restraints manager: 17.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16272 1.33 - 1.45: 15046 1.45 - 1.57: 42986 1.57 - 1.70: 75 1.70 - 1.82: 640 Bond restraints: 75019 Sorted by residual: bond pdb=" CB MET e 89 " pdb=" CG MET e 89 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.07e+00 bond pdb=" CB TRP C 381 " pdb=" CG TRP C 381 " ideal model delta sigma weight residual 1.498 1.557 -0.059 3.10e-02 1.04e+03 3.68e+00 bond pdb=" CG ARG B 296 " pdb=" CD ARG B 296 " ideal model delta sigma weight residual 1.520 1.469 0.051 3.00e-02 1.11e+03 2.94e+00 bond pdb=" C HIS L 388 " pdb=" N PRO L 389 " ideal model delta sigma weight residual 1.334 1.370 -0.037 2.34e-02 1.83e+03 2.44e+00 bond pdb=" SD MET e 89 " pdb=" CE MET e 89 " ideal model delta sigma weight residual 1.791 1.753 0.038 2.50e-02 1.60e+03 2.32e+00 ... (remaining 75014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.02: 100196 3.02 - 6.03: 891 6.03 - 9.05: 99 9.05 - 12.07: 9 12.07 - 15.09: 5 Bond angle restraints: 101200 Sorted by residual: angle pdb=" N MET P 380 " pdb=" CA MET P 380 " pdb=" CB MET P 380 " ideal model delta sigma weight residual 110.39 118.76 -8.37 1.66e+00 3.63e-01 2.54e+01 angle pdb=" C PHE A 413 " pdb=" N GLU A 414 " pdb=" CA GLU A 414 " ideal model delta sigma weight residual 122.06 112.92 9.14 1.86e+00 2.89e-01 2.42e+01 angle pdb=" CB MET P 380 " pdb=" CG MET P 380 " pdb=" SD MET P 380 " ideal model delta sigma weight residual 112.70 126.97 -14.27 3.00e+00 1.11e-01 2.26e+01 angle pdb=" N GLU o 128 " pdb=" CA GLU o 128 " pdb=" CB GLU o 128 " ideal model delta sigma weight residual 110.28 117.29 -7.01 1.55e+00 4.16e-01 2.04e+01 angle pdb=" C LYS P 379 " pdb=" N MET P 380 " pdb=" CA MET P 380 " ideal model delta sigma weight residual 120.72 113.28 7.44 1.67e+00 3.59e-01 1.99e+01 ... (remaining 101195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 41585 17.82 - 35.65: 4187 35.65 - 53.47: 727 53.47 - 71.29: 152 71.29 - 89.12: 75 Dihedral angle restraints: 46726 sinusoidal: 19746 harmonic: 26980 Sorted by residual: dihedral pdb=" CA GLU G 226 " pdb=" C GLU G 226 " pdb=" N VAL G 227 " pdb=" CA VAL G 227 " ideal model delta harmonic sigma weight residual 180.00 -152.36 -27.64 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA MET G 415 " pdb=" C MET G 415 " pdb=" N MET G 416 " pdb=" CA MET G 416 " ideal model delta harmonic sigma weight residual 180.00 155.57 24.43 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA PHE C 62 " pdb=" C PHE C 62 " pdb=" N GLY C 63 " pdb=" CA GLY C 63 " ideal model delta harmonic sigma weight residual -180.00 -155.65 -24.35 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 46723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 9436 0.058 - 0.116: 1804 0.116 - 0.174: 171 0.174 - 0.233: 5 0.233 - 0.291: 2 Chirality restraints: 11418 Sorted by residual: chirality pdb=" CG LEU p 104 " pdb=" CB LEU p 104 " pdb=" CD1 LEU p 104 " pdb=" CD2 LEU p 104 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB ILE H 400 " pdb=" CA ILE H 400 " pdb=" CG1 ILE H 400 " pdb=" CG2 ILE H 400 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE B 316 " pdb=" CA ILE B 316 " pdb=" CG1 ILE B 316 " pdb=" CG2 ILE B 316 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 11415 not shown) Planarity restraints: 13205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 381 " 0.033 2.00e-02 2.50e+03 3.61e-02 3.25e+01 pdb=" CG TRP C 381 " -0.095 2.00e-02 2.50e+03 pdb=" CD1 TRP C 381 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 381 " 0.010 2.00e-02 2.50e+03 pdb=" NE1 TRP C 381 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 381 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP C 381 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 381 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 381 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP C 381 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR a 170 " 0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO a 171 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO a 171 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO a 171 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 381 " 0.018 2.00e-02 2.50e+03 1.76e-02 7.79e+00 pdb=" CG TRP A 381 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TRP A 381 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 381 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 381 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 381 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 381 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 381 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 381 " 0.001 2.00e-02 2.50e+03 ... (remaining 13202 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 1198 2.60 - 3.18: 68652 3.18 - 3.75: 128382 3.75 - 4.33: 162100 4.33 - 4.90: 258520 Nonbonded interactions: 618852 Sorted by model distance: nonbonded pdb=" OG1 THR j 170 " pdb=" OE1 GLN j 173 " model vdw 2.031 3.040 nonbonded pdb=" OG1 THR E 185 " pdb="MG MG E 502 " model vdw 2.061 2.170 nonbonded pdb=" OG1 THR D 185 " pdb="MG MG D 502 " model vdw 2.070 2.170 nonbonded pdb=" OG1 THR O 185 " pdb="MG MG O 502 " model vdw 2.070 2.170 nonbonded pdb=" OG1 THR N 185 " pdb="MG MG N 502 " model vdw 2.071 2.170 ... (remaining 618847 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 1 through 419) selection = (chain 'B' and resid 1 through 419) selection = (chain 'C' and resid 1 through 419) selection = (chain 'D' and resid 1 through 419) selection = (chain 'E' and resid 1 through 419) selection = (chain 'F' and resid 1 through 419) selection = (chain 'G' and resid 1 through 419) selection = (chain 'H' and resid 1 through 419) selection = (chain 'J' and resid 1 through 419) selection = (chain 'K' and resid 1 through 419) selection = (chain 'L' and resid 1 through 419) selection = (chain 'M' and resid 1 through 419) selection = (chain 'N' and resid 1 through 419) selection = (chain 'O' and resid 1 through 419) selection = (chain 'P' and resid 1 through 419) selection = chain 'Y' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'o' selection = chain 'p' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.630 Check model and map are aligned: 0.430 Set scattering table: 0.540 Process input model: 138.900 Find NCS groups from input model: 3.400 Set up NCS constraints: 0.710 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: 0.020 Load rotamer database and sin/cos tables:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 156.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 : 0.003 0.061 75019 Z= 0.176 Angle : 0.700 15.087 101200 Z= 0.358 Chirality : 0.044 0.291 11418 Planarity : 0.004 0.087 13205 Dihedral : 14.771 89.116 29206 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.92 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.09), residues: 9262 helix: 0.68 (0.07), residues: 5012 sheet: 0.18 (0.17), residues: 984 loop : -0.58 (0.11), residues: 3266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP C 381 HIS 0.009 0.001 HIS K 344 PHE 0.038 0.001 PHE C 412 TYR 0.033 0.001 TYR N 80 ARG 0.026 0.001 ARG f 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1022 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1022 time to evaluate : 6.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7423 (t80) cc_final: 0.7184 (t80) REVERT: B 197 TYR cc_start: 0.7881 (t80) cc_final: 0.7603 (t80) REVERT: C 164 LEU cc_start: 0.9184 (mm) cc_final: 0.8970 (mm) REVERT: C 329 GLU cc_start: 0.8854 (mp0) cc_final: 0.8379 (mp0) REVERT: D 1 MET cc_start: 0.8306 (tmm) cc_final: 0.7715 (tmm) REVERT: D 139 LEU cc_start: 0.8740 (mt) cc_final: 0.8459 (mt) REVERT: D 147 MET cc_start: 0.9204 (mmm) cc_final: 0.8980 (mmm) REVERT: D 186 MET cc_start: 0.8122 (ptp) cc_final: 0.7827 (ptt) REVERT: D 333 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7946 (tp30) REVERT: F 1 MET cc_start: 0.8471 (ppp) cc_final: 0.8134 (ppp) REVERT: G 1 MET cc_start: 0.8283 (ppp) cc_final: 0.7741 (ppp) REVERT: G 21 MET cc_start: 0.1517 (tpp) cc_final: 0.1228 (tpt) REVERT: G 29 MET cc_start: 0.4414 (pmm) cc_final: 0.3407 (pmm) REVERT: G 381 TRP cc_start: 0.8027 (m-10) cc_final: 0.7675 (m-10) REVERT: H 205 MET cc_start: 0.7453 (pmm) cc_final: 0.6966 (pmm) REVERT: H 299 ARG cc_start: 0.9117 (tpm170) cc_final: 0.8686 (mtt180) REVERT: J 21 MET cc_start: 0.7100 (ppp) cc_final: 0.6637 (ppp) REVERT: J 72 TYR cc_start: 0.8571 (m-10) cc_final: 0.8313 (m-10) REVERT: J 219 MET cc_start: 0.8352 (mmt) cc_final: 0.8134 (mmt) REVERT: J 374 GLN cc_start: 0.8238 (tp-100) cc_final: 0.7839 (tp-100) REVERT: J 416 MET cc_start: 0.6259 (ppp) cc_final: 0.5838 (ppp) REVERT: K 73 LEU cc_start: 0.8928 (tp) cc_final: 0.8721 (tp) REVERT: L 244 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8146 (mm-30) REVERT: L 333 GLU cc_start: 0.9035 (tt0) cc_final: 0.8826 (pp20) REVERT: L 341 MET cc_start: 0.8356 (tmm) cc_final: 0.7931 (tmm) REVERT: L 342 GLU cc_start: 0.8464 (mp0) cc_final: 0.8132 (mp0) REVERT: L 397 GLU cc_start: 0.9145 (mp0) cc_final: 0.8732 (mp0) REVERT: L 405 MET cc_start: 0.8086 (ppp) cc_final: 0.7661 (ppp) REVERT: L 406 THR cc_start: 0.7098 (p) cc_final: 0.6655 (p) REVERT: N 21 MET cc_start: 0.7978 (tmm) cc_final: 0.7313 (tmm) REVERT: N 126 ASN cc_start: 0.9235 (t0) cc_final: 0.8914 (t0) REVERT: N 292 ASN cc_start: 0.9002 (m110) cc_final: 0.8738 (m110) REVERT: O 168 ILE cc_start: 0.8630 (mm) cc_final: 0.8332 (mm) REVERT: O 380 MET cc_start: 0.9412 (mtm) cc_final: 0.9078 (mtm) REVERT: P 396 MET cc_start: 0.7547 (ppp) cc_final: 0.7193 (ppp) REVERT: Y 205 MET cc_start: 0.2825 (ppp) cc_final: 0.2555 (ppp) REVERT: a 53 ASN cc_start: 0.9080 (m110) cc_final: 0.8871 (m110) REVERT: a 59 LYS cc_start: 0.8960 (ptpp) cc_final: 0.8720 (ptpp) REVERT: b 163 ASP cc_start: 0.6872 (p0) cc_final: 0.6669 (p0) REVERT: c 25 ASN cc_start: 0.9336 (m110) cc_final: 0.9089 (m110) REVERT: e 124 ASP cc_start: 0.9242 (m-30) cc_final: 0.8980 (p0) REVERT: f 83 ASP cc_start: 0.9201 (t0) cc_final: 0.8821 (t0) REVERT: g 83 ASP cc_start: 0.8898 (t70) cc_final: 0.8507 (t0) REVERT: i 83 ASP cc_start: 0.9156 (t70) cc_final: 0.8814 (t0) REVERT: i 89 MET cc_start: 0.8376 (tpt) cc_final: 0.8171 (tmm) REVERT: i 105 MET cc_start: 0.9100 (mmp) cc_final: 0.8569 (mmm) REVERT: i 128 GLU cc_start: 0.9511 (tm-30) cc_final: 0.9265 (tm-30) REVERT: j 128 GLU cc_start: 0.9328 (mp0) cc_final: 0.9086 (mp0) REVERT: j 175 MET cc_start: 0.9028 (ppp) cc_final: 0.8747 (ppp) outliers start: 0 outliers final: 0 residues processed: 1022 average time/residue: 0.6905 time to fit residues: 1242.5667 Evaluate side-chains 738 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 8.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 766 optimal weight: 5.9990 chunk 688 optimal weight: 0.8980 chunk 381 optimal weight: 7.9990 chunk 235 optimal weight: 0.7980 chunk 464 optimal weight: 0.3980 chunk 367 optimal weight: 7.9990 chunk 711 optimal weight: 0.9980 chunk 275 optimal weight: 0.9990 chunk 432 optimal weight: 7.9990 chunk 529 optimal weight: 6.9990 chunk 824 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 189 GLN B 340 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 ASN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 374 GLN F 135 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 220 GLN F 239 HIS G 85 GLN ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN J 295 HIS ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 306 ASN L 42 HIS L 306 ASN M 85 GLN M 90 ASN ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 292 ASN N 25 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 241 GLN a 25 ASN ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 174 ASN ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN k 63 ASN k 120 GLN l 63 ASN o 16 ASN o 53 ASN o 86 ASN p 73 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.086818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.063531 restraints weight = 428108.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065199 restraints weight = 221319.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.065320 restraints weight = 136114.147| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 75019 Z= 0.189 Angle : 0.691 16.290 101200 Z= 0.350 Chirality : 0.044 0.246 11418 Planarity : 0.005 0.068 13205 Dihedral : 7.987 86.727 10718 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.12 % Allowed : 9.71 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.09), residues: 9262 helix: 0.79 (0.07), residues: 5118 sheet: 0.13 (0.17), residues: 968 loop : -0.63 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP o 133 HIS 0.007 0.001 HIS Y 256 PHE 0.041 0.001 PHE C 412 TYR 0.023 0.002 TYR N 80 ARG 0.008 0.001 ARG o 166 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 854 time to evaluate : 6.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 TYR cc_start: 0.8785 (m-80) cc_final: 0.7823 (m-80) REVERT: A 341 MET cc_start: 0.8307 (tmm) cc_final: 0.8024 (tmm) REVERT: B 1 MET cc_start: 0.8153 (tmm) cc_final: 0.7870 (ppp) REVERT: B 80 TYR cc_start: 0.7092 (t80) cc_final: 0.6862 (t80) REVERT: B 197 TYR cc_start: 0.8045 (t80) cc_final: 0.7695 (t80) REVERT: B 380 MET cc_start: 0.9391 (mpp) cc_final: 0.9160 (mpp) REVERT: C 1 MET cc_start: 0.8565 (tpp) cc_final: 0.8360 (tpp) REVERT: C 164 LEU cc_start: 0.9412 (mm) cc_final: 0.9095 (mm) REVERT: C 215 GLU cc_start: 0.7965 (pm20) cc_final: 0.7743 (pm20) REVERT: C 240 VAL cc_start: 0.8955 (t) cc_final: 0.8750 (p) REVERT: C 329 GLU cc_start: 0.8735 (mp0) cc_final: 0.8334 (mp0) REVERT: C 351 GLU cc_start: 0.8997 (mp0) cc_final: 0.8653 (mp0) REVERT: C 369 GLU cc_start: 0.8438 (mp0) cc_final: 0.8009 (mp0) REVERT: D 1 MET cc_start: 0.7967 (tmm) cc_final: 0.7525 (tmm) REVERT: E 341 MET cc_start: 0.9383 (tmm) cc_final: 0.8808 (tmm) REVERT: E 405 MET cc_start: 0.8661 (ppp) cc_final: 0.8416 (ppp) REVERT: E 416 MET cc_start: 0.8343 (tpp) cc_final: 0.8130 (tpp) REVERT: F 369 GLU cc_start: 0.8899 (pm20) cc_final: 0.8317 (pm20) REVERT: G 1 MET cc_start: 0.8713 (ppp) cc_final: 0.8027 (ppp) REVERT: G 2 ASN cc_start: 0.8994 (t0) cc_final: 0.8761 (t0) REVERT: G 21 MET cc_start: 0.2404 (tpp) cc_final: 0.2190 (tpt) REVERT: G 29 MET cc_start: 0.5200 (pmm) cc_final: 0.4283 (pmm) REVERT: G 381 TRP cc_start: 0.9187 (m-10) cc_final: 0.8843 (m-10) REVERT: G 415 MET cc_start: 0.9100 (ppp) cc_final: 0.8688 (ppp) REVERT: G 416 MET cc_start: 0.9188 (mmm) cc_final: 0.8803 (mmm) REVERT: H 205 MET cc_start: 0.7715 (pmm) cc_final: 0.7492 (pmm) REVERT: H 245 MET cc_start: 0.5691 (ptm) cc_final: 0.5169 (ppp) REVERT: H 327 MET cc_start: 0.4811 (mmt) cc_final: 0.4126 (ttm) REVERT: J 13 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8198 (tm-30) REVERT: J 21 MET cc_start: 0.7539 (ppp) cc_final: 0.7055 (ppp) REVERT: J 205 MET cc_start: 0.6981 (ppp) cc_final: 0.6002 (ppp) REVERT: J 219 MET cc_start: 0.9148 (mmt) cc_final: 0.8920 (mmm) REVERT: J 374 GLN cc_start: 0.8625 (tp-100) cc_final: 0.8255 (tp-100) REVERT: J 396 MET cc_start: 0.9103 (mmm) cc_final: 0.8890 (mmm) REVERT: J 416 MET cc_start: 0.6492 (ppp) cc_final: 0.6117 (ppp) REVERT: K 380 MET cc_start: 0.9191 (mtm) cc_final: 0.8990 (mtm) REVERT: L 341 MET cc_start: 0.8581 (tmm) cc_final: 0.8123 (tmm) REVERT: L 342 GLU cc_start: 0.8257 (mp0) cc_final: 0.7993 (mp0) REVERT: L 362 ARG cc_start: 0.8940 (mtp-110) cc_final: 0.8237 (ttm110) REVERT: L 405 MET cc_start: 0.7754 (ppp) cc_final: 0.7272 (ppp) REVERT: L 406 THR cc_start: 0.6739 (p) cc_final: 0.6134 (p) REVERT: L 415 MET cc_start: 0.8454 (tmm) cc_final: 0.8180 (tmm) REVERT: M 219 MET cc_start: 0.8616 (mmp) cc_final: 0.8381 (mmp) REVERT: N 21 MET cc_start: 0.7772 (tmm) cc_final: 0.7027 (tmm) REVERT: N 126 ASN cc_start: 0.9155 (t0) cc_final: 0.8813 (t0) REVERT: N 241 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: N 245 MET cc_start: 0.8920 (ppp) cc_final: 0.8546 (ppp) REVERT: O 1 MET cc_start: 0.7571 (tmm) cc_final: 0.6893 (ppp) REVERT: O 136 LEU cc_start: 0.9465 (mt) cc_final: 0.9063 (pp) REVERT: O 219 MET cc_start: 0.9270 (mmp) cc_final: 0.9059 (mmm) REVERT: O 380 MET cc_start: 0.9514 (mtm) cc_final: 0.9072 (mtm) REVERT: P 186 MET cc_start: 0.9194 (pmm) cc_final: 0.8993 (pmm) REVERT: P 245 MET cc_start: 0.8720 (mpp) cc_final: 0.8361 (mpp) REVERT: P 381 TRP cc_start: 0.8568 (t60) cc_final: 0.8320 (t60) REVERT: P 396 MET cc_start: 0.8411 (ppp) cc_final: 0.7979 (ppp) REVERT: P 405 MET cc_start: 0.8388 (pmm) cc_final: 0.7980 (pmm) REVERT: Y 29 MET cc_start: 0.4280 (pmm) cc_final: 0.3669 (ppp) REVERT: Y 245 MET cc_start: 0.1414 (tpt) cc_final: 0.0796 (mmm) REVERT: Y 414 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8686 (pp20) REVERT: Y 415 MET cc_start: 0.7804 (ppp) cc_final: 0.7199 (ppp) REVERT: a 59 LYS cc_start: 0.9474 (ptpp) cc_final: 0.9161 (pttm) REVERT: a 87 ASP cc_start: 0.9190 (m-30) cc_final: 0.8911 (p0) REVERT: b 89 MET cc_start: 0.8603 (tmm) cc_final: 0.7940 (tmm) REVERT: b 105 MET cc_start: 0.8454 (mpp) cc_final: 0.8245 (mpp) REVERT: b 175 MET cc_start: 0.9088 (ppp) cc_final: 0.8776 (ppp) REVERT: c 25 ASN cc_start: 0.9369 (m110) cc_final: 0.9080 (m-40) REVERT: f 83 ASP cc_start: 0.9063 (t0) cc_final: 0.8808 (t0) REVERT: g 83 ASP cc_start: 0.8902 (t70) cc_final: 0.8592 (t0) REVERT: h 175 MET cc_start: 0.8778 (ppp) cc_final: 0.8491 (ppp) REVERT: i 83 ASP cc_start: 0.9030 (t70) cc_final: 0.8717 (t0) REVERT: i 89 MET cc_start: 0.8456 (tpt) cc_final: 0.8107 (tmm) REVERT: i 128 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8872 (tm-30) REVERT: j 175 MET cc_start: 0.8765 (ppp) cc_final: 0.8440 (ppp) REVERT: k 105 MET cc_start: 0.8934 (mmt) cc_final: 0.8431 (mmt) REVERT: k 168 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8338 (tptp) REVERT: p 167 GLU cc_start: 0.7851 (pm20) cc_final: 0.7589 (pm20) REVERT: p 169 PHE cc_start: 0.7002 (m-80) cc_final: 0.6713 (m-80) REVERT: p 176 ILE cc_start: 0.9033 (tp) cc_final: 0.8800 (tp) REVERT: p 180 LYS cc_start: 0.6943 (mmtt) cc_final: 0.6527 (mmtt) outliers start: 88 outliers final: 39 residues processed: 909 average time/residue: 0.6478 time to fit residues: 1033.8167 Evaluate side-chains 789 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 748 time to evaluate : 6.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 378 GLN Chi-restraints excluded: chain E residue 398 PHE Chi-restraints excluded: chain F residue 274 TYR Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain J residue 193 GLN Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain K residue 228 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain i residue 159 VAL Chi-restraints excluded: chain j residue 53 ASN Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain o residue 128 GLU Chi-restraints excluded: chain o residue 130 LEU Chi-restraints excluded: chain o residue 170 THR Chi-restraints excluded: chain p residue 45 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 258 optimal weight: 3.9990 chunk 468 optimal weight: 2.9990 chunk 808 optimal weight: 9.9990 chunk 644 optimal weight: 4.9990 chunk 825 optimal weight: 10.0000 chunk 282 optimal weight: 20.0000 chunk 387 optimal weight: 1.9990 chunk 301 optimal weight: 50.0000 chunk 118 optimal weight: 6.9990 chunk 492 optimal weight: 10.0000 chunk 530 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS D 239 HIS ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 292 ASN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 239 HIS L 190 ASN L 239 HIS ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 306 ASN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 199 HIS ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 361 ASN ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 117 ASN ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 64 GLN ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 174 ASN k 77 GLN ** k 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.083814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.059741 restraints weight = 417921.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.061145 restraints weight = 226339.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.060845 restraints weight = 134200.495| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 75019 Z= 0.268 Angle : 0.666 15.817 101200 Z= 0.344 Chirality : 0.044 0.279 11418 Planarity : 0.004 0.066 13205 Dihedral : 7.893 77.146 10718 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.69 % Allowed : 13.38 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.09), residues: 9262 helix: 0.85 (0.07), residues: 5193 sheet: -0.08 (0.16), residues: 1013 loop : -0.62 (0.11), residues: 3056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP o 133 HIS 0.015 0.001 HIS J 295 PHE 0.031 0.002 PHE C 412 TYR 0.025 0.002 TYR i 142 ARG 0.013 0.001 ARG J 296 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 794 time to evaluate : 6.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.9326 (mmm) cc_final: 0.9110 (mmm) REVERT: A 341 MET cc_start: 0.8599 (tmm) cc_final: 0.8179 (tmm) REVERT: A 390 MET cc_start: 0.7194 (pmm) cc_final: 0.6937 (pmm) REVERT: B 80 TYR cc_start: 0.7360 (t80) cc_final: 0.7138 (t80) REVERT: B 326 LYS cc_start: 0.9511 (mmmt) cc_final: 0.9311 (tppt) REVERT: B 380 MET cc_start: 0.9515 (mpp) cc_final: 0.9247 (mpp) REVERT: C 1 MET cc_start: 0.8573 (tpp) cc_final: 0.8345 (tpp) REVERT: C 164 LEU cc_start: 0.9497 (mm) cc_final: 0.9237 (mm) REVERT: C 177 VAL cc_start: 0.8961 (t) cc_final: 0.8733 (t) REVERT: D 1 MET cc_start: 0.7986 (tmm) cc_final: 0.7616 (tmm) REVERT: D 147 MET cc_start: 0.8787 (mmm) cc_final: 0.8442 (mmm) REVERT: D 341 MET cc_start: 0.9212 (tmm) cc_final: 0.8710 (ppp) REVERT: E 415 MET cc_start: 0.8846 (ptm) cc_final: 0.8556 (ptp) REVERT: E 416 MET cc_start: 0.8169 (tpp) cc_final: 0.7906 (tpp) REVERT: F 265 ASP cc_start: 0.8352 (t0) cc_final: 0.7513 (p0) REVERT: F 380 MET cc_start: 0.9373 (pmm) cc_final: 0.9132 (pmm) REVERT: G 1 MET cc_start: 0.8825 (ppp) cc_final: 0.8224 (ppp) REVERT: G 29 MET cc_start: 0.5255 (pmm) cc_final: 0.4368 (pmm) REVERT: G 54 VAL cc_start: 0.4075 (OUTLIER) cc_final: 0.3859 (t) REVERT: G 164 LEU cc_start: 0.9193 (tt) cc_final: 0.8974 (pp) REVERT: G 396 MET cc_start: 0.6966 (ptt) cc_final: 0.6722 (ptt) REVERT: J 21 MET cc_start: 0.7507 (ppp) cc_final: 0.6824 (ppp) REVERT: J 205 MET cc_start: 0.7031 (ppp) cc_final: 0.6284 (ppp) REVERT: J 219 MET cc_start: 0.9223 (mmt) cc_final: 0.8977 (mmm) REVERT: J 374 GLN cc_start: 0.8704 (tp-100) cc_final: 0.8352 (tp-100) REVERT: J 396 MET cc_start: 0.9066 (mmm) cc_final: 0.8792 (mmm) REVERT: J 416 MET cc_start: 0.6652 (ppp) cc_final: 0.6300 (ppp) REVERT: K 193 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8307 (pm20) REVERT: L 341 MET cc_start: 0.8889 (tmm) cc_final: 0.8601 (tmm) REVERT: L 405 MET cc_start: 0.7976 (ppp) cc_final: 0.7381 (ppp) REVERT: L 406 THR cc_start: 0.7095 (p) cc_final: 0.6354 (p) REVERT: L 415 MET cc_start: 0.8362 (tmm) cc_final: 0.8093 (tmm) REVERT: M 147 MET cc_start: 0.8826 (mmm) cc_final: 0.8560 (mmm) REVERT: M 219 MET cc_start: 0.9022 (mmp) cc_final: 0.8791 (mmp) REVERT: M 415 MET cc_start: 0.9220 (tmm) cc_final: 0.8980 (tmm) REVERT: N 21 MET cc_start: 0.7989 (tmm) cc_final: 0.7384 (tmm) REVERT: N 126 ASN cc_start: 0.9198 (t0) cc_final: 0.8800 (t0) REVERT: N 241 GLN cc_start: 0.8016 (OUTLIER) cc_final: 0.7544 (pm20) REVERT: N 244 GLU cc_start: 0.8707 (pp20) cc_final: 0.8455 (pp20) REVERT: N 245 MET cc_start: 0.8672 (ppp) cc_final: 0.8425 (ppp) REVERT: O 219 MET cc_start: 0.9340 (mmp) cc_final: 0.9073 (mmt) REVERT: O 380 MET cc_start: 0.9557 (mtm) cc_final: 0.9270 (mtm) REVERT: P 245 MET cc_start: 0.8800 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: P 396 MET cc_start: 0.8426 (ppp) cc_final: 0.8030 (ppp) REVERT: P 405 MET cc_start: 0.8465 (pmm) cc_final: 0.8226 (pmm) REVERT: Y 245 MET cc_start: 0.1656 (tpt) cc_final: 0.1337 (mmm) REVERT: Y 405 MET cc_start: 0.8515 (mmp) cc_final: 0.8196 (pmm) REVERT: Y 414 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.8688 (pp20) REVERT: a 59 LYS cc_start: 0.9476 (ptpp) cc_final: 0.9178 (ptpp) REVERT: a 87 ASP cc_start: 0.9195 (m-30) cc_final: 0.8932 (p0) REVERT: b 89 MET cc_start: 0.8635 (tmm) cc_final: 0.7991 (tmm) REVERT: c 25 ASN cc_start: 0.9369 (m110) cc_final: 0.9081 (m-40) REVERT: f 83 ASP cc_start: 0.9070 (t0) cc_final: 0.8810 (t0) REVERT: g 83 ASP cc_start: 0.8855 (t70) cc_final: 0.8593 (t0) REVERT: h 175 MET cc_start: 0.8864 (ppp) cc_final: 0.8637 (ppp) REVERT: i 89 MET cc_start: 0.8679 (tpt) cc_final: 0.8159 (tmm) REVERT: i 128 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8909 (tp30) REVERT: j 175 MET cc_start: 0.8863 (ppp) cc_final: 0.8605 (ppp) REVERT: k 105 MET cc_start: 0.9014 (mmt) cc_final: 0.8427 (mmm) REVERT: o 58 ARG cc_start: 0.7127 (tpm170) cc_final: 0.6339 (tpp80) REVERT: p 78 HIS cc_start: 0.9229 (m90) cc_final: 0.8907 (m90) outliers start: 133 outliers final: 76 residues processed: 885 average time/residue: 0.6301 time to fit residues: 984.0338 Evaluate side-chains 794 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 713 time to evaluate : 6.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 330 VAL Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 274 TYR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain J residue 193 GLN Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 274 TYR Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain O residue 414 GLU Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain P residue 332 TYR Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 193 GLN Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 86 ASN Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain e residue 94 THR Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain h residue 94 THR Chi-restraints excluded: chain i residue 159 VAL Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain l residue 27 LEU Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 181 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 797 optimal weight: 5.9990 chunk 449 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 468 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 896 optimal weight: 20.0000 chunk 195 optimal weight: 7.9990 chunk 189 optimal weight: 0.9990 chunk 132 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 GLN ** H 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 HIS K 140 HIS ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 344 HIS ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 120 GLN g 120 GLN ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN k 116 ASN o 44 ASN o 77 GLN p 25 ASN p 63 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.084541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.061012 restraints weight = 424755.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.062131 restraints weight = 223892.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.062651 restraints weight = 134828.646| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 75019 Z= 0.178 Angle : 0.651 15.844 101200 Z= 0.329 Chirality : 0.043 0.335 11418 Planarity : 0.004 0.064 13205 Dihedral : 7.702 81.273 10718 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.89 % Allowed : 15.19 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.09), residues: 9262 helix: 0.86 (0.07), residues: 5204 sheet: -0.07 (0.16), residues: 1014 loop : -0.57 (0.11), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP o 133 HIS 0.013 0.001 HIS H 344 PHE 0.032 0.001 PHE C 412 TYR 0.018 0.001 TYR A 274 ARG 0.012 0.000 ARG N 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 785 time to evaluate : 6.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.6976 (tpp) cc_final: 0.6469 (mmm) REVERT: A 219 MET cc_start: 0.9256 (mmm) cc_final: 0.9047 (mmm) REVERT: A 341 MET cc_start: 0.8748 (tmm) cc_final: 0.8298 (tmm) REVERT: A 380 MET cc_start: 0.9056 (ppp) cc_final: 0.8729 (ppp) REVERT: A 390 MET cc_start: 0.7124 (pmm) cc_final: 0.6917 (pmm) REVERT: B 80 TYR cc_start: 0.7537 (t80) cc_final: 0.7308 (t80) REVERT: B 240 VAL cc_start: 0.8893 (m) cc_final: 0.8669 (p) REVERT: B 380 MET cc_start: 0.9520 (mpp) cc_final: 0.9223 (mtm) REVERT: C 1 MET cc_start: 0.8603 (tpp) cc_final: 0.8373 (tpp) REVERT: C 164 LEU cc_start: 0.9530 (mm) cc_final: 0.9256 (mm) REVERT: C 177 VAL cc_start: 0.8891 (t) cc_final: 0.8624 (t) REVERT: C 329 GLU cc_start: 0.8676 (mp0) cc_final: 0.8301 (mp0) REVERT: D 1 MET cc_start: 0.7999 (tmm) cc_final: 0.7637 (tmm) REVERT: D 147 MET cc_start: 0.8859 (mmm) cc_final: 0.8568 (mmm) REVERT: D 341 MET cc_start: 0.9221 (tmm) cc_final: 0.9005 (tmm) REVERT: E 193 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: E 327 MET cc_start: 0.8791 (ppp) cc_final: 0.7708 (ppp) REVERT: E 397 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8427 (mt-10) REVERT: E 415 MET cc_start: 0.8848 (ptm) cc_final: 0.8638 (ptp) REVERT: E 416 MET cc_start: 0.8148 (tpp) cc_final: 0.7901 (tpp) REVERT: F 244 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8427 (pm20) REVERT: F 245 MET cc_start: 0.9329 (mmt) cc_final: 0.8717 (mmm) REVERT: F 265 ASP cc_start: 0.8361 (t0) cc_final: 0.7425 (p0) REVERT: F 380 MET cc_start: 0.9387 (OUTLIER) cc_final: 0.9121 (pmm) REVERT: G 1 MET cc_start: 0.8729 (ppp) cc_final: 0.8098 (ppp) REVERT: G 29 MET cc_start: 0.5198 (pmm) cc_final: 0.4288 (pmm) REVERT: G 415 MET cc_start: 0.9095 (ppp) cc_final: 0.8725 (ppp) REVERT: G 416 MET cc_start: 0.9179 (mmm) cc_final: 0.8781 (mmm) REVERT: J 21 MET cc_start: 0.7545 (ppp) cc_final: 0.6757 (ppp) REVERT: J 205 MET cc_start: 0.7012 (ppp) cc_final: 0.6474 (ppp) REVERT: J 219 MET cc_start: 0.9182 (mmt) cc_final: 0.8942 (mmm) REVERT: J 234 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8069 (pm20) REVERT: J 344 HIS cc_start: 0.8807 (m90) cc_final: 0.8292 (m-70) REVERT: J 396 MET cc_start: 0.9118 (mmm) cc_final: 0.8786 (mmm) REVERT: J 416 MET cc_start: 0.6738 (ppp) cc_final: 0.6408 (ppp) REVERT: K 21 MET cc_start: 0.7958 (ptp) cc_final: 0.7537 (tpt) REVERT: K 193 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8264 (pm20) REVERT: K 380 MET cc_start: 0.9221 (mtm) cc_final: 0.8803 (mtm) REVERT: L 186 MET cc_start: 0.8034 (ptp) cc_final: 0.7546 (ptp) REVERT: L 189 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8891 (pm20) REVERT: L 205 MET cc_start: 0.8306 (mtp) cc_final: 0.8052 (mtp) REVERT: L 220 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: L 334 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8304 (tm-30) REVERT: L 335 PHE cc_start: 0.9157 (OUTLIER) cc_final: 0.8941 (m-10) REVERT: L 362 ARG cc_start: 0.8999 (mtp-110) cc_final: 0.8585 (ttm110) REVERT: L 405 MET cc_start: 0.8028 (ppp) cc_final: 0.7472 (ppp) REVERT: L 406 THR cc_start: 0.7112 (p) cc_final: 0.6354 (p) REVERT: M 147 MET cc_start: 0.8925 (mmm) cc_final: 0.8628 (mmm) REVERT: N 21 MET cc_start: 0.8027 (tmm) cc_final: 0.7444 (tmm) REVERT: N 47 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6520 (pm20) REVERT: N 126 ASN cc_start: 0.9185 (t0) cc_final: 0.8778 (t0) REVERT: N 241 GLN cc_start: 0.8028 (OUTLIER) cc_final: 0.7539 (pm20) REVERT: N 244 GLU cc_start: 0.8722 (pp20) cc_final: 0.8419 (pp20) REVERT: N 245 MET cc_start: 0.8638 (ppp) cc_final: 0.8359 (ppp) REVERT: O 219 MET cc_start: 0.9342 (mmp) cc_final: 0.9061 (mmt) REVERT: O 380 MET cc_start: 0.9569 (mtm) cc_final: 0.9070 (mtm) REVERT: P 205 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.6669 (tpp) REVERT: P 245 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8513 (mpp) REVERT: P 380 MET cc_start: 0.9026 (pmm) cc_final: 0.8723 (pmm) REVERT: P 396 MET cc_start: 0.8511 (ppp) cc_final: 0.8071 (ppp) REVERT: P 405 MET cc_start: 0.8489 (pmm) cc_final: 0.8267 (pmm) REVERT: Y 245 MET cc_start: 0.1810 (tpt) cc_final: 0.1053 (mmm) REVERT: Y 405 MET cc_start: 0.8589 (mmp) cc_final: 0.8280 (pmm) REVERT: Y 414 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8667 (pp20) REVERT: Y 415 MET cc_start: 0.7869 (ppp) cc_final: 0.7641 (ppp) REVERT: a 59 LYS cc_start: 0.9473 (ptpp) cc_final: 0.9178 (pttm) REVERT: a 87 ASP cc_start: 0.9191 (m-30) cc_final: 0.8923 (p0) REVERT: b 89 MET cc_start: 0.8654 (tmm) cc_final: 0.7874 (ppp) REVERT: b 100 LEU cc_start: 0.8536 (tp) cc_final: 0.8131 (pp) REVERT: c 25 ASN cc_start: 0.9380 (m110) cc_final: 0.9094 (m110) REVERT: f 83 ASP cc_start: 0.9068 (t0) cc_final: 0.8801 (t0) REVERT: g 83 ASP cc_start: 0.8850 (t70) cc_final: 0.8533 (t0) REVERT: g 96 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8597 (pp) REVERT: h 175 MET cc_start: 0.8864 (ppp) cc_final: 0.8655 (ppp) REVERT: i 89 MET cc_start: 0.8777 (tpt) cc_final: 0.8284 (tmm) REVERT: i 128 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9001 (tp30) REVERT: j 175 MET cc_start: 0.8901 (ppp) cc_final: 0.8691 (ppp) REVERT: k 105 MET cc_start: 0.9073 (mmt) cc_final: 0.8430 (mmm) REVERT: k 168 LYS cc_start: 0.8932 (mmmt) cc_final: 0.8677 (tmtt) REVERT: o 23 ARG cc_start: 0.8281 (mtm180) cc_final: 0.7964 (ptp90) REVERT: o 58 ARG cc_start: 0.6972 (tpm170) cc_final: 0.6376 (tpp80) REVERT: p 78 HIS cc_start: 0.9178 (m90) cc_final: 0.8836 (m90) REVERT: p 167 GLU cc_start: 0.7058 (pm20) cc_final: 0.6703 (pm20) REVERT: p 177 PHE cc_start: 0.8197 (m-10) cc_final: 0.7705 (m-10) outliers start: 149 outliers final: 77 residues processed: 889 average time/residue: 0.6472 time to fit residues: 1008.0857 Evaluate side-chains 811 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 719 time to evaluate : 6.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 378 GLN Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 274 TYR Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 126 ASN Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 300 PHE Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 335 PHE Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 191 ILE Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 372 THR Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 205 MET Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain P residue 332 TYR Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 193 GLN Chi-restraints excluded: chain Y residue 256 HIS Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 31 GLU Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 86 ASN Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 96 LEU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 26 GLU Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain o residue 188 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 181 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 34 optimal weight: 8.9990 chunk 864 optimal weight: 0.8980 chunk 235 optimal weight: 3.9990 chunk 496 optimal weight: 6.9990 chunk 539 optimal weight: 30.0000 chunk 70 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 874 optimal weight: 6.9990 chunk 520 optimal weight: 4.9990 chunk 528 optimal weight: 0.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 239 HIS J 193 GLN ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 239 HIS ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 173 GLN ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.083151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.058479 restraints weight = 400459.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.058799 restraints weight = 202451.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.059575 restraints weight = 125315.432| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 75019 Z= 0.210 Angle : 0.659 15.565 101200 Z= 0.333 Chirality : 0.043 0.280 11418 Planarity : 0.004 0.062 13205 Dihedral : 7.592 83.331 10718 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.41 % Allowed : 15.76 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 9262 helix: 0.90 (0.07), residues: 5212 sheet: -0.07 (0.16), residues: 1058 loop : -0.52 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP p 60 HIS 0.031 0.001 HIS J 295 PHE 0.025 0.001 PHE C 412 TYR 0.023 0.001 TYR C 332 ARG 0.011 0.000 ARG E 30 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 952 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 190 poor density : 762 time to evaluate : 6.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.6994 (tpp) cc_final: 0.6657 (mmm) REVERT: A 219 MET cc_start: 0.9319 (mmm) cc_final: 0.9101 (mmm) REVERT: A 341 MET cc_start: 0.8783 (tmm) cc_final: 0.8325 (tmm) REVERT: A 380 MET cc_start: 0.9046 (ppp) cc_final: 0.8740 (ppp) REVERT: B 380 MET cc_start: 0.9463 (mpp) cc_final: 0.9161 (mtm) REVERT: C 1 MET cc_start: 0.8705 (tpp) cc_final: 0.8446 (tpp) REVERT: C 164 LEU cc_start: 0.9530 (mm) cc_final: 0.9319 (mm) REVERT: C 177 VAL cc_start: 0.8941 (t) cc_final: 0.8738 (t) REVERT: C 329 GLU cc_start: 0.8832 (mp0) cc_final: 0.8435 (mp0) REVERT: D 92 ARG cc_start: 0.7303 (OUTLIER) cc_final: 0.6445 (mtm180) REVERT: D 147 MET cc_start: 0.8933 (mmm) cc_final: 0.8704 (mmm) REVERT: D 341 MET cc_start: 0.9209 (tmm) cc_final: 0.8851 (tmm) REVERT: E 193 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8659 (pm20) REVERT: E 244 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8350 (mm-30) REVERT: E 327 MET cc_start: 0.8931 (ppp) cc_final: 0.7972 (ppp) REVERT: E 416 MET cc_start: 0.8245 (tpp) cc_final: 0.7973 (tpp) REVERT: F 245 MET cc_start: 0.9341 (mmt) cc_final: 0.8815 (mmm) REVERT: F 265 ASP cc_start: 0.8405 (t0) cc_final: 0.8122 (t0) REVERT: F 313 LEU cc_start: 0.9200 (tp) cc_final: 0.8965 (tt) REVERT: F 380 MET cc_start: 0.9306 (OUTLIER) cc_final: 0.9048 (pmm) REVERT: G 1 MET cc_start: 0.8729 (ppp) cc_final: 0.8153 (ppp) REVERT: G 21 MET cc_start: 0.2066 (tpt) cc_final: 0.1192 (tpt) REVERT: G 29 MET cc_start: 0.5209 (pmm) cc_final: 0.4361 (pmm) REVERT: G 54 VAL cc_start: 0.5038 (OUTLIER) cc_final: 0.4775 (t) REVERT: G 139 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8932 (mm) REVERT: G 415 MET cc_start: 0.9108 (ppp) cc_final: 0.8690 (ppp) REVERT: G 416 MET cc_start: 0.9384 (mmm) cc_final: 0.9051 (mmm) REVERT: J 21 MET cc_start: 0.7339 (ppp) cc_final: 0.6445 (ppp) REVERT: J 204 LEU cc_start: 0.6201 (OUTLIER) cc_final: 0.5902 (mm) REVERT: J 219 MET cc_start: 0.9165 (mmt) cc_final: 0.8940 (mmm) REVERT: J 234 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: J 344 HIS cc_start: 0.8638 (m90) cc_final: 0.8137 (m-70) REVERT: J 374 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8645 (tp-100) REVERT: J 396 MET cc_start: 0.9095 (mmm) cc_final: 0.8776 (mmm) REVERT: K 21 MET cc_start: 0.7987 (ptp) cc_final: 0.7635 (tpt) REVERT: K 189 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8415 (mm-40) REVERT: K 283 LYS cc_start: 0.8174 (tttt) cc_final: 0.7849 (tptp) REVERT: L 189 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8915 (pm20) REVERT: L 220 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8189 (mp10) REVERT: L 334 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8259 (tm-30) REVERT: L 335 PHE cc_start: 0.9129 (OUTLIER) cc_final: 0.8723 (m-10) REVERT: L 362 ARG cc_start: 0.9002 (mtp-110) cc_final: 0.8654 (ttm110) REVERT: M 147 MET cc_start: 0.9070 (mmm) cc_final: 0.8726 (mmm) REVERT: M 219 MET cc_start: 0.9018 (mmp) cc_final: 0.8763 (mmp) REVERT: M 244 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8077 (mm-30) REVERT: M 327 MET cc_start: 0.8721 (ppp) cc_final: 0.8494 (ptm) REVERT: N 21 MET cc_start: 0.8076 (tmm) cc_final: 0.7470 (tmm) REVERT: N 126 ASN cc_start: 0.9165 (t0) cc_final: 0.8781 (t0) REVERT: N 241 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: N 244 GLU cc_start: 0.8765 (pp20) cc_final: 0.8434 (pp20) REVERT: O 219 MET cc_start: 0.9332 (mmp) cc_final: 0.9019 (mmt) REVERT: O 380 MET cc_start: 0.9537 (mtm) cc_final: 0.9195 (mtt) REVERT: P 205 MET cc_start: 0.7677 (pmm) cc_final: 0.7347 (ppp) REVERT: P 245 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8595 (mpp) REVERT: P 396 MET cc_start: 0.8381 (ppp) cc_final: 0.7911 (ppp) REVERT: Y 245 MET cc_start: 0.2934 (tpt) cc_final: 0.2165 (mmm) REVERT: Y 405 MET cc_start: 0.8581 (mmp) cc_final: 0.8354 (pmm) REVERT: Y 414 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8721 (pp20) REVERT: a 27 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8730 (tp) REVERT: a 59 LYS cc_start: 0.9500 (ptpp) cc_final: 0.9218 (ptpp) REVERT: a 89 MET cc_start: 0.7415 (tmm) cc_final: 0.7063 (tmm) REVERT: b 89 MET cc_start: 0.8701 (tmm) cc_final: 0.7619 (ppp) REVERT: b 100 LEU cc_start: 0.8581 (tp) cc_final: 0.8163 (pp) REVERT: c 25 ASN cc_start: 0.9371 (m110) cc_final: 0.9100 (m110) REVERT: e 105 MET cc_start: 0.8848 (mpp) cc_final: 0.8453 (mpp) REVERT: g 83 ASP cc_start: 0.8895 (t70) cc_final: 0.8628 (t70) REVERT: h 175 MET cc_start: 0.8858 (ppp) cc_final: 0.8656 (ppp) REVERT: i 89 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8324 (tmm) REVERT: i 128 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8973 (tp30) REVERT: k 105 MET cc_start: 0.9008 (mmt) cc_final: 0.8481 (mmm) REVERT: p 78 HIS cc_start: 0.9306 (m90) cc_final: 0.9099 (m90) outliers start: 190 outliers final: 116 residues processed: 897 average time/residue: 0.6480 time to fit residues: 1023.3143 Evaluate side-chains 838 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 706 time to evaluate : 7.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 274 TYR Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 274 TYR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 300 PHE Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 246 VAL Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 335 PHE Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 286 THR Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 372 THR Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 193 GLN Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 256 HIS Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 27 LEU Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 86 ASN Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 96 LEU Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain j residue 53 ASN Chi-restraints excluded: chain j residue 100 LEU Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain l residue 34 TYR Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain l residue 128 GLU Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 170 THR Chi-restraints excluded: chain o residue 188 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 136 LYS Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 181 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 340 optimal weight: 0.9980 chunk 903 optimal weight: 30.0000 chunk 425 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 700 optimal weight: 4.9990 chunk 384 optimal weight: 0.5980 chunk 694 optimal weight: 10.0000 chunk 510 optimal weight: 9.9990 chunk 499 optimal weight: 10.0000 chunk 329 optimal weight: 2.9990 chunk 442 optimal weight: 0.9980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 199 HIS F 135 ASN ** F 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 HIS ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 188 GLN ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.083616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.058823 restraints weight = 418254.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.059187 restraints weight = 200172.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.060050 restraints weight = 128389.191| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 75019 Z= 0.181 Angle : 0.665 15.410 101200 Z= 0.333 Chirality : 0.043 0.277 11418 Planarity : 0.004 0.058 13205 Dihedral : 7.464 84.849 10718 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.32 % Allowed : 16.83 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.09), residues: 9262 helix: 0.92 (0.07), residues: 5203 sheet: -0.06 (0.16), residues: 1056 loop : -0.52 (0.11), residues: 3003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.001 TRP p 60 HIS 0.008 0.001 HIS G 239 PHE 0.034 0.001 PHE C 412 TYR 0.025 0.001 TYR J 274 ARG 0.008 0.000 ARG f 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 751 time to evaluate : 6.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8886 (pp30) REVERT: A 205 MET cc_start: 0.7135 (tpp) cc_final: 0.6808 (mmm) REVERT: A 341 MET cc_start: 0.8850 (tmm) cc_final: 0.8417 (tmm) REVERT: A 380 MET cc_start: 0.9051 (ppp) cc_final: 0.8765 (ppp) REVERT: A 417 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8590 (mtmm) REVERT: B 80 TYR cc_start: 0.7703 (t80) cc_final: 0.7339 (t80) REVERT: B 348 LYS cc_start: 0.8331 (pptt) cc_final: 0.7845 (ptmm) REVERT: C 1 MET cc_start: 0.8684 (tpp) cc_final: 0.8437 (tpp) REVERT: C 164 LEU cc_start: 0.9533 (mm) cc_final: 0.9310 (mm) REVERT: C 177 VAL cc_start: 0.8993 (t) cc_final: 0.8714 (t) REVERT: C 329 GLU cc_start: 0.8809 (mp0) cc_final: 0.8376 (mp0) REVERT: D 92 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6937 (mtm-85) REVERT: D 147 MET cc_start: 0.8938 (mmm) cc_final: 0.8729 (mmm) REVERT: D 186 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7936 (ptp) REVERT: D 341 MET cc_start: 0.9153 (tmm) cc_final: 0.8771 (tmm) REVERT: D 415 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8961 (tmm) REVERT: E 193 GLN cc_start: 0.9122 (OUTLIER) cc_final: 0.8673 (pm20) REVERT: E 244 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8271 (mm-30) REVERT: E 327 MET cc_start: 0.8930 (ppp) cc_final: 0.7963 (ppp) REVERT: E 397 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.8435 (mt-10) REVERT: F 244 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8469 (pm20) REVERT: F 245 MET cc_start: 0.9331 (mmt) cc_final: 0.8759 (mmm) REVERT: F 265 ASP cc_start: 0.8356 (t70) cc_final: 0.8070 (t0) REVERT: F 313 LEU cc_start: 0.9186 (tp) cc_final: 0.8967 (tt) REVERT: F 380 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9012 (pmm) REVERT: G 1 MET cc_start: 0.8788 (ppp) cc_final: 0.8229 (ppp) REVERT: G 21 MET cc_start: 0.2504 (tpt) cc_final: 0.1638 (tpt) REVERT: G 29 MET cc_start: 0.5411 (pmm) cc_final: 0.4671 (pmm) REVERT: G 139 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.8980 (mm) REVERT: G 245 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8292 (mmt) REVERT: G 399 LEU cc_start: 0.9712 (tt) cc_final: 0.9473 (pp) REVERT: G 416 MET cc_start: 0.9440 (mmm) cc_final: 0.9203 (mmm) REVERT: J 21 MET cc_start: 0.7335 (ppp) cc_final: 0.6435 (ppp) REVERT: J 73 LEU cc_start: 0.8353 (tp) cc_final: 0.7854 (mt) REVERT: J 204 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5992 (mm) REVERT: J 219 MET cc_start: 0.9138 (mmt) cc_final: 0.8937 (mmm) REVERT: J 234 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8142 (pm20) REVERT: J 344 HIS cc_start: 0.8610 (m90) cc_final: 0.8120 (m-70) REVERT: J 396 MET cc_start: 0.9115 (mmm) cc_final: 0.8805 (mmm) REVERT: K 21 MET cc_start: 0.8020 (ptp) cc_final: 0.7696 (tpt) REVERT: K 189 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.7898 (mm-40) REVERT: K 193 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.8154 (pm20) REVERT: K 267 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9261 (mp) REVERT: K 380 MET cc_start: 0.9309 (mtm) cc_final: 0.9058 (mtm) REVERT: L 189 GLN cc_start: 0.9113 (OUTLIER) cc_final: 0.8881 (pm20) REVERT: L 205 MET cc_start: 0.8320 (mtp) cc_final: 0.8101 (mtp) REVERT: L 220 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: L 334 GLU cc_start: 0.8520 (tm-30) cc_final: 0.8198 (tm-30) REVERT: L 335 PHE cc_start: 0.9176 (OUTLIER) cc_final: 0.8747 (m-10) REVERT: L 362 ARG cc_start: 0.8982 (mtp-110) cc_final: 0.8647 (ttm110) REVERT: L 405 MET cc_start: 0.8126 (ppp) cc_final: 0.7471 (ppp) REVERT: M 327 MET cc_start: 0.8730 (ppp) cc_final: 0.8516 (ptm) REVERT: N 1 MET cc_start: 0.7910 (tmm) cc_final: 0.7566 (tmm) REVERT: N 21 MET cc_start: 0.8083 (tmm) cc_final: 0.7490 (tmm) REVERT: N 47 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6526 (pm20) REVERT: N 126 ASN cc_start: 0.9164 (t0) cc_final: 0.8774 (t0) REVERT: N 241 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7594 (pm20) REVERT: N 244 GLU cc_start: 0.8740 (pp20) cc_final: 0.8381 (pp20) REVERT: O 219 MET cc_start: 0.9321 (mmp) cc_final: 0.9013 (mmt) REVERT: O 380 MET cc_start: 0.9531 (mtm) cc_final: 0.9200 (mtt) REVERT: P 327 MET cc_start: 0.7847 (tpp) cc_final: 0.6128 (ptm) REVERT: P 396 MET cc_start: 0.8269 (ppp) cc_final: 0.7881 (ppp) REVERT: Y 245 MET cc_start: 0.4104 (tpt) cc_final: 0.3507 (mmm) REVERT: Y 313 LEU cc_start: 0.4891 (OUTLIER) cc_final: 0.4048 (mp) REVERT: Y 414 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8614 (pp20) REVERT: Y 415 MET cc_start: 0.7943 (ppp) cc_final: 0.7607 (ppp) REVERT: Y 418 ARG cc_start: 0.8482 (mmp80) cc_final: 0.8251 (mmp80) REVERT: a 59 LYS cc_start: 0.9532 (ptpp) cc_final: 0.9215 (pttm) REVERT: a 89 MET cc_start: 0.7337 (tmm) cc_final: 0.7109 (tmm) REVERT: a 175 MET cc_start: 0.9455 (mmp) cc_final: 0.9250 (mmp) REVERT: c 25 ASN cc_start: 0.9363 (m110) cc_final: 0.9087 (m110) REVERT: d 59 LYS cc_start: 0.9126 (mtmt) cc_final: 0.8922 (mttp) REVERT: g 83 ASP cc_start: 0.8884 (t70) cc_final: 0.8604 (t0) REVERT: i 89 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8353 (tmm) REVERT: i 128 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8979 (tp30) REVERT: k 105 MET cc_start: 0.9017 (mmt) cc_final: 0.8462 (mmm) outliers start: 183 outliers final: 103 residues processed: 881 average time/residue: 0.6309 time to fit residues: 980.2352 Evaluate side-chains 834 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 708 time to evaluate : 6.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 342 GLU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain J residue 204 LEU Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 335 PHE Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 286 THR Chi-restraints excluded: chain N residue 320 LEU Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 376 GLU Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 332 TYR Chi-restraints excluded: chain P residue 380 MET Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 193 GLN Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 256 HIS Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain g residue 96 LEU Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain j residue 100 LEU Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain l residue 34 TYR Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain l residue 128 GLU Chi-restraints excluded: chain o residue 78 HIS Chi-restraints excluded: chain o residue 188 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 153 ILE Chi-restraints excluded: chain p residue 164 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 557 optimal weight: 0.9990 chunk 2 optimal weight: 40.0000 chunk 544 optimal weight: 40.0000 chunk 68 optimal weight: 2.9990 chunk 261 optimal weight: 8.9990 chunk 703 optimal weight: 7.9990 chunk 740 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 837 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 437 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN A 344 HIS ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 GLN ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 32 GLN ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 90 GLN ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.083180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.058448 restraints weight = 417065.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.058800 restraints weight = 207175.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.059654 restraints weight = 131167.590| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 75019 Z= 0.197 Angle : 0.685 15.390 101200 Z= 0.342 Chirality : 0.043 0.300 11418 Planarity : 0.004 0.056 13205 Dihedral : 7.416 85.174 10718 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.40 % Allowed : 17.54 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.09), residues: 9262 helix: 0.95 (0.07), residues: 5195 sheet: -0.06 (0.16), residues: 1047 loop : -0.49 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.001 TRP p 60 HIS 0.020 0.001 HIS J 295 PHE 0.037 0.001 PHE C 412 TYR 0.020 0.001 TYR d 107 ARG 0.007 0.000 ARG l 36 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 739 time to evaluate : 7.056 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7202 (tpp) cc_final: 0.6857 (mmm) REVERT: A 341 MET cc_start: 0.8846 (tmm) cc_final: 0.8430 (tmm) REVERT: A 380 MET cc_start: 0.9052 (ppp) cc_final: 0.8765 (ppp) REVERT: B 80 TYR cc_start: 0.7767 (t80) cc_final: 0.7402 (t80) REVERT: B 326 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9315 (mmmm) REVERT: B 348 LYS cc_start: 0.8381 (pptt) cc_final: 0.7949 (ptmm) REVERT: C 1 MET cc_start: 0.8665 (tpp) cc_final: 0.8424 (tpp) REVERT: C 164 LEU cc_start: 0.9546 (mm) cc_final: 0.9333 (mm) REVERT: C 177 VAL cc_start: 0.9011 (t) cc_final: 0.8769 (t) REVERT: C 329 GLU cc_start: 0.8755 (mp0) cc_final: 0.8340 (mp0) REVERT: C 396 MET cc_start: 0.8886 (tmm) cc_final: 0.8641 (tmm) REVERT: D 21 MET cc_start: 0.8643 (ttm) cc_final: 0.8347 (ttt) REVERT: D 92 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.6916 (mtm-85) REVERT: D 147 MET cc_start: 0.8951 (mmm) cc_final: 0.8713 (mmm) REVERT: D 186 MET cc_start: 0.8405 (ptp) cc_final: 0.7956 (ptp) REVERT: D 341 MET cc_start: 0.9129 (tmm) cc_final: 0.8730 (tmm) REVERT: D 415 MET cc_start: 0.9225 (OUTLIER) cc_final: 0.8952 (tmm) REVERT: E 193 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.8663 (pm20) REVERT: E 244 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8234 (mm-30) REVERT: E 327 MET cc_start: 0.8922 (ppp) cc_final: 0.8014 (ppp) REVERT: E 416 MET cc_start: 0.8562 (tpp) cc_final: 0.8030 (tpp) REVERT: F 245 MET cc_start: 0.9301 (mmt) cc_final: 0.8881 (mmm) REVERT: F 265 ASP cc_start: 0.8363 (t70) cc_final: 0.8083 (t0) REVERT: F 380 MET cc_start: 0.9283 (OUTLIER) cc_final: 0.9013 (pmm) REVERT: G 1 MET cc_start: 0.8819 (ppp) cc_final: 0.8270 (ppp) REVERT: G 21 MET cc_start: 0.2212 (tpt) cc_final: 0.1302 (tpt) REVERT: G 29 MET cc_start: 0.5462 (pmm) cc_final: 0.4651 (pmm) REVERT: G 139 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8984 (mm) REVERT: G 245 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8230 (mmt) REVERT: G 399 LEU cc_start: 0.9686 (tt) cc_final: 0.9462 (pp) REVERT: G 415 MET cc_start: 0.8970 (ppp) cc_final: 0.8472 (ppp) REVERT: G 416 MET cc_start: 0.9514 (mmm) cc_final: 0.9307 (mmm) REVERT: J 21 MET cc_start: 0.7381 (ppp) cc_final: 0.6471 (ppp) REVERT: J 73 LEU cc_start: 0.8495 (tp) cc_final: 0.8187 (mt) REVERT: J 234 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8165 (pm20) REVERT: J 344 HIS cc_start: 0.8576 (m90) cc_final: 0.8105 (m-70) REVERT: J 396 MET cc_start: 0.9107 (mmm) cc_final: 0.8828 (mmm) REVERT: K 21 MET cc_start: 0.8026 (ptp) cc_final: 0.7766 (tpt) REVERT: K 136 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7968 (mt) REVERT: K 189 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8411 (mm-40) REVERT: K 244 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8146 (mm-30) REVERT: K 267 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9263 (mp) REVERT: K 283 LYS cc_start: 0.8148 (tttt) cc_final: 0.7901 (tptp) REVERT: L 189 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8863 (pm20) REVERT: L 205 MET cc_start: 0.8326 (mtp) cc_final: 0.8119 (mtp) REVERT: L 220 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8193 (mp10) REVERT: L 334 GLU cc_start: 0.8476 (tm-30) cc_final: 0.8150 (tm-30) REVERT: L 335 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8717 (m-10) REVERT: L 362 ARG cc_start: 0.8981 (mtp-110) cc_final: 0.8647 (ttm110) REVERT: L 405 MET cc_start: 0.8207 (ppp) cc_final: 0.7435 (ppp) REVERT: M 244 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7988 (mm-30) REVERT: N 1 MET cc_start: 0.7880 (tmm) cc_final: 0.7587 (tmm) REVERT: N 21 MET cc_start: 0.8073 (tmm) cc_final: 0.7464 (tmm) REVERT: N 47 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6554 (pm20) REVERT: N 126 ASN cc_start: 0.9138 (t0) cc_final: 0.8761 (t0) REVERT: N 241 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7571 (pm20) REVERT: N 244 GLU cc_start: 0.8757 (pp20) cc_final: 0.8392 (pp20) REVERT: O 219 MET cc_start: 0.9299 (mmp) cc_final: 0.8972 (mmt) REVERT: O 376 GLU cc_start: 0.9071 (OUTLIER) cc_final: 0.8715 (pt0) REVERT: O 380 MET cc_start: 0.9512 (mtm) cc_final: 0.9157 (mtt) REVERT: P 147 MET cc_start: 0.5915 (tpt) cc_final: 0.5395 (tpt) REVERT: P 245 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8565 (mpp) REVERT: P 327 MET cc_start: 0.7730 (tpp) cc_final: 0.5979 (ptm) REVERT: P 396 MET cc_start: 0.8364 (ppp) cc_final: 0.7936 (ppp) REVERT: Y 245 MET cc_start: 0.3001 (tpt) cc_final: 0.2342 (mmm) REVERT: Y 313 LEU cc_start: 0.5293 (OUTLIER) cc_final: 0.4338 (mp) REVERT: Y 414 GLU cc_start: 0.8971 (OUTLIER) cc_final: 0.8531 (pp20) REVERT: Y 415 MET cc_start: 0.8133 (ppp) cc_final: 0.7485 (ppp) REVERT: Y 418 ARG cc_start: 0.8512 (mmp80) cc_final: 0.8265 (mmp80) REVERT: a 59 LYS cc_start: 0.9506 (ptpp) cc_final: 0.9208 (pttm) REVERT: b 100 LEU cc_start: 0.8534 (tp) cc_final: 0.8185 (pp) REVERT: c 25 ASN cc_start: 0.9346 (m110) cc_final: 0.9079 (m110) REVERT: d 59 LYS cc_start: 0.9123 (mtmt) cc_final: 0.8917 (mttp) REVERT: e 104 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8478 (mp) REVERT: g 83 ASP cc_start: 0.8857 (t70) cc_final: 0.8588 (t70) REVERT: i 89 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.8357 (tmm) REVERT: i 128 GLU cc_start: 0.9188 (tm-30) cc_final: 0.8951 (tp30) REVERT: k 105 MET cc_start: 0.9014 (mmt) cc_final: 0.8478 (mmm) REVERT: p 180 LYS cc_start: 0.6776 (mmtt) cc_final: 0.6561 (mmmt) outliers start: 189 outliers final: 125 residues processed: 873 average time/residue: 0.6372 time to fit residues: 984.6537 Evaluate side-chains 856 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 710 time to evaluate : 6.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 378 GLN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 378 GLN Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 220 GLN Chi-restraints excluded: chain G residue 245 MET Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 300 PHE Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 294 LEU Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 267 ILE Chi-restraints excluded: chain K residue 318 THR Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 335 PHE Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 284 VAL Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 264 LEU Chi-restraints excluded: chain N residue 286 THR Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 205 MET Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 372 THR Chi-restraints excluded: chain O residue 376 GLU Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 175 LEU Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain P residue 332 TYR Chi-restraints excluded: chain P residue 380 MET Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 193 GLN Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 256 HIS Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain g residue 81 ILE Chi-restraints excluded: chain g residue 96 LEU Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain j residue 100 LEU Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain l residue 34 TYR Chi-restraints excluded: chain l residue 78 HIS Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain l residue 128 GLU Chi-restraints excluded: chain o residue 11 ASP Chi-restraints excluded: chain o residue 188 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 153 ILE Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 181 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 393 optimal weight: 7.9990 chunk 770 optimal weight: 7.9990 chunk 373 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 chunk 363 optimal weight: 9.9990 chunk 27 optimal weight: 9.9990 chunk 376 optimal weight: 7.9990 chunk 453 optimal weight: 9.9990 chunk 184 optimal weight: 0.9980 chunk 549 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 190 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 190 ASN ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 ASN ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 135 ASN ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 374 GLN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 239 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 140 HIS ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 7 GLN ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN k 145 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.080514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.055653 restraints weight = 402665.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.056594 restraints weight = 216591.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056765 restraints weight = 127831.151| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 75019 Z= 0.313 Angle : 0.741 15.443 101200 Z= 0.377 Chirality : 0.044 0.315 11418 Planarity : 0.005 0.056 13205 Dihedral : 7.538 82.045 10718 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.46 % Allowed : 18.13 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.09), residues: 9262 helix: 0.87 (0.07), residues: 5165 sheet: -0.21 (0.16), residues: 1088 loop : -0.42 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.132 0.002 TRP p 60 HIS 0.012 0.001 HIS e 73 PHE 0.030 0.002 PHE C 412 TYR 0.027 0.002 TYR C 332 ARG 0.007 0.001 ARG j 127 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 715 time to evaluate : 6.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7113 (tpp) cc_final: 0.6825 (mmm) REVERT: A 341 MET cc_start: 0.8962 (tmm) cc_final: 0.8584 (tmm) REVERT: B 298 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8393 (mtpt) REVERT: C 1 MET cc_start: 0.8759 (tpp) cc_final: 0.8502 (tpp) REVERT: C 177 VAL cc_start: 0.9173 (t) cc_final: 0.8946 (t) REVERT: C 329 GLU cc_start: 0.8716 (mp0) cc_final: 0.8364 (mp0) REVERT: C 342 GLU cc_start: 0.8298 (mp0) cc_final: 0.8024 (mp0) REVERT: D 92 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6593 (mtm180) REVERT: D 147 MET cc_start: 0.9005 (mmm) cc_final: 0.8591 (mmm) REVERT: D 327 MET cc_start: 0.8802 (ppp) cc_final: 0.7970 (ppp) REVERT: D 341 MET cc_start: 0.9126 (tmm) cc_final: 0.8684 (tmm) REVERT: D 358 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9000 (mp) REVERT: E 29 MET cc_start: 0.7187 (pmm) cc_final: 0.6896 (pmm) REVERT: E 193 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8697 (pm20) REVERT: E 234 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: E 327 MET cc_start: 0.8948 (ppp) cc_final: 0.8121 (ppp) REVERT: E 397 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8490 (mt-10) REVERT: F 58 LEU cc_start: 0.9460 (OUTLIER) cc_final: 0.9149 (mt) REVERT: F 265 ASP cc_start: 0.8410 (t70) cc_final: 0.8109 (t0) REVERT: F 380 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.9073 (pmm) REVERT: G 1 MET cc_start: 0.8830 (ppp) cc_final: 0.8268 (ppp) REVERT: G 21 MET cc_start: 0.2064 (tpt) cc_final: 0.1090 (tpt) REVERT: G 29 MET cc_start: 0.5159 (pmm) cc_final: 0.4220 (pmm) REVERT: G 139 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8899 (mm) REVERT: G 415 MET cc_start: 0.8929 (ppp) cc_final: 0.8457 (ppp) REVERT: G 416 MET cc_start: 0.9533 (mmm) cc_final: 0.9332 (mmm) REVERT: J 21 MET cc_start: 0.7572 (ppp) cc_final: 0.6747 (ppp) REVERT: J 73 LEU cc_start: 0.8611 (tp) cc_final: 0.8314 (mt) REVERT: J 205 MET cc_start: 0.7776 (ppp) cc_final: 0.6568 (ppp) REVERT: J 234 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8225 (pm20) REVERT: J 396 MET cc_start: 0.9153 (mmm) cc_final: 0.8818 (mmm) REVERT: K 1 MET cc_start: 0.8778 (pmm) cc_final: 0.8356 (pmm) REVERT: K 189 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8089 (mm-40) REVERT: K 193 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.8128 (pm20) REVERT: K 283 LYS cc_start: 0.8330 (tttt) cc_final: 0.8118 (tptp) REVERT: L 189 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.8915 (pm20) REVERT: L 220 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.8265 (mp10) REVERT: L 334 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8248 (tm-30) REVERT: L 335 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8664 (m-10) REVERT: L 362 ARG cc_start: 0.9018 (mtp-110) cc_final: 0.8367 (ttm110) REVERT: M 219 MET cc_start: 0.8928 (mmp) cc_final: 0.8508 (mmp) REVERT: N 21 MET cc_start: 0.8233 (tmm) cc_final: 0.7691 (tmm) REVERT: N 47 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6518 (pm20) REVERT: N 126 ASN cc_start: 0.9187 (t0) cc_final: 0.8860 (t0) REVERT: N 241 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7617 (pm20) REVERT: N 244 GLU cc_start: 0.8944 (pp20) cc_final: 0.8580 (pp20) REVERT: O 1 MET cc_start: 0.8184 (tpt) cc_final: 0.7177 (ppp) REVERT: O 219 MET cc_start: 0.9321 (mmp) cc_final: 0.9106 (mmp) REVERT: O 380 MET cc_start: 0.9613 (mtm) cc_final: 0.9206 (mtt) REVERT: P 245 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8414 (mpp) REVERT: P 327 MET cc_start: 0.7760 (tpp) cc_final: 0.5998 (ptm) REVERT: P 396 MET cc_start: 0.8351 (ppp) cc_final: 0.7985 (ppp) REVERT: P 405 MET cc_start: 0.8597 (pmm) cc_final: 0.8193 (pmm) REVERT: Y 245 MET cc_start: 0.2377 (tpt) cc_final: 0.1908 (mmm) REVERT: Y 313 LEU cc_start: 0.6008 (OUTLIER) cc_final: 0.4940 (mp) REVERT: Y 414 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8414 (pp20) REVERT: Y 415 MET cc_start: 0.8174 (ppp) cc_final: 0.7359 (ppp) REVERT: Y 418 ARG cc_start: 0.8616 (mmp80) cc_final: 0.8347 (mmp80) REVERT: a 59 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9210 (pttm) REVERT: a 87 ASP cc_start: 0.9125 (m-30) cc_final: 0.8873 (p0) REVERT: a 100 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8339 (mm) REVERT: b 100 LEU cc_start: 0.8670 (tp) cc_final: 0.8314 (pp) REVERT: d 175 MET cc_start: 0.9165 (tmm) cc_final: 0.8945 (ppp) REVERT: e 104 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8496 (mm) REVERT: g 83 ASP cc_start: 0.8806 (t70) cc_final: 0.8547 (t70) REVERT: i 89 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8422 (tmm) REVERT: i 128 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8897 (tp30) REVERT: j 175 MET cc_start: 0.8888 (ppp) cc_final: 0.8626 (ppp) REVERT: k 105 MET cc_start: 0.9092 (mmt) cc_final: 0.8516 (mmm) REVERT: l 175 MET cc_start: 0.9313 (ppp) cc_final: 0.9104 (ppp) REVERT: o 20 TRP cc_start: 0.4905 (t60) cc_final: 0.4536 (t60) outliers start: 194 outliers final: 128 residues processed: 853 average time/residue: 0.6347 time to fit residues: 957.7064 Evaluate side-chains 830 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 679 time to evaluate : 6.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 298 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 358 ILE Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 219 MET Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 351 GLU Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain J residue 374 GLN Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 274 TYR Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 320 LEU Chi-restraints excluded: chain L residue 335 PHE Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 262 ILE Chi-restraints excluded: chain N residue 286 THR Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 372 THR Chi-restraints excluded: chain O residue 376 GLU Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain P residue 332 TYR Chi-restraints excluded: chain P residue 380 MET Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 256 HIS Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain a residue 100 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 170 THR Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 81 ILE Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain j residue 53 ASN Chi-restraints excluded: chain j residue 100 LEU Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain l residue 34 TYR Chi-restraints excluded: chain l residue 78 HIS Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain l residue 128 GLU Chi-restraints excluded: chain o residue 170 THR Chi-restraints excluded: chain o residue 188 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 86 ASN Chi-restraints excluded: chain p residue 153 ILE Chi-restraints excluded: chain p residue 164 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 811 optimal weight: 4.9990 chunk 524 optimal weight: 0.1980 chunk 569 optimal weight: 5.9990 chunk 255 optimal weight: 50.0000 chunk 601 optimal weight: 4.9990 chunk 575 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 768 optimal weight: 5.9990 chunk 706 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 189 GLN ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 189 GLN ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 HIS J 374 GLN ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 173 GLN ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 174 ASN ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 174 ASN f 7 GLN ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.080580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055558 restraints weight = 399974.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 74)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.055993 restraints weight = 199919.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.056398 restraints weight = 126511.288| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 75019 Z= 0.268 Angle : 0.743 15.586 101200 Z= 0.375 Chirality : 0.045 0.294 11418 Planarity : 0.004 0.057 13205 Dihedral : 7.527 88.034 10718 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.24 % Allowed : 18.81 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.09), residues: 9262 helix: 0.83 (0.07), residues: 5179 sheet: -0.25 (0.16), residues: 1085 loop : -0.40 (0.12), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.112 0.002 TRP p 60 HIS 0.009 0.001 HIS e 73 PHE 0.035 0.001 PHE C 412 TYR 0.028 0.002 TYR o 69 ARG 0.009 0.000 ARG G 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 717 time to evaluate : 6.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7069 (tpp) cc_final: 0.6800 (mmm) REVERT: A 341 MET cc_start: 0.8976 (tmm) cc_final: 0.8628 (tmm) REVERT: A 380 MET cc_start: 0.9001 (ppp) cc_final: 0.8739 (ppp) REVERT: B 80 TYR cc_start: 0.7955 (t80) cc_final: 0.7614 (t80) REVERT: B 147 MET cc_start: 0.8632 (mmm) cc_final: 0.8402 (mmm) REVERT: C 1 MET cc_start: 0.8744 (tpp) cc_final: 0.8486 (tpp) REVERT: C 329 GLU cc_start: 0.8768 (mp0) cc_final: 0.8437 (mp0) REVERT: C 342 GLU cc_start: 0.8266 (mp0) cc_final: 0.7971 (mp0) REVERT: C 396 MET cc_start: 0.9025 (tmm) cc_final: 0.8722 (tmm) REVERT: D 91 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9073 (pp) REVERT: D 92 ARG cc_start: 0.7386 (OUTLIER) cc_final: 0.6656 (mtm180) REVERT: D 147 MET cc_start: 0.9025 (mmm) cc_final: 0.8640 (mmm) REVERT: D 327 MET cc_start: 0.8859 (ppp) cc_final: 0.7790 (ppp) REVERT: D 328 ASP cc_start: 0.8678 (m-30) cc_final: 0.8103 (m-30) REVERT: D 341 MET cc_start: 0.9057 (tmm) cc_final: 0.8660 (tmm) REVERT: D 358 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9126 (mp) REVERT: D 415 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8949 (tmm) REVERT: E 193 GLN cc_start: 0.9115 (OUTLIER) cc_final: 0.8637 (pm20) REVERT: E 327 MET cc_start: 0.9019 (ppp) cc_final: 0.8179 (ppp) REVERT: E 397 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8483 (mt-10) REVERT: F 21 MET cc_start: 0.8449 (ppp) cc_final: 0.8247 (ppp) REVERT: F 58 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9174 (mt) REVERT: F 244 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8443 (pm20) REVERT: F 265 ASP cc_start: 0.8378 (t70) cc_final: 0.8107 (t0) REVERT: F 274 TYR cc_start: 0.9635 (OUTLIER) cc_final: 0.9422 (m-10) REVERT: F 380 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.9054 (pmm) REVERT: G 1 MET cc_start: 0.8911 (ppp) cc_final: 0.8354 (ppp) REVERT: G 21 MET cc_start: 0.2854 (tpt) cc_final: 0.1952 (tpt) REVERT: G 29 MET cc_start: 0.5139 (pmm) cc_final: 0.4311 (pmm) REVERT: G 139 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8936 (mm) REVERT: G 415 MET cc_start: 0.8973 (ppp) cc_final: 0.8507 (ppp) REVERT: H 197 TYR cc_start: 0.9007 (m-80) cc_final: 0.8781 (m-80) REVERT: J 21 MET cc_start: 0.7410 (ppp) cc_final: 0.6570 (ppp) REVERT: J 73 LEU cc_start: 0.8790 (tp) cc_final: 0.8436 (mt) REVERT: J 205 MET cc_start: 0.7895 (ppp) cc_final: 0.6876 (ppp) REVERT: J 234 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8181 (pm20) REVERT: J 396 MET cc_start: 0.9184 (mmm) cc_final: 0.8836 (mmm) REVERT: K 1 MET cc_start: 0.8751 (pmm) cc_final: 0.8305 (pmm) REVERT: K 189 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8122 (mm-40) REVERT: K 193 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8110 (pm20) REVERT: K 228 VAL cc_start: 0.9222 (t) cc_final: 0.8937 (p) REVERT: K 244 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8214 (mm-30) REVERT: K 352 LYS cc_start: 0.9006 (mmmt) cc_final: 0.8339 (ttpt) REVERT: L 186 MET cc_start: 0.8444 (ptp) cc_final: 0.7953 (ptt) REVERT: L 189 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.8934 (pm20) REVERT: L 220 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: L 334 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8261 (tm-30) REVERT: L 335 PHE cc_start: 0.9210 (OUTLIER) cc_final: 0.8711 (m-10) REVERT: L 362 ARG cc_start: 0.9024 (mtp-110) cc_final: 0.8354 (ttm110) REVERT: L 396 MET cc_start: 0.9364 (tpp) cc_final: 0.9082 (tpp) REVERT: N 1 MET cc_start: 0.7717 (tmm) cc_final: 0.7320 (tmm) REVERT: N 21 MET cc_start: 0.8133 (tmm) cc_final: 0.7636 (tmm) REVERT: N 47 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: N 126 ASN cc_start: 0.9167 (t0) cc_final: 0.8835 (t0) REVERT: N 219 MET cc_start: 0.9435 (mmt) cc_final: 0.9161 (mmt) REVERT: N 241 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7865 (pm20) REVERT: N 244 GLU cc_start: 0.8928 (pp20) cc_final: 0.8704 (pp20) REVERT: O 1 MET cc_start: 0.8183 (tpt) cc_final: 0.7078 (ppp) REVERT: O 219 MET cc_start: 0.9290 (mmp) cc_final: 0.9047 (mmp) REVERT: O 380 MET cc_start: 0.9527 (mtm) cc_final: 0.8967 (mtm) REVERT: P 245 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8498 (mpp) REVERT: P 396 MET cc_start: 0.8293 (ppp) cc_final: 0.8004 (ppp) REVERT: P 405 MET cc_start: 0.8604 (pmm) cc_final: 0.8230 (pmm) REVERT: Y 245 MET cc_start: 0.3150 (tpt) cc_final: 0.2704 (mmm) REVERT: Y 313 LEU cc_start: 0.5372 (OUTLIER) cc_final: 0.4425 (mp) REVERT: Y 414 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8653 (pp20) REVERT: Y 415 MET cc_start: 0.8106 (ppp) cc_final: 0.7631 (ppp) REVERT: a 59 LYS cc_start: 0.9480 (ptpp) cc_final: 0.9212 (pttm) REVERT: a 87 ASP cc_start: 0.9113 (m-30) cc_final: 0.8865 (p0) REVERT: b 100 LEU cc_start: 0.8526 (tp) cc_final: 0.8184 (pp) REVERT: e 104 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8559 (mm) REVERT: g 83 ASP cc_start: 0.8776 (t70) cc_final: 0.8532 (t70) REVERT: i 89 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8396 (tmm) REVERT: i 128 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8927 (tp30) REVERT: j 175 MET cc_start: 0.8891 (ppp) cc_final: 0.8615 (ppp) REVERT: k 105 MET cc_start: 0.8945 (mmt) cc_final: 0.8430 (mmm) REVERT: l 175 MET cc_start: 0.9149 (ppp) cc_final: 0.8915 (ppp) REVERT: o 81 ILE cc_start: 0.5337 (mm) cc_final: 0.5122 (mm) outliers start: 177 outliers final: 127 residues processed: 853 average time/residue: 0.6407 time to fit residues: 959.6630 Evaluate side-chains 827 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 676 time to evaluate : 6.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 50 PHE Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 320 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 274 TYR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain J residue 234 GLU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 335 PHE Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 260 VAL Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 47 GLU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 262 ILE Chi-restraints excluded: chain N residue 286 THR Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 372 THR Chi-restraints excluded: chain O residue 376 GLU Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain P residue 332 TYR Chi-restraints excluded: chain P residue 380 MET Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 256 HIS Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain d residue 94 THR Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 81 ILE Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain i residue 159 VAL Chi-restraints excluded: chain j residue 53 ASN Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 100 LEU Chi-restraints excluded: chain j residue 170 THR Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain k residue 145 GLN Chi-restraints excluded: chain l residue 34 TYR Chi-restraints excluded: chain l residue 78 HIS Chi-restraints excluded: chain l residue 111 THR Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain l residue 128 GLU Chi-restraints excluded: chain o residue 188 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 86 ASN Chi-restraints excluded: chain p residue 153 ILE Chi-restraints excluded: chain p residue 164 ASP Chi-restraints excluded: chain p residue 181 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 575 optimal weight: 10.0000 chunk 349 optimal weight: 0.9980 chunk 493 optimal weight: 4.9990 chunk 583 optimal weight: 50.0000 chunk 108 optimal weight: 0.9990 chunk 842 optimal weight: 6.9990 chunk 864 optimal weight: 4.9990 chunk 704 optimal weight: 2.9990 chunk 315 optimal weight: 0.0050 chunk 4 optimal weight: 9.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 HIS ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 HIS ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN ** l 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 174 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.081172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.056286 restraints weight = 404308.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.058102 restraints weight = 201611.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.057977 restraints weight = 110608.942| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 75019 Z= 0.214 Angle : 0.758 15.523 101200 Z= 0.378 Chirality : 0.045 0.316 11418 Planarity : 0.004 0.064 13205 Dihedral : 7.483 89.004 10718 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.02 % Allowed : 19.30 % Favored : 78.68 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.09), residues: 9262 helix: 0.85 (0.07), residues: 5147 sheet: -0.22 (0.16), residues: 1088 loop : -0.40 (0.11), residues: 3027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.170 0.002 TRP p 60 HIS 0.011 0.001 HIS J 295 PHE 0.037 0.001 PHE C 412 TYR 0.048 0.002 TYR J 274 ARG 0.014 0.000 ARG d 36 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18524 Ramachandran restraints generated. 9262 Oldfield, 0 Emsley, 9262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 717 time to evaluate : 6.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 205 MET cc_start: 0.7026 (tpp) cc_final: 0.6781 (mmm) REVERT: A 341 MET cc_start: 0.9029 (tmm) cc_final: 0.8741 (tmm) REVERT: A 380 MET cc_start: 0.9156 (ppp) cc_final: 0.8861 (ppp) REVERT: B 80 TYR cc_start: 0.8064 (t80) cc_final: 0.7699 (t80) REVERT: B 147 MET cc_start: 0.8661 (mmm) cc_final: 0.8444 (mmm) REVERT: B 328 ASP cc_start: 0.9215 (m-30) cc_final: 0.8866 (m-30) REVERT: C 1 MET cc_start: 0.8788 (tpp) cc_final: 0.8520 (tpp) REVERT: C 329 GLU cc_start: 0.8728 (mp0) cc_final: 0.8441 (mp0) REVERT: C 342 GLU cc_start: 0.8227 (mp0) cc_final: 0.7918 (mp0) REVERT: C 396 MET cc_start: 0.9062 (tmm) cc_final: 0.8738 (tmm) REVERT: D 91 LEU cc_start: 0.9553 (OUTLIER) cc_final: 0.9087 (pp) REVERT: D 92 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6583 (mtm180) REVERT: D 147 MET cc_start: 0.9066 (mmm) cc_final: 0.8663 (mmm) REVERT: D 327 MET cc_start: 0.8880 (ppp) cc_final: 0.7961 (ppp) REVERT: D 341 MET cc_start: 0.9096 (tmm) cc_final: 0.8665 (tmm) REVERT: D 358 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9055 (mp) REVERT: D 415 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8952 (tmm) REVERT: E 52 ASP cc_start: 0.8170 (p0) cc_final: 0.7907 (p0) REVERT: E 193 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8653 (pm20) REVERT: E 234 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8236 (pm20) REVERT: E 327 MET cc_start: 0.9077 (ppp) cc_final: 0.8208 (ppp) REVERT: E 397 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8454 (mt-10) REVERT: F 21 MET cc_start: 0.8573 (ppp) cc_final: 0.8328 (ppp) REVERT: F 245 MET cc_start: 0.9363 (mmt) cc_final: 0.8654 (mmm) REVERT: F 265 ASP cc_start: 0.8547 (t70) cc_final: 0.8342 (t0) REVERT: F 274 TYR cc_start: 0.9642 (OUTLIER) cc_final: 0.9371 (m-10) REVERT: F 380 MET cc_start: 0.9384 (OUTLIER) cc_final: 0.9073 (pmm) REVERT: G 1 MET cc_start: 0.8871 (ppp) cc_final: 0.8338 (ppp) REVERT: G 21 MET cc_start: 0.2519 (tpt) cc_final: 0.1565 (tpt) REVERT: G 29 MET cc_start: 0.5240 (pmm) cc_final: 0.4391 (pmm) REVERT: G 139 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8898 (mm) REVERT: G 219 MET cc_start: 0.9583 (mmm) cc_final: 0.9381 (mmm) REVERT: G 415 MET cc_start: 0.9086 (ppp) cc_final: 0.8861 (ppp) REVERT: H 147 MET cc_start: 0.6472 (tmm) cc_final: 0.6210 (tmm) REVERT: H 197 TYR cc_start: 0.9108 (m-80) cc_final: 0.8833 (m-80) REVERT: J 21 MET cc_start: 0.7726 (ppp) cc_final: 0.6928 (ppp) REVERT: J 73 LEU cc_start: 0.8565 (tp) cc_final: 0.8278 (mt) REVERT: J 205 MET cc_start: 0.7614 (ppp) cc_final: 0.6679 (ppp) REVERT: J 396 MET cc_start: 0.9192 (mmm) cc_final: 0.8824 (mmm) REVERT: J 415 MET cc_start: 0.8996 (ptp) cc_final: 0.8784 (pmm) REVERT: K 1 MET cc_start: 0.8823 (pmm) cc_final: 0.8276 (pmm) REVERT: K 189 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8573 (mm-40) REVERT: K 228 VAL cc_start: 0.9208 (t) cc_final: 0.8915 (p) REVERT: K 244 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8246 (mm-30) REVERT: K 352 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8803 (tppt) REVERT: L 186 MET cc_start: 0.8507 (ptp) cc_final: 0.7946 (ptt) REVERT: L 189 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8956 (pm20) REVERT: L 220 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8238 (mp10) REVERT: L 334 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8226 (tm-30) REVERT: L 335 PHE cc_start: 0.9167 (OUTLIER) cc_final: 0.8755 (m-10) REVERT: L 362 ARG cc_start: 0.9053 (mtp-110) cc_final: 0.8379 (ttm110) REVERT: L 396 MET cc_start: 0.9425 (tpp) cc_final: 0.9146 (tpp) REVERT: L 403 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8524 (mm) REVERT: L 405 MET cc_start: 0.8466 (ppp) cc_final: 0.7801 (ppp) REVERT: M 219 MET cc_start: 0.8895 (mmp) cc_final: 0.8502 (mmp) REVERT: M 333 GLU cc_start: 0.8835 (tp30) cc_final: 0.8623 (tp30) REVERT: N 1 MET cc_start: 0.7924 (tmm) cc_final: 0.7545 (tmm) REVERT: N 21 MET cc_start: 0.8289 (tmm) cc_final: 0.7754 (tmm) REVERT: N 126 ASN cc_start: 0.9265 (t0) cc_final: 0.8920 (t0) REVERT: N 219 MET cc_start: 0.9466 (mmt) cc_final: 0.9202 (mmt) REVERT: N 241 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: N 244 GLU cc_start: 0.8888 (pp20) cc_final: 0.8675 (pp20) REVERT: N 348 LYS cc_start: 0.9093 (tptp) cc_final: 0.8589 (mmtm) REVERT: O 1 MET cc_start: 0.8351 (tpt) cc_final: 0.7219 (ppp) REVERT: O 219 MET cc_start: 0.9321 (mmp) cc_final: 0.9034 (mmp) REVERT: O 376 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.9016 (pt0) REVERT: O 380 MET cc_start: 0.9619 (mtm) cc_final: 0.9130 (mtm) REVERT: P 205 MET cc_start: 0.7291 (pmm) cc_final: 0.5641 (ttm) REVERT: P 245 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8464 (mpp) REVERT: P 327 MET cc_start: 0.7853 (tpp) cc_final: 0.6213 (ptt) REVERT: P 396 MET cc_start: 0.8228 (ppp) cc_final: 0.7875 (ppp) REVERT: P 405 MET cc_start: 0.8643 (pmm) cc_final: 0.8244 (pmm) REVERT: Y 245 MET cc_start: 0.2582 (tpt) cc_final: 0.2117 (mmm) REVERT: Y 313 LEU cc_start: 0.5768 (OUTLIER) cc_final: 0.4734 (mp) REVERT: Y 414 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8618 (pp20) REVERT: Y 415 MET cc_start: 0.8136 (ppp) cc_final: 0.7548 (ppp) REVERT: a 59 LYS cc_start: 0.9482 (ptpp) cc_final: 0.9225 (pttm) REVERT: b 100 LEU cc_start: 0.8647 (tp) cc_final: 0.8279 (pp) REVERT: g 83 ASP cc_start: 0.8848 (t70) cc_final: 0.8576 (t70) REVERT: i 89 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8398 (tmm) REVERT: i 128 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8998 (tp30) REVERT: j 175 MET cc_start: 0.9019 (ppp) cc_final: 0.8779 (ppp) REVERT: k 105 MET cc_start: 0.9084 (mmt) cc_final: 0.8453 (mmm) REVERT: o 81 ILE cc_start: 0.5598 (mm) cc_final: 0.5381 (mm) REVERT: p 180 LYS cc_start: 0.6345 (mmtt) cc_final: 0.6037 (mmmt) outliers start: 159 outliers final: 123 residues processed: 836 average time/residue: 0.6579 time to fit residues: 971.5373 Evaluate side-chains 831 residues out of total 7886 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 687 time to evaluate : 6.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 333 GLU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 351 GLU Chi-restraints excluded: chain B residue 394 ASP Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 234 GLU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 338 THR Chi-restraints excluded: chain C residue 354 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 91 LEU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 186 MET Chi-restraints excluded: chain D residue 188 LEU Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 354 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 415 MET Chi-restraints excluded: chain E residue 193 GLN Chi-restraints excluded: chain E residue 234 GLU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 377 LEU Chi-restraints excluded: chain E residue 397 GLU Chi-restraints excluded: chain F residue 20 ASN Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 157 LEU Chi-restraints excluded: chain F residue 244 GLU Chi-restraints excluded: chain F residue 274 TYR Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 372 THR Chi-restraints excluded: chain F residue 380 MET Chi-restraints excluded: chain F residue 397 GLU Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 284 VAL Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 289 VAL Chi-restraints excluded: chain H residue 300 PHE Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 295 HIS Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 175 LEU Chi-restraints excluded: chain K residue 189 GLN Chi-restraints excluded: chain K residue 193 GLN Chi-restraints excluded: chain K residue 206 VAL Chi-restraints excluded: chain K residue 227 VAL Chi-restraints excluded: chain K residue 316 ILE Chi-restraints excluded: chain K residue 346 SER Chi-restraints excluded: chain K residue 354 VAL Chi-restraints excluded: chain L residue 52 ASP Chi-restraints excluded: chain L residue 62 PHE Chi-restraints excluded: chain L residue 116 VAL Chi-restraints excluded: chain L residue 189 GLN Chi-restraints excluded: chain L residue 219 MET Chi-restraints excluded: chain L residue 220 GLN Chi-restraints excluded: chain L residue 227 VAL Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 289 VAL Chi-restraints excluded: chain L residue 335 PHE Chi-restraints excluded: chain L residue 388 HIS Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain M residue 73 LEU Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 175 LEU Chi-restraints excluded: chain M residue 190 ASN Chi-restraints excluded: chain M residue 354 VAL Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain N residue 241 GLN Chi-restraints excluded: chain N residue 245 MET Chi-restraints excluded: chain N residue 286 THR Chi-restraints excluded: chain N residue 330 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 177 VAL Chi-restraints excluded: chain O residue 233 ASP Chi-restraints excluded: chain O residue 295 HIS Chi-restraints excluded: chain O residue 372 THR Chi-restraints excluded: chain O residue 376 GLU Chi-restraints excluded: chain O residue 377 LEU Chi-restraints excluded: chain O residue 388 HIS Chi-restraints excluded: chain P residue 245 MET Chi-restraints excluded: chain P residue 332 TYR Chi-restraints excluded: chain P residue 380 MET Chi-restraints excluded: chain P residue 397 GLU Chi-restraints excluded: chain Y residue 193 GLN Chi-restraints excluded: chain Y residue 247 ILE Chi-restraints excluded: chain Y residue 286 THR Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 414 GLU Chi-restraints excluded: chain a residue 11 ASP Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 96 LEU Chi-restraints excluded: chain a residue 162 VAL Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 78 HIS Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain c residue 45 VAL Chi-restraints excluded: chain d residue 11 ASP Chi-restraints excluded: chain d residue 53 ASN Chi-restraints excluded: chain d residue 78 HIS Chi-restraints excluded: chain e residue 59 LYS Chi-restraints excluded: chain g residue 49 ASP Chi-restraints excluded: chain g residue 81 ILE Chi-restraints excluded: chain g residue 111 THR Chi-restraints excluded: chain g residue 136 LYS Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 51 LEU Chi-restraints excluded: chain i residue 89 MET Chi-restraints excluded: chain i residue 96 LEU Chi-restraints excluded: chain j residue 53 ASN Chi-restraints excluded: chain j residue 81 ILE Chi-restraints excluded: chain j residue 100 LEU Chi-restraints excluded: chain j residue 184 LEU Chi-restraints excluded: chain k residue 78 HIS Chi-restraints excluded: chain k residue 128 GLU Chi-restraints excluded: chain k residue 145 GLN Chi-restraints excluded: chain l residue 34 TYR Chi-restraints excluded: chain l residue 78 HIS Chi-restraints excluded: chain l residue 111 THR Chi-restraints excluded: chain l residue 123 THR Chi-restraints excluded: chain l residue 128 GLU Chi-restraints excluded: chain o residue 188 GLN Chi-restraints excluded: chain p residue 45 VAL Chi-restraints excluded: chain p residue 56 GLU Chi-restraints excluded: chain p residue 86 ASN Chi-restraints excluded: chain p residue 153 ILE Chi-restraints excluded: chain p residue 164 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 908 random chunks: chunk 60 optimal weight: 8.9990 chunk 679 optimal weight: 7.9990 chunk 406 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 774 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 573 optimal weight: 0.0970 chunk 478 optimal weight: 3.9990 chunk 396 optimal weight: 0.7980 chunk 857 optimal weight: 8.9990 chunk 896 optimal weight: 6.9990 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 295 HIS ** K 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 378 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 344 HIS ** N 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 374 GLN ** O 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 174 ASN ** c 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 174 ASN ** j 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 53 ASN ** k 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.081475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.056990 restraints weight = 410460.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.057917 restraints weight = 212106.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.058525 restraints weight = 137286.184| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 75019 Z= 0.202 Angle : 0.760 16.922 101200 Z= 0.377 Chirality : 0.045 0.330 11418 Planarity : 0.004 0.079 13205 Dihedral : 7.399 89.211 10718 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 19.48 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.10 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.09), residues: 9262 helix: 0.86 (0.07), residues: 5152 sheet: -0.15 (0.16), residues: 1058 loop : -0.42 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.186 0.002 TRP p 60 HIS 0.020 0.001 HIS J 295 PHE 0.035 0.001 PHE C 412 TYR 0.040 0.001 TYR J 274 ARG 0.017 0.000 ARG B 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27938.65 seconds wall clock time: 483 minutes 34.61 seconds (29014.61 seconds total)