Starting phenix.real_space_refine on Mon Aug 25 20:43:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6jcw_9799/08_2025/6jcw_9799.cif Found real_map, /net/cci-nas-00/data/ceres_data/6jcw_9799/08_2025/6jcw_9799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6jcw_9799/08_2025/6jcw_9799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6jcw_9799/08_2025/6jcw_9799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6jcw_9799/08_2025/6jcw_9799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6jcw_9799/08_2025/6jcw_9799.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.339 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: 5 Type Number sf(0) Gaussians Mg 24 5.21 5 S 120 5.16 5 C 19889 2.51 5 N 5043 2.21 5 O 5812 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 141 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30888 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "B" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "C" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "D" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "E" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "F" Number of atoms: 2571 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Conformer: "B" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} bond proxies already assigned to first conformer: 2607 Chain: "G" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "H" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "I" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "J" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "K" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "L" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2563 Classifications: {'peptide': 326} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 314} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "D" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "L" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 7.51, per 1000 atoms: 0.24 Number of scatterers: 30888 At special positions: 0 Unit cell: (144.84, 145.52, 144.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 Mg 24 11.99 O 5812 8.00 N 5043 7.00 C 19889 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7130 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 12 sheets defined 55.1% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'A' and resid 24 through 37 removed outlier: 3.783A pdb=" N ARG A 28 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET A 34 " --> pdb=" O GLN A 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A 36 " --> pdb=" O THR A 32 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN A 37 " --> pdb=" O ILE A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 54 removed outlier: 3.771A pdb=" N LEU A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 3.582A pdb=" N GLU A 88 " --> pdb=" O LYS A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 113 removed outlier: 3.714A pdb=" N ALA A 112 " --> pdb=" O GLY A 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 113' Processing helix chain 'A' and resid 136 through 141 removed outlier: 4.240A pdb=" N LYS A 141 " --> pdb=" O MET A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.606A pdb=" N ALA A 164 " --> pdb=" O ALA A 160 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS A 165 " --> pdb=" O TRP A 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 166 " --> pdb=" O ASP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.708A pdb=" N LEU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU A 195 " --> pdb=" O ASP A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.717A pdb=" N ILE A 201 " --> pdb=" O THR A 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.509A pdb=" N PHE A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR A 229 " --> pdb=" O LEU A 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 224 through 229' Processing helix chain 'A' and resid 238 through 245 removed outlier: 3.782A pdb=" N ALA A 242 " --> pdb=" O ALA A 238 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS A 252 " --> pdb=" O GLN A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG A 264 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 285 removed outlier: 3.692A pdb=" N VAL A 272 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 274 " --> pdb=" O ASP A 270 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASN A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 299 removed outlier: 3.628A pdb=" N LYS A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 296 " --> pdb=" O TRP A 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR A 304 " --> pdb=" O TYR A 300 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG A 305 " --> pdb=" O PRO A 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR A 311 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 323 removed outlier: 3.592A pdb=" N ALA A 318 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 321 " --> pdb=" O LYS A 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 37 removed outlier: 3.783A pdb=" N ARG B 28 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET B 34 " --> pdb=" O GLN B 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 removed outlier: 3.779A pdb=" N LEU B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG B 69 " --> pdb=" O ASP B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 removed outlier: 3.508A pdb=" N GLU B 88 " --> pdb=" O LYS B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 108 through 113' Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.607A pdb=" N ALA B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS B 165 " --> pdb=" O TRP B 161 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ALA B 166 " --> pdb=" O ASP B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 218 removed outlier: 3.717A pdb=" N ILE B 201 " --> pdb=" O THR B 197 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA B 208 " --> pdb=" O GLY B 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY B 218 " --> pdb=" O VAL B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 removed outlier: 3.552A pdb=" N PHE B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 224 through 229' Processing helix chain 'B' and resid 238 through 245 removed outlier: 3.794A pdb=" N ALA B 242 " --> pdb=" O ALA B 238 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU B 243 " --> pdb=" O ARG B 239 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 245 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 253 removed outlier: 3.720A pdb=" N HIS B 252 " --> pdb=" O GLN B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG B 264 " --> pdb=" O GLY B 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL B 272 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 274 " --> pdb=" O ASP B 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 281 " --> pdb=" O GLU B 277 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 283 " --> pdb=" O GLU B 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP B 285 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN B 297 " --> pdb=" O SER B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR B 304 " --> pdb=" O TYR B 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 305 " --> pdb=" O PRO B 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP B 307 " --> pdb=" O PHE B 303 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 308 " --> pdb=" O TYR B 304 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR B 311 " --> pdb=" O TRP B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA B 318 " --> pdb=" O GLU B 314 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU B 321 " --> pdb=" O LYS B 317 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 37 removed outlier: 3.778A pdb=" N ARG C 28 " --> pdb=" O GLY C 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET C 34 " --> pdb=" O GLN C 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 54 removed outlier: 3.772A pdb=" N LEU C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 71 removed outlier: 3.814A pdb=" N ARG C 69 " --> pdb=" O ASP C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 removed outlier: 3.535A pdb=" N GLU C 88 " --> pdb=" O LYS C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 113 removed outlier: 3.713A pdb=" N ALA C 112 " --> pdb=" O GLY C 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.600A pdb=" N ALA C 164 " --> pdb=" O ALA C 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS C 165 " --> pdb=" O TRP C 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA C 166 " --> pdb=" O ASP C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU C 195 " --> pdb=" O ASP C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 218 removed outlier: 3.700A pdb=" N ILE C 201 " --> pdb=" O THR C 197 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA C 208 " --> pdb=" O GLY C 204 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY C 218 " --> pdb=" O VAL C 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 removed outlier: 3.506A pdb=" N PHE C 228 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR C 229 " --> pdb=" O LEU C 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 224 through 229' Processing helix chain 'C' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA C 242 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU C 243 " --> pdb=" O ARG C 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY C 245 " --> pdb=" O ILE C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.716A pdb=" N HIS C 252 " --> pdb=" O GLN C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.809A pdb=" N ARG C 264 " --> pdb=" O GLY C 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 285 removed outlier: 3.677A pdb=" N VAL C 272 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG C 274 " --> pdb=" O ASP C 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE C 275 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL C 276 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN C 278 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS C 281 " --> pdb=" O GLU C 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE C 283 " --> pdb=" O GLU C 279 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP C 285 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN C 296 " --> pdb=" O TRP C 292 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLN C 297 " --> pdb=" O SER C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR C 304 " --> pdb=" O TYR C 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG C 305 " --> pdb=" O PRO C 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP C 307 " --> pdb=" O PHE C 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 308 " --> pdb=" O TYR C 304 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR C 311 " --> pdb=" O TRP C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA C 318 " --> pdb=" O GLU C 314 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU C 321 " --> pdb=" O LYS C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 37 removed outlier: 3.777A pdb=" N ARG D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N VAL D 29 " --> pdb=" O ASN D 25 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET D 34 " --> pdb=" O GLN D 30 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU D 36 " --> pdb=" O THR D 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 37 " --> pdb=" O ILE D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 54 removed outlier: 3.759A pdb=" N LEU D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 71 removed outlier: 3.818A pdb=" N ARG D 69 " --> pdb=" O ASP D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 removed outlier: 3.509A pdb=" N GLU D 88 " --> pdb=" O LYS D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 113 removed outlier: 3.714A pdb=" N ALA D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 108 through 113' Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.550A pdb=" N ALA D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 165 " --> pdb=" O TRP D 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 166 " --> pdb=" O ASP D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.706A pdb=" N LEU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 218 removed outlier: 3.726A pdb=" N ILE D 201 " --> pdb=" O THR D 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA D 208 " --> pdb=" O GLY D 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP D 211 " --> pdb=" O LYS D 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY D 218 " --> pdb=" O VAL D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.509A pdb=" N PHE D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR D 229 " --> pdb=" O LEU D 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 224 through 229' Processing helix chain 'D' and resid 238 through 245 removed outlier: 3.773A pdb=" N ALA D 242 " --> pdb=" O ALA D 238 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU D 243 " --> pdb=" O ARG D 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 245 " --> pdb=" O ILE D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS D 252 " --> pdb=" O GLN D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG D 264 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL D 272 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG D 274 " --> pdb=" O ASP D 270 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ILE D 275 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N VAL D 276 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP D 285 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 299 removed outlier: 3.636A pdb=" N LYS D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN D 296 " --> pdb=" O TRP D 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN D 297 " --> pdb=" O SER D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR D 304 " --> pdb=" O TYR D 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG D 305 " --> pdb=" O PRO D 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP D 307 " --> pdb=" O PHE D 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 308 " --> pdb=" O TYR D 304 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR D 311 " --> pdb=" O TRP D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 323 removed outlier: 3.594A pdb=" N ALA D 318 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU D 321 " --> pdb=" O LYS D 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN E 37 " --> pdb=" O ILE E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 54 removed outlier: 3.737A pdb=" N LEU E 53 " --> pdb=" O LYS E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 71 removed outlier: 3.817A pdb=" N ARG E 69 " --> pdb=" O ASP E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 88 removed outlier: 3.534A pdb=" N GLU E 88 " --> pdb=" O LYS E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE E 113 " --> pdb=" O TYR E 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 108 through 113' Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.601A pdb=" N ALA E 164 " --> pdb=" O ALA E 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS E 165 " --> pdb=" O TRP E 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA E 166 " --> pdb=" O ASP E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.708A pdb=" N LEU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N SER E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 218 removed outlier: 3.654A pdb=" N ILE E 201 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP E 211 " --> pdb=" O LYS E 207 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY E 218 " --> pdb=" O VAL E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 229 removed outlier: 3.554A pdb=" N PHE E 228 " --> pdb=" O ALA E 224 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR E 229 " --> pdb=" O LEU E 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 224 through 229' Processing helix chain 'E' and resid 238 through 245 removed outlier: 3.791A pdb=" N ALA E 242 " --> pdb=" O ALA E 238 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 253 removed outlier: 3.719A pdb=" N HIS E 252 " --> pdb=" O GLN E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG E 264 " --> pdb=" O GLY E 260 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 268 through 285 removed outlier: 3.676A pdb=" N VAL E 272 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG E 274 " --> pdb=" O ASP E 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE E 275 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL E 276 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN E 278 " --> pdb=" O ARG E 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS E 281 " --> pdb=" O GLU E 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 283 " --> pdb=" O GLU E 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP E 285 " --> pdb=" O LYS E 281 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS E 290 " --> pdb=" O GLY E 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN E 296 " --> pdb=" O TRP E 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN E 297 " --> pdb=" O SER E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 312 removed outlier: 3.810A pdb=" N TYR E 304 " --> pdb=" O TYR E 300 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 305 " --> pdb=" O PRO E 301 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TRP E 307 " --> pdb=" O PHE E 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 308 " --> pdb=" O TYR E 304 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU E 309 " --> pdb=" O ARG E 305 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR E 311 " --> pdb=" O TRP E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 323 removed outlier: 3.610A pdb=" N ALA E 318 " --> pdb=" O GLU E 314 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLU E 321 " --> pdb=" O LYS E 317 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 37 removed outlier: 3.884A pdb=" N VAL F 29 " --> pdb=" O ASN F 25 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN F 30 " --> pdb=" O GLN F 26 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET F 34 " --> pdb=" O GLN F 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN F 37 " --> pdb=" O ILE F 33 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 54 removed outlier: 3.810A pdb=" N LEU F 53 " --> pdb=" O LYS F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 71 removed outlier: 3.838A pdb=" N ARG F 69 " --> pdb=" O ASP F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 88 removed outlier: 3.521A pdb=" N GLU F 88 " --> pdb=" O LYS F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 4.204A pdb=" N GLN F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 113 removed outlier: 3.675A pdb=" N ALA F 112 " --> pdb=" O GLY F 108 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE F 113 " --> pdb=" O TYR F 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 108 through 113' Processing helix chain 'F' and resid 136 through 141 removed outlier: 4.199A pdb=" N LYS F 141 " --> pdb=" O MET F 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.598A pdb=" N ALA F 164 " --> pdb=" O ALA F 160 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LYS F 165 " --> pdb=" O TRP F 161 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.583A pdb=" N ALA F 188 " --> pdb=" O PHE F 184 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 218 removed outlier: 3.724A pdb=" N ILE F 201 " --> pdb=" O THR F 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA F 208 " --> pdb=" O GLY F 204 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 211 " --> pdb=" O LYS F 207 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY F 218 " --> pdb=" O VAL F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 229 removed outlier: 3.527A pdb=" N PHE F 228 " --> pdb=" O ALA F 224 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR F 229 " --> pdb=" O LEU F 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 224 through 229' Processing helix chain 'F' and resid 238 through 245 removed outlier: 3.802A pdb=" N ALA F 242 " --> pdb=" O ALA F 238 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLU F 243 " --> pdb=" O ARG F 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY F 245 " --> pdb=" O ILE F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 253 removed outlier: 3.774A pdb=" N HIS F 252 " --> pdb=" O GLN F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.796A pdb=" N ARG F 264 " --> pdb=" O GLY F 260 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 268 through 285 removed outlier: 3.634A pdb=" N VAL F 272 " --> pdb=" O TYR F 268 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG F 274 " --> pdb=" O ASP F 270 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE F 275 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL F 276 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN F 278 " --> pdb=" O ARG F 274 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS F 281 " --> pdb=" O GLU F 277 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE F 283 " --> pdb=" O GLU F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 299 removed outlier: 3.628A pdb=" N LYS F 290 " --> pdb=" O GLY F 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN F 296 " --> pdb=" O TRP F 292 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN F 297 " --> pdb=" O SER F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 312 removed outlier: 3.802A pdb=" N TYR F 304 " --> pdb=" O TYR F 300 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG F 305 " --> pdb=" O PRO F 301 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TRP F 307 " --> pdb=" O PHE F 303 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU F 308 " --> pdb=" O TYR F 304 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU F 309 " --> pdb=" O ARG F 305 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR F 311 " --> pdb=" O TRP F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 323 removed outlier: 3.593A pdb=" N ALA F 318 " --> pdb=" O GLU F 314 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU F 321 " --> pdb=" O LYS F 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET G 34 " --> pdb=" O GLN G 30 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.756A pdb=" N LEU G 53 " --> pdb=" O LYS G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 71 removed outlier: 3.817A pdb=" N ARG G 69 " --> pdb=" O ASP G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 88 removed outlier: 3.507A pdb=" N GLU G 88 " --> pdb=" O LYS G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 113 removed outlier: 3.716A pdb=" N ALA G 112 " --> pdb=" O GLY G 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE G 113 " --> pdb=" O TYR G 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 108 through 113' Processing helix chain 'G' and resid 159 through 171 removed outlier: 3.547A pdb=" N ALA G 164 " --> pdb=" O ALA G 160 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS G 165 " --> pdb=" O TRP G 161 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA G 166 " --> pdb=" O ASP G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 195 removed outlier: 3.720A pdb=" N LEU G 190 " --> pdb=" O GLU G 186 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU G 195 " --> pdb=" O ASP G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 218 removed outlier: 3.716A pdb=" N ILE G 201 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA G 208 " --> pdb=" O GLY G 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP G 211 " --> pdb=" O LYS G 207 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY G 218 " --> pdb=" O VAL G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 229 removed outlier: 3.506A pdb=" N PHE G 228 " --> pdb=" O ALA G 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR G 229 " --> pdb=" O LEU G 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 224 through 229' Processing helix chain 'G' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA G 242 " --> pdb=" O ALA G 238 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU G 243 " --> pdb=" O ARG G 239 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.718A pdb=" N HIS G 252 " --> pdb=" O GLN G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG G 264 " --> pdb=" O GLY G 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE G 266 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL G 272 " --> pdb=" O TYR G 268 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 274 " --> pdb=" O ASP G 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE G 275 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL G 276 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN G 278 " --> pdb=" O ARG G 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS G 281 " --> pdb=" O GLU G 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP G 285 " --> pdb=" O LYS G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 299 removed outlier: 3.629A pdb=" N LYS G 290 " --> pdb=" O GLY G 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN G 296 " --> pdb=" O TRP G 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN G 297 " --> pdb=" O SER G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 300 through 312 removed outlier: 3.810A pdb=" N TYR G 304 " --> pdb=" O TYR G 300 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG G 305 " --> pdb=" O PRO G 301 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP G 307 " --> pdb=" O PHE G 303 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU G 308 " --> pdb=" O TYR G 304 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR G 311 " --> pdb=" O TRP G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 313 through 323 removed outlier: 3.577A pdb=" N ALA G 318 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU G 321 " --> pdb=" O LYS G 317 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 37 removed outlier: 3.783A pdb=" N ARG H 28 " --> pdb=" O GLY H 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL H 29 " --> pdb=" O ASN H 25 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N MET H 34 " --> pdb=" O GLN H 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 36 " --> pdb=" O THR H 32 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN H 37 " --> pdb=" O ILE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 54 removed outlier: 3.764A pdb=" N LEU H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 71 removed outlier: 3.819A pdb=" N ARG H 69 " --> pdb=" O ASP H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 88 removed outlier: 3.521A pdb=" N GLU H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 113 removed outlier: 3.714A pdb=" N ALA H 112 " --> pdb=" O GLY H 108 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE H 113 " --> pdb=" O TYR H 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 108 through 113' Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 159 through 171 removed outlier: 3.551A pdb=" N ALA H 164 " --> pdb=" O ALA H 160 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 165 " --> pdb=" O TRP H 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA H 166 " --> pdb=" O ASP H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU H 190 " --> pdb=" O GLU H 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 218 removed outlier: 3.718A pdb=" N ILE H 201 " --> pdb=" O THR H 197 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 208 " --> pdb=" O GLY H 204 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP H 211 " --> pdb=" O LYS H 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY H 218 " --> pdb=" O VAL H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 229 removed outlier: 3.511A pdb=" N PHE H 228 " --> pdb=" O ALA H 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR H 229 " --> pdb=" O LEU H 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 224 through 229' Processing helix chain 'H' and resid 238 through 245 removed outlier: 3.774A pdb=" N ALA H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU H 243 " --> pdb=" O ARG H 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY H 245 " --> pdb=" O ILE H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS H 252 " --> pdb=" O GLN H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG H 264 " --> pdb=" O GLY H 260 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE H 266 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL H 272 " --> pdb=" O TYR H 268 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG H 274 " --> pdb=" O ASP H 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE H 275 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL H 276 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN H 278 " --> pdb=" O ARG H 274 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS H 281 " --> pdb=" O GLU H 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE H 283 " --> pdb=" O GLU H 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP H 285 " --> pdb=" O LYS H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS H 290 " --> pdb=" O GLY H 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN H 296 " --> pdb=" O TRP H 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN H 297 " --> pdb=" O SER H 293 " (cutoff:3.500A) Processing helix chain 'H' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR H 304 " --> pdb=" O TYR H 300 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG H 305 " --> pdb=" O PRO H 301 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TRP H 307 " --> pdb=" O PHE H 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU H 308 " --> pdb=" O TYR H 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR H 311 " --> pdb=" O TRP H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA H 318 " --> pdb=" O GLU H 314 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLU H 321 " --> pdb=" O LYS H 317 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET I 34 " --> pdb=" O GLN I 30 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASN I 37 " --> pdb=" O ILE I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.733A pdb=" N LEU I 53 " --> pdb=" O LYS I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG I 69 " --> pdb=" O ASP I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 88 removed outlier: 3.506A pdb=" N GLU I 88 " --> pdb=" O LYS I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA I 112 " --> pdb=" O GLY I 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE I 113 " --> pdb=" O TYR I 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 108 through 113' Processing helix chain 'I' and resid 136 through 141 removed outlier: 4.240A pdb=" N LYS I 141 " --> pdb=" O MET I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 171 removed outlier: 3.601A pdb=" N ALA I 164 " --> pdb=" O ALA I 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS I 165 " --> pdb=" O TRP I 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA I 166 " --> pdb=" O ASP I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 195 removed outlier: 3.706A pdb=" N LEU I 190 " --> pdb=" O GLU I 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU I 192 " --> pdb=" O ALA I 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER I 194 " --> pdb=" O LEU I 190 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU I 195 " --> pdb=" O ASP I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 218 removed outlier: 3.725A pdb=" N ILE I 201 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 208 " --> pdb=" O GLY I 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP I 211 " --> pdb=" O LYS I 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY I 218 " --> pdb=" O VAL I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 224 through 229 removed outlier: 3.508A pdb=" N PHE I 228 " --> pdb=" O ALA I 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR I 229 " --> pdb=" O LEU I 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 224 through 229' Processing helix chain 'I' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA I 242 " --> pdb=" O ALA I 238 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU I 243 " --> pdb=" O ARG I 239 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY I 245 " --> pdb=" O ILE I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 253 removed outlier: 3.718A pdb=" N HIS I 252 " --> pdb=" O GLN I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG I 264 " --> pdb=" O GLY I 260 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE I 266 " --> pdb=" O LEU I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 268 through 285 removed outlier: 3.679A pdb=" N VAL I 272 " --> pdb=" O TYR I 268 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG I 274 " --> pdb=" O ASP I 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE I 275 " --> pdb=" O VAL I 271 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL I 276 " --> pdb=" O VAL I 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN I 278 " --> pdb=" O ARG I 274 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS I 281 " --> pdb=" O GLU I 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE I 283 " --> pdb=" O GLU I 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP I 285 " --> pdb=" O LYS I 281 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 299 removed outlier: 3.636A pdb=" N LYS I 290 " --> pdb=" O GLY I 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN I 296 " --> pdb=" O TRP I 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN I 297 " --> pdb=" O SER I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 312 removed outlier: 3.809A pdb=" N TYR I 304 " --> pdb=" O TYR I 300 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG I 305 " --> pdb=" O PRO I 301 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP I 307 " --> pdb=" O PHE I 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU I 308 " --> pdb=" O TYR I 304 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU I 309 " --> pdb=" O ARG I 305 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR I 311 " --> pdb=" O TRP I 307 " (cutoff:3.500A) Processing helix chain 'I' and resid 313 through 323 removed outlier: 3.592A pdb=" N ALA I 318 " --> pdb=" O GLU I 314 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU I 321 " --> pdb=" O LYS I 317 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 37 removed outlier: 3.781A pdb=" N ARG J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL J 29 " --> pdb=" O ASN J 25 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET J 34 " --> pdb=" O GLN J 30 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU J 36 " --> pdb=" O THR J 32 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASN J 37 " --> pdb=" O ILE J 33 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 removed outlier: 3.746A pdb=" N LEU J 53 " --> pdb=" O LYS J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 71 removed outlier: 3.818A pdb=" N ARG J 69 " --> pdb=" O ASP J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 88 removed outlier: 3.519A pdb=" N GLU J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA J 112 " --> pdb=" O GLY J 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 108 through 113' Processing helix chain 'J' and resid 136 through 140 Processing helix chain 'J' and resid 159 through 171 removed outlier: 3.551A pdb=" N ALA J 164 " --> pdb=" O ALA J 160 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS J 165 " --> pdb=" O TRP J 161 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA J 166 " --> pdb=" O ASP J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU J 190 " --> pdb=" O GLU J 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU J 192 " --> pdb=" O ALA J 188 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU J 195 " --> pdb=" O ASP J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 218 removed outlier: 3.702A pdb=" N ILE J 201 " --> pdb=" O THR J 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA J 208 " --> pdb=" O GLY J 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP J 211 " --> pdb=" O LYS J 207 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY J 218 " --> pdb=" O VAL J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 229 removed outlier: 3.507A pdb=" N PHE J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR J 229 " --> pdb=" O LEU J 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 224 through 229' Processing helix chain 'J' and resid 238 through 245 removed outlier: 3.776A pdb=" N ALA J 242 " --> pdb=" O ALA J 238 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLU J 243 " --> pdb=" O ARG J 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY J 245 " --> pdb=" O ILE J 241 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 253 removed outlier: 3.716A pdb=" N HIS J 252 " --> pdb=" O GLN J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 266 removed outlier: 3.805A pdb=" N ARG J 264 " --> pdb=" O GLY J 260 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE J 266 " --> pdb=" O LEU J 262 " (cutoff:3.500A) Processing helix chain 'J' and resid 268 through 285 removed outlier: 3.678A pdb=" N VAL J 272 " --> pdb=" O TYR J 268 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG J 274 " --> pdb=" O ASP J 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE J 275 " --> pdb=" O VAL J 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL J 276 " --> pdb=" O VAL J 272 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN J 278 " --> pdb=" O ARG J 274 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS J 281 " --> pdb=" O GLU J 277 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE J 283 " --> pdb=" O GLU J 279 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP J 285 " --> pdb=" O LYS J 281 " (cutoff:3.500A) Processing helix chain 'J' and resid 286 through 299 removed outlier: 3.642A pdb=" N LYS J 290 " --> pdb=" O GLY J 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN J 296 " --> pdb=" O TRP J 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN J 297 " --> pdb=" O SER J 293 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR J 304 " --> pdb=" O TYR J 300 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG J 305 " --> pdb=" O PRO J 301 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TRP J 307 " --> pdb=" O PHE J 303 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU J 308 " --> pdb=" O TYR J 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR J 311 " --> pdb=" O TRP J 307 " (cutoff:3.500A) Processing helix chain 'J' and resid 313 through 323 removed outlier: 3.576A pdb=" N ALA J 318 " --> pdb=" O GLU J 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU J 321 " --> pdb=" O LYS J 317 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 37 removed outlier: 3.782A pdb=" N ARG K 28 " --> pdb=" O GLY K 24 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET K 34 " --> pdb=" O GLN K 30 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ASN K 37 " --> pdb=" O ILE K 33 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 54 removed outlier: 3.738A pdb=" N LEU K 53 " --> pdb=" O LYS K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 71 removed outlier: 3.816A pdb=" N ARG K 69 " --> pdb=" O ASP K 65 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 88 removed outlier: 3.505A pdb=" N GLU K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 113 removed outlier: 3.715A pdb=" N ALA K 112 " --> pdb=" O GLY K 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE K 113 " --> pdb=" O TYR K 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 108 through 113' Processing helix chain 'K' and resid 159 through 171 removed outlier: 3.592A pdb=" N ALA K 164 " --> pdb=" O ALA K 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS K 165 " --> pdb=" O TRP K 161 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ALA K 166 " --> pdb=" O ASP K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 195 removed outlier: 3.708A pdb=" N LEU K 190 " --> pdb=" O GLU K 186 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER K 194 " --> pdb=" O LEU K 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 218 removed outlier: 3.716A pdb=" N ILE K 201 " --> pdb=" O THR K 197 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA K 208 " --> pdb=" O GLY K 204 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY K 218 " --> pdb=" O VAL K 214 " (cutoff:3.500A) Processing helix chain 'K' and resid 224 through 229 removed outlier: 3.550A pdb=" N PHE K 228 " --> pdb=" O ALA K 224 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR K 229 " --> pdb=" O LEU K 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 224 through 229' Processing helix chain 'K' and resid 238 through 245 removed outlier: 3.797A pdb=" N ALA K 242 " --> pdb=" O ALA K 238 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU K 243 " --> pdb=" O ARG K 239 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY K 245 " --> pdb=" O ILE K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 253 removed outlier: 3.713A pdb=" N HIS K 252 " --> pdb=" O GLN K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG K 264 " --> pdb=" O GLY K 260 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE K 266 " --> pdb=" O LEU K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 268 through 285 removed outlier: 3.677A pdb=" N VAL K 272 " --> pdb=" O TYR K 268 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG K 274 " --> pdb=" O ASP K 270 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE K 275 " --> pdb=" O VAL K 271 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL K 276 " --> pdb=" O VAL K 272 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN K 278 " --> pdb=" O ARG K 274 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS K 281 " --> pdb=" O GLU K 277 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE K 283 " --> pdb=" O GLU K 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP K 285 " --> pdb=" O LYS K 281 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 299 removed outlier: 3.636A pdb=" N LYS K 290 " --> pdb=" O GLY K 286 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN K 296 " --> pdb=" O TRP K 292 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN K 297 " --> pdb=" O SER K 293 " (cutoff:3.500A) Processing helix chain 'K' and resid 300 through 312 removed outlier: 3.807A pdb=" N TYR K 304 " --> pdb=" O TYR K 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG K 305 " --> pdb=" O PRO K 301 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP K 307 " --> pdb=" O PHE K 303 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU K 308 " --> pdb=" O TYR K 304 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR K 311 " --> pdb=" O TRP K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 313 through 323 removed outlier: 3.578A pdb=" N ALA K 318 " --> pdb=" O GLU K 314 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLU K 321 " --> pdb=" O LYS K 317 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 37 removed outlier: 3.773A pdb=" N ARG L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N MET L 34 " --> pdb=" O GLN L 30 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU L 36 " --> pdb=" O THR L 32 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN L 37 " --> pdb=" O ILE L 33 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 71 removed outlier: 3.813A pdb=" N ARG L 69 " --> pdb=" O ASP L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 88 removed outlier: 3.582A pdb=" N GLU L 88 " --> pdb=" O LYS L 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 108 through 113 removed outlier: 3.716A pdb=" N ALA L 112 " --> pdb=" O GLY L 108 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE L 113 " --> pdb=" O TYR L 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 108 through 113' Processing helix chain 'L' and resid 136 through 140 Processing helix chain 'L' and resid 159 through 171 removed outlier: 3.602A pdb=" N ALA L 164 " --> pdb=" O ALA L 160 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS L 165 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA L 166 " --> pdb=" O ASP L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 195 removed outlier: 3.707A pdb=" N LEU L 190 " --> pdb=" O GLU L 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU L 192 " --> pdb=" O ALA L 188 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER L 194 " --> pdb=" O LEU L 190 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLU L 195 " --> pdb=" O ASP L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 218 removed outlier: 3.716A pdb=" N ILE L 201 " --> pdb=" O THR L 197 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA L 208 " --> pdb=" O GLY L 204 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP L 211 " --> pdb=" O LYS L 207 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLY L 218 " --> pdb=" O VAL L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 229 removed outlier: 3.509A pdb=" N PHE L 228 " --> pdb=" O ALA L 224 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N TYR L 229 " --> pdb=" O LEU L 225 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 224 through 229' Processing helix chain 'L' and resid 238 through 245 removed outlier: 3.773A pdb=" N ALA L 242 " --> pdb=" O ALA L 238 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU L 243 " --> pdb=" O ARG L 239 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY L 245 " --> pdb=" O ILE L 241 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 253 removed outlier: 3.717A pdb=" N HIS L 252 " --> pdb=" O GLN L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 254 through 266 removed outlier: 3.808A pdb=" N ARG L 264 " --> pdb=" O GLY L 260 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N PHE L 266 " --> pdb=" O LEU L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 268 through 285 removed outlier: 3.680A pdb=" N VAL L 272 " --> pdb=" O TYR L 268 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG L 274 " --> pdb=" O ASP L 270 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE L 275 " --> pdb=" O VAL L 271 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N VAL L 276 " --> pdb=" O VAL L 272 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASN L 278 " --> pdb=" O ARG L 274 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS L 281 " --> pdb=" O GLU L 277 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE L 283 " --> pdb=" O GLU L 279 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP L 285 " --> pdb=" O LYS L 281 " (cutoff:3.500A) Processing helix chain 'L' and resid 286 through 299 removed outlier: 3.635A pdb=" N LYS L 290 " --> pdb=" O GLY L 286 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN L 296 " --> pdb=" O TRP L 292 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN L 297 " --> pdb=" O SER L 293 " (cutoff:3.500A) Processing helix chain 'L' and resid 300 through 312 removed outlier: 3.808A pdb=" N TYR L 304 " --> pdb=" O TYR L 300 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG L 305 " --> pdb=" O PRO L 301 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TRP L 307 " --> pdb=" O PHE L 303 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU L 308 " --> pdb=" O TYR L 304 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR L 311 " --> pdb=" O TRP L 307 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 323 removed outlier: 3.592A pdb=" N ALA L 318 " --> pdb=" O GLU L 314 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU L 321 " --> pdb=" O LYS L 317 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 9.313A pdb=" N TYR A 62 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ILE A 18 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY A 44 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL A 20 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR A 124 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 61 through 62 removed outlier: 9.312A pdb=" N TYR B 62 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N VAL B 43 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ILE B 18 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLY B 44 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N VAL B 20 " --> pdb=" O GLY B 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR B 124 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 61 through 62 removed outlier: 9.312A pdb=" N TYR C 62 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N VAL C 43 " --> pdb=" O TYR C 62 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N THR C 124 " --> pdb=" O LYS C 153 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 61 through 62 removed outlier: 9.308A pdb=" N TYR D 62 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N VAL D 43 " --> pdb=" O TYR D 62 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR D 124 " --> pdb=" O LYS D 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 61 through 62 removed outlier: 9.323A pdb=" N TYR E 62 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL E 43 " --> pdb=" O TYR E 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE E 18 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N GLY E 44 " --> pdb=" O ILE E 18 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL E 20 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR E 124 " --> pdb=" O LYS E 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 61 through 62 removed outlier: 9.303A pdb=" N TYR F 62 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL F 43 " --> pdb=" O TYR F 62 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR F 124 " --> pdb=" O LYS F 153 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 61 through 62 removed outlier: 9.321A pdb=" N TYR G 62 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL G 43 " --> pdb=" O TYR G 62 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE G 18 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY G 44 " --> pdb=" O ILE G 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL G 20 " --> pdb=" O GLY G 44 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR G 124 " --> pdb=" O LYS G 153 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 61 through 62 removed outlier: 9.311A pdb=" N TYR H 62 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL H 43 " --> pdb=" O TYR H 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE H 18 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N GLY H 44 " --> pdb=" O ILE H 18 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL H 20 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N THR H 124 " --> pdb=" O LYS H 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 61 through 62 removed outlier: 9.311A pdb=" N TYR I 62 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL I 43 " --> pdb=" O TYR I 62 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE I 18 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N GLY I 44 " --> pdb=" O ILE I 18 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL I 20 " --> pdb=" O GLY I 44 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR I 124 " --> pdb=" O LYS I 153 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 61 through 62 removed outlier: 9.321A pdb=" N TYR J 62 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL J 43 " --> pdb=" O TYR J 62 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ILE J 18 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY J 44 " --> pdb=" O ILE J 18 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL J 20 " --> pdb=" O GLY J 44 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR J 124 " --> pdb=" O LYS J 153 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 61 through 62 removed outlier: 9.322A pdb=" N TYR K 62 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL K 43 " --> pdb=" O TYR K 62 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE K 18 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N GLY K 44 " --> pdb=" O ILE K 18 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL K 20 " --> pdb=" O GLY K 44 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR K 124 " --> pdb=" O LYS K 153 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 61 through 62 removed outlier: 9.343A pdb=" N TYR L 62 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N VAL L 43 " --> pdb=" O TYR L 62 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE L 18 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N GLY L 44 " --> pdb=" O ILE L 18 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N VAL L 20 " --> pdb=" O GLY L 44 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR L 124 " --> pdb=" O LYS L 153 " (cutoff:3.500A) 1051 hydrogen bonds defined for protein. 3063 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: 5.29 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9780 1.34 - 1.45: 4771 1.45 - 1.57: 16622 1.57 - 1.69: 0 1.69 - 1.80: 228 Bond restraints: 31401 Sorted by residual: bond pdb=" N ARG L 35 " pdb=" CA ARG L 35 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.21e-02 6.83e+03 4.88e+00 bond pdb=" CB PRO D 200 " pdb=" CG PRO D 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.41e+00 bond pdb=" CB PRO B 200 " pdb=" CG PRO B 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.40e+00 bond pdb=" CB PRO I 200 " pdb=" CG PRO I 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.37e+00 bond pdb=" CB PRO G 200 " pdb=" CG PRO G 200 " ideal model delta sigma weight residual 1.492 1.400 0.092 5.00e-02 4.00e+02 3.36e+00 ... (remaining 31396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 41271 2.30 - 4.59: 969 4.59 - 6.89: 137 6.89 - 9.19: 20 9.19 - 11.48: 12 Bond angle restraints: 42409 Sorted by residual: angle pdb=" N VAL J 111 " pdb=" CA VAL J 111 " pdb=" C VAL J 111 " ideal model delta sigma weight residual 112.96 109.03 3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL E 111 " pdb=" CA VAL E 111 " pdb=" C VAL E 111 " ideal model delta sigma weight residual 112.96 109.03 3.93 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL C 111 " pdb=" CA VAL C 111 " pdb=" C VAL C 111 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL D 111 " pdb=" CA VAL D 111 " pdb=" C VAL D 111 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N VAL A 111 " pdb=" CA VAL A 111 " pdb=" C VAL A 111 " ideal model delta sigma weight residual 112.96 109.04 3.92 1.00e+00 1.00e+00 1.54e+01 ... (remaining 42404 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 16716 18.14 - 36.29: 1637 36.29 - 54.43: 347 54.43 - 72.57: 26 72.57 - 90.72: 51 Dihedral angle restraints: 18777 sinusoidal: 7529 harmonic: 11248 Sorted by residual: dihedral pdb=" CA SER G 157 " pdb=" C SER G 157 " pdb=" N GLY G 158 " pdb=" CA GLY G 158 " ideal model delta harmonic sigma weight residual -180.00 -156.23 -23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA SER F 157 " pdb=" C SER F 157 " pdb=" N GLY F 158 " pdb=" CA GLY F 158 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA SER A 157 " pdb=" C SER A 157 " pdb=" N GLY A 158 " pdb=" CA GLY A 158 " ideal model delta harmonic sigma weight residual -180.00 -158.15 -21.85 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 18774 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2548 0.038 - 0.076: 1449 0.076 - 0.114: 438 0.114 - 0.152: 168 0.152 - 0.190: 42 Chirality restraints: 4645 Sorted by residual: chirality pdb=" CA ASP H 11 " pdb=" N ASP H 11 " pdb=" C ASP H 11 " pdb=" CB ASP H 11 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CA ASP D 11 " pdb=" N ASP D 11 " pdb=" C ASP D 11 " pdb=" CB ASP D 11 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.00e-01 chirality pdb=" CA ASP G 11 " pdb=" N ASP G 11 " pdb=" C ASP G 11 " pdb=" CB ASP G 11 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.99e-01 ... (remaining 4642 not shown) Planarity restraints: 5390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP G 11 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO G 12 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 12 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 12 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP H 11 " 0.046 5.00e-02 4.00e+02 6.92e-02 7.67e+00 pdb=" N PRO H 12 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO H 12 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 12 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP J 11 " -0.046 5.00e-02 4.00e+02 6.92e-02 7.65e+00 pdb=" N PRO J 12 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO J 12 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO J 12 " -0.039 5.00e-02 4.00e+02 ... (remaining 5387 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1223 2.71 - 3.26: 25322 3.26 - 3.81: 44566 3.81 - 4.35: 60408 4.35 - 4.90: 104257 Nonbonded interactions: 235776 Sorted by model distance: nonbonded pdb=" OE2 GLU F 227 " pdb="MG MG F 401 " model vdw 2.168 2.170 nonbonded pdb=" OE2 GLU E 227 " pdb="MG MG E 402 " model vdw 2.172 2.170 nonbonded pdb=" OE2 GLU K 227 " pdb="MG MG K 402 " model vdw 2.175 2.170 nonbonded pdb=" OE2 GLU B 227 " pdb="MG MG B 401 " model vdw 2.176 2.170 nonbonded pdb=" OE2 GLU C 227 " pdb="MG MG C 402 " model vdw 2.206 2.170 ... (remaining 235771 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 3 through 27 or resid 29 through 402)) selection = (chain 'B' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'C' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'D' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'E' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'F' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'G' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'H' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'I' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'J' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'K' and (resid 3 through 27 or resid 29 through 402)) selection = (chain 'L' and (resid 3 through 27 or resid 29 through 402)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.990 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: 0.030 Extract box with map and model: 0.600 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.420 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 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 : 0.007 0.092 31401 Z= 0.297 Angle : 0.883 11.483 42409 Z= 0.475 Chirality : 0.054 0.190 4645 Planarity : 0.007 0.069 5390 Dihedral : 15.375 90.716 11647 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.35 % Allowed : 5.25 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.55 (0.08), residues: 3889 helix: -5.10 (0.03), residues: 2161 sheet: -2.32 (0.17), residues: 564 loop : -3.15 (0.14), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 130 TYR 0.017 0.003 TYR B 217 PHE 0.015 0.003 PHE F 184 TRP 0.015 0.003 TRP A 284 HIS 0.004 0.001 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00714 (31401) covalent geometry : angle 0.88349 (42409) hydrogen bonds : bond 0.39384 ( 1051) hydrogen bonds : angle 11.06294 ( 3063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 472 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 142 GLN cc_start: 0.9031 (mm110) cc_final: 0.8810 (mp10) REVERT: C 142 GLN cc_start: 0.9037 (mm110) cc_final: 0.8819 (mp10) REVERT: E 142 GLN cc_start: 0.9042 (mm110) cc_final: 0.8814 (mp10) REVERT: H 142 GLN cc_start: 0.8796 (mp10) cc_final: 0.8546 (mp10) REVERT: K 142 GLN cc_start: 0.9033 (mm110) cc_final: 0.8832 (mp10) outliers start: 11 outliers final: 0 residues processed: 483 average time/residue: 0.1728 time to fit residues: 133.5781 Evaluate side-chains 378 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 378 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 196 HIS F 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.056537 restraints weight = 114866.990| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 4.60 r_work: 0.2557 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 31401 Z= 0.125 Angle : 0.573 9.145 42409 Z= 0.295 Chirality : 0.044 0.134 4645 Planarity : 0.005 0.051 5390 Dihedral : 4.466 16.357 4263 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.69 (0.10), residues: 3889 helix: -3.54 (0.07), residues: 2089 sheet: -1.70 (0.19), residues: 540 loop : -2.49 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 130 TYR 0.015 0.001 TYR A 217 PHE 0.005 0.001 PHE F 184 TRP 0.017 0.001 TRP F 198 HIS 0.002 0.001 HIS I 140 Details of bonding type rmsd covalent geometry : bond 0.00280 (31401) covalent geometry : angle 0.57294 (42409) hydrogen bonds : bond 0.05028 ( 1051) hydrogen bonds : angle 4.84331 ( 3063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 417 time to evaluate : 1.218 Fit side-chains REVERT: A 142 GLN cc_start: 0.8728 (mp10) cc_final: 0.8518 (mp10) REVERT: B 142 GLN cc_start: 0.9481 (mm110) cc_final: 0.8816 (mp10) REVERT: C 142 GLN cc_start: 0.9488 (mm110) cc_final: 0.8823 (mp10) REVERT: E 142 GLN cc_start: 0.9485 (mm110) cc_final: 0.8821 (mp10) REVERT: F 26 GLN cc_start: 0.9345 (mm-40) cc_final: 0.8979 (mm-40) REVERT: F 126 MET cc_start: 0.9468 (ttp) cc_final: 0.9256 (ttp) REVERT: F 312 GLN cc_start: 0.8785 (mm110) cc_final: 0.8571 (mm110) REVERT: G 142 GLN cc_start: 0.9468 (mm110) cc_final: 0.8802 (mp10) REVERT: H 126 MET cc_start: 0.9447 (ttp) cc_final: 0.9240 (ttp) REVERT: H 142 GLN cc_start: 0.9205 (mp10) cc_final: 0.8614 (mp10) REVERT: K 142 GLN cc_start: 0.9474 (mm110) cc_final: 0.8820 (mp10) outliers start: 0 outliers final: 0 residues processed: 417 average time/residue: 0.1750 time to fit residues: 118.2141 Evaluate side-chains 374 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 162 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 318 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 131 optimal weight: 0.0050 overall best weight: 3.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN A 196 HIS B 110 ASN B 196 HIS C 110 ASN C 196 HIS D 110 ASN D 196 HIS E 110 ASN F 96 GLN F 196 HIS G 96 GLN G 110 ASN G 196 HIS H 96 GLN H 110 ASN H 196 HIS I 110 ASN I 196 HIS J 96 GLN J 110 ASN J 196 HIS K 96 GLN K 110 ASN K 196 HIS L 110 ASN L 196 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.077082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.053103 restraints weight = 105538.330| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 4.31 r_work: 0.2504 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2470 r_free = 0.2470 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 31401 Z= 0.194 Angle : 0.580 9.678 42409 Z= 0.296 Chirality : 0.045 0.142 4645 Planarity : 0.004 0.044 5390 Dihedral : 4.063 14.243 4263 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 0.19 % Allowed : 11.13 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.43 (0.12), residues: 3889 helix: -2.29 (0.10), residues: 2089 sheet: -1.37 (0.19), residues: 540 loop : -2.25 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 274 TYR 0.014 0.001 TYR F 217 PHE 0.007 0.001 PHE C 113 TRP 0.018 0.002 TRP F 198 HIS 0.003 0.001 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00437 (31401) covalent geometry : angle 0.58046 (42409) hydrogen bonds : bond 0.05301 ( 1051) hydrogen bonds : angle 4.44475 ( 3063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 340 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: B 142 GLN cc_start: 0.9505 (mm110) cc_final: 0.8834 (mp10) REVERT: C 142 GLN cc_start: 0.9493 (mm110) cc_final: 0.8814 (mp10) REVERT: E 142 GLN cc_start: 0.9494 (mm110) cc_final: 0.8818 (mp10) REVERT: F 26 GLN cc_start: 0.9396 (mm-40) cc_final: 0.9137 (mm110) REVERT: F 297 GLN cc_start: 0.9550 (mt0) cc_final: 0.9301 (mt0) REVERT: G 142 GLN cc_start: 0.9503 (mm110) cc_final: 0.8833 (mp10) REVERT: H 142 GLN cc_start: 0.9278 (mp10) cc_final: 0.8641 (mp10) REVERT: K 142 GLN cc_start: 0.9495 (mm110) cc_final: 0.8828 (mp10) outliers start: 6 outliers final: 4 residues processed: 345 average time/residue: 0.1790 time to fit residues: 99.1912 Evaluate side-chains 327 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 323 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 168 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 348 optimal weight: 0.6980 chunk 180 optimal weight: 3.9990 chunk 233 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 38 optimal weight: 7.9990 chunk 210 optimal weight: 7.9990 chunk 287 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN B 25 ASN C 25 ASN D 25 ASN E 25 ASN F 96 GLN G 25 ASN G 96 GLN H 25 ASN H 96 GLN I 25 ASN J 25 ASN J 96 GLN K 25 ASN K 96 GLN L 25 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.079778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.056169 restraints weight = 115177.778| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 4.47 r_work: 0.2555 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 31401 Z= 0.090 Angle : 0.494 8.891 42409 Z= 0.245 Chirality : 0.043 0.126 4645 Planarity : 0.003 0.038 5390 Dihedral : 3.653 13.414 4263 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.31 % Allowed : 11.29 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.58 (0.12), residues: 3889 helix: -1.65 (0.11), residues: 2101 sheet: -0.66 (0.22), residues: 444 loop : -1.87 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 274 TYR 0.009 0.001 TYR A 217 PHE 0.005 0.001 PHE F 184 TRP 0.018 0.001 TRP F 198 HIS 0.001 0.000 HIS B 140 Details of bonding type rmsd covalent geometry : bond 0.00205 (31401) covalent geometry : angle 0.49372 (42409) hydrogen bonds : bond 0.03485 ( 1051) hydrogen bonds : angle 4.12279 ( 3063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 366 time to evaluate : 1.020 Fit side-chains REVERT: A 25 ASN cc_start: 0.9058 (m-40) cc_final: 0.8742 (p0) REVERT: A 142 GLN cc_start: 0.8814 (mp10) cc_final: 0.8470 (mp10) REVERT: B 25 ASN cc_start: 0.9063 (m-40) cc_final: 0.8754 (p0) REVERT: B 142 GLN cc_start: 0.9494 (mm110) cc_final: 0.8848 (mp10) REVERT: C 25 ASN cc_start: 0.9049 (m-40) cc_final: 0.8741 (p0) REVERT: C 142 GLN cc_start: 0.9481 (mm110) cc_final: 0.8841 (mp10) REVERT: D 25 ASN cc_start: 0.9067 (m-40) cc_final: 0.8758 (p0) REVERT: E 25 ASN cc_start: 0.9065 (m-40) cc_final: 0.8752 (p0) REVERT: E 142 GLN cc_start: 0.9493 (mm110) cc_final: 0.8846 (mp10) REVERT: F 26 GLN cc_start: 0.9370 (mm-40) cc_final: 0.8197 (mm110) REVERT: F 30 GLN cc_start: 0.9219 (mt0) cc_final: 0.8609 (mp10) REVERT: G 25 ASN cc_start: 0.9062 (m-40) cc_final: 0.8754 (p0) REVERT: G 142 GLN cc_start: 0.9483 (mm110) cc_final: 0.8838 (mp10) REVERT: H 25 ASN cc_start: 0.9066 (m-40) cc_final: 0.8753 (p0) REVERT: H 142 GLN cc_start: 0.9277 (mp10) cc_final: 0.8651 (mp10) REVERT: I 25 ASN cc_start: 0.9057 (m-40) cc_final: 0.8747 (p0) REVERT: J 25 ASN cc_start: 0.9057 (m-40) cc_final: 0.8748 (p0) REVERT: K 25 ASN cc_start: 0.9060 (m-40) cc_final: 0.8754 (p0) REVERT: K 142 GLN cc_start: 0.9484 (mm110) cc_final: 0.8833 (mp10) REVERT: L 25 ASN cc_start: 0.9062 (m-40) cc_final: 0.8752 (p0) outliers start: 10 outliers final: 10 residues processed: 375 average time/residue: 0.1645 time to fit residues: 99.2521 Evaluate side-chains 362 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 352 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 187 optimal weight: 4.9990 chunk 126 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 354 optimal weight: 9.9990 chunk 206 optimal weight: 9.9990 chunk 379 optimal weight: 1.9990 chunk 286 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 188 optimal weight: 0.8980 chunk 19 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN F 96 GLN G 96 GLN H 96 GLN J 96 GLN K 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.077716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.053825 restraints weight = 116355.183| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 4.49 r_work: 0.2505 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2506 r_free = 0.2506 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 31401 Z= 0.164 Angle : 0.538 8.690 42409 Z= 0.269 Chirality : 0.044 0.142 4645 Planarity : 0.003 0.034 5390 Dihedral : 3.603 12.192 4263 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.82 % Allowed : 11.51 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.12 (0.13), residues: 3889 helix: -1.27 (0.11), residues: 2197 sheet: -0.46 (0.22), residues: 444 loop : -1.67 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 274 TYR 0.012 0.001 TYR F 217 PHE 0.006 0.001 PHE B 113 TRP 0.016 0.001 TRP F 198 HIS 0.002 0.000 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00374 (31401) covalent geometry : angle 0.53770 (42409) hydrogen bonds : bond 0.04496 ( 1051) hydrogen bonds : angle 4.17323 ( 3063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 336 time to evaluate : 1.480 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.9058 (m-40) cc_final: 0.8771 (p0) REVERT: B 25 ASN cc_start: 0.9067 (m-40) cc_final: 0.8776 (p0) REVERT: B 142 GLN cc_start: 0.9488 (mm110) cc_final: 0.8841 (mp10) REVERT: C 25 ASN cc_start: 0.9037 (m-40) cc_final: 0.8759 (p0) REVERT: C 142 GLN cc_start: 0.9490 (mm110) cc_final: 0.8849 (mp10) REVERT: D 25 ASN cc_start: 0.9042 (m-40) cc_final: 0.8760 (p0) REVERT: E 25 ASN cc_start: 0.9070 (m-40) cc_final: 0.8779 (p0) REVERT: E 142 GLN cc_start: 0.9485 (mm110) cc_final: 0.8845 (mp10) REVERT: F 26 GLN cc_start: 0.9367 (mm-40) cc_final: 0.8389 (tp40) REVERT: F 30 GLN cc_start: 0.9219 (mt0) cc_final: 0.8661 (mp10) REVERT: G 25 ASN cc_start: 0.9054 (m-40) cc_final: 0.8773 (p0) REVERT: G 142 GLN cc_start: 0.9483 (mm110) cc_final: 0.8833 (mp10) REVERT: H 25 ASN cc_start: 0.9067 (m-40) cc_final: 0.8782 (p0) REVERT: H 142 GLN cc_start: 0.9316 (mp10) cc_final: 0.8678 (mp10) REVERT: I 25 ASN cc_start: 0.9056 (m-40) cc_final: 0.8769 (p0) REVERT: J 25 ASN cc_start: 0.9063 (m-40) cc_final: 0.8777 (p0) REVERT: K 25 ASN cc_start: 0.9060 (m-40) cc_final: 0.8774 (p0) REVERT: K 142 GLN cc_start: 0.9478 (mm110) cc_final: 0.8830 (mp10) REVERT: L 25 ASN cc_start: 0.9063 (m-40) cc_final: 0.8769 (p0) outliers start: 26 outliers final: 15 residues processed: 362 average time/residue: 0.2002 time to fit residues: 117.8949 Evaluate side-chains 341 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 326 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain F residue 71 SER Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 81 optimal weight: 0.0000 chunk 369 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 361 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 363 optimal weight: 0.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 GLN G 96 GLN H 96 GLN J 96 GLN K 96 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.078251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.054103 restraints weight = 131375.641| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 4.78 r_work: 0.2491 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2491 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2509 r_free = 0.2509 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31401 Z= 0.133 Angle : 0.517 9.052 42409 Z= 0.257 Chirality : 0.044 0.136 4645 Planarity : 0.003 0.033 5390 Dihedral : 3.494 11.996 4263 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.66 % Allowed : 12.92 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.44 (0.13), residues: 3889 helix: -0.66 (0.11), residues: 2125 sheet: -0.18 (0.22), residues: 444 loop : -1.48 (0.17), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 274 TYR 0.011 0.001 TYR F 217 PHE 0.005 0.001 PHE F 113 TRP 0.017 0.001 TRP F 198 HIS 0.002 0.000 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00307 (31401) covalent geometry : angle 0.51705 (42409) hydrogen bonds : bond 0.04015 ( 1051) hydrogen bonds : angle 4.07164 ( 3063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 325 time to evaluate : 1.239 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.9011 (m-40) cc_final: 0.8732 (p0) REVERT: B 25 ASN cc_start: 0.9015 (m-40) cc_final: 0.8732 (p0) REVERT: B 142 GLN cc_start: 0.9499 (mm110) cc_final: 0.8859 (mp10) REVERT: C 25 ASN cc_start: 0.8980 (m-40) cc_final: 0.8718 (p0) REVERT: C 142 GLN cc_start: 0.9491 (mm110) cc_final: 0.8855 (mp10) REVERT: D 25 ASN cc_start: 0.8988 (m-40) cc_final: 0.8725 (p0) REVERT: E 25 ASN cc_start: 0.9015 (m-40) cc_final: 0.8743 (p0) REVERT: E 142 GLN cc_start: 0.9482 (mm110) cc_final: 0.8849 (mp10) REVERT: F 26 GLN cc_start: 0.9359 (mm-40) cc_final: 0.8411 (tp40) REVERT: F 30 GLN cc_start: 0.9218 (mt0) cc_final: 0.8683 (mp10) REVERT: F 178 ILE cc_start: 0.9035 (mm) cc_final: 0.8584 (tp) REVERT: G 25 ASN cc_start: 0.9016 (m-40) cc_final: 0.8744 (p0) REVERT: G 142 GLN cc_start: 0.9496 (mm110) cc_final: 0.8863 (mp10) REVERT: H 25 ASN cc_start: 0.9013 (m-40) cc_final: 0.8740 (p0) REVERT: H 142 GLN cc_start: 0.9351 (mp10) cc_final: 0.8695 (mp10) REVERT: I 25 ASN cc_start: 0.8998 (m-40) cc_final: 0.8728 (p0) REVERT: J 25 ASN cc_start: 0.9014 (m-40) cc_final: 0.8736 (p0) REVERT: K 25 ASN cc_start: 0.9002 (m-40) cc_final: 0.8725 (p0) REVERT: K 142 GLN cc_start: 0.9480 (mm110) cc_final: 0.8837 (mp10) REVERT: L 25 ASN cc_start: 0.9017 (m-40) cc_final: 0.8736 (p0) outliers start: 21 outliers final: 20 residues processed: 346 average time/residue: 0.2018 time to fit residues: 112.7428 Evaluate side-chains 342 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 322 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain D residue 182 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 182 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain K residue 71 SER Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain L residue 71 SER Chi-restraints excluded: chain L residue 182 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 141 optimal weight: 4.9990 chunk 338 optimal weight: 9.9990 chunk 161 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 353 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 264 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 180 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN C 96 GLN D 96 GLN G 96 GLN H 96 GLN K 96 GLN L 96 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.075684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.051874 restraints weight = 114689.318| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 4.40 r_work: 0.2430 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2461 r_free = 0.2461 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2461 r_free = 0.2461 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 31401 Z= 0.267 Angle : 0.599 8.541 42409 Z= 0.303 Chirality : 0.048 0.159 4645 Planarity : 0.003 0.034 5390 Dihedral : 3.745 12.277 4263 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.69 % Allowed : 13.80 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.33 (0.13), residues: 3889 helix: -0.47 (0.11), residues: 2185 sheet: -0.06 (0.22), residues: 444 loop : -1.72 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 274 TYR 0.013 0.001 TYR F 217 PHE 0.008 0.001 PHE D 228 TRP 0.018 0.002 TRP F 198 HIS 0.003 0.001 HIS F 140 Details of bonding type rmsd covalent geometry : bond 0.00607 (31401) covalent geometry : angle 0.59902 (42409) hydrogen bonds : bond 0.05228 ( 1051) hydrogen bonds : angle 4.37470 ( 3063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 320 time to evaluate : 1.307 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8991 (m-40) cc_final: 0.8717 (p0) REVERT: B 25 ASN cc_start: 0.8996 (m-40) cc_final: 0.8722 (p0) REVERT: B 142 GLN cc_start: 0.9470 (mm110) cc_final: 0.8824 (mp10) REVERT: C 25 ASN cc_start: 0.8959 (m-40) cc_final: 0.8720 (p0) REVERT: C 142 GLN cc_start: 0.9466 (mm110) cc_final: 0.8827 (mp10) REVERT: D 25 ASN cc_start: 0.8957 (m-40) cc_final: 0.8720 (p0) REVERT: E 25 ASN cc_start: 0.9004 (m-40) cc_final: 0.8731 (p0) REVERT: E 142 GLN cc_start: 0.9464 (mm110) cc_final: 0.8826 (mp10) REVERT: F 26 GLN cc_start: 0.9355 (mm-40) cc_final: 0.8450 (tp40) REVERT: F 30 GLN cc_start: 0.9223 (mt0) cc_final: 0.8683 (mp10) REVERT: F 312 GLN cc_start: 0.9096 (mm110) cc_final: 0.8828 (mm110) REVERT: G 25 ASN cc_start: 0.8978 (m-40) cc_final: 0.8721 (p0) REVERT: G 142 GLN cc_start: 0.9475 (mm110) cc_final: 0.8838 (mp10) REVERT: G 182 SER cc_start: 0.9394 (OUTLIER) cc_final: 0.9182 (p) REVERT: H 25 ASN cc_start: 0.8999 (m-40) cc_final: 0.8729 (p0) REVERT: I 25 ASN cc_start: 0.8970 (m-40) cc_final: 0.8713 (p0) REVERT: J 25 ASN cc_start: 0.8994 (m-40) cc_final: 0.8725 (p0) REVERT: K 25 ASN cc_start: 0.8991 (m-40) cc_final: 0.8720 (p0) REVERT: K 142 GLN cc_start: 0.9465 (mm110) cc_final: 0.8827 (mp10) REVERT: L 25 ASN cc_start: 0.8987 (m-40) cc_final: 0.8718 (p0) outliers start: 22 outliers final: 11 residues processed: 342 average time/residue: 0.1970 time to fit residues: 108.5181 Evaluate side-chains 328 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 316 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain B residue 71 SER Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 71 SER Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 182 SER Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain I residue 71 SER Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain K residue 71 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 161 optimal weight: 5.9990 chunk 381 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 134 optimal weight: 2.9990 chunk 111 optimal weight: 0.4980 chunk 225 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 115 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 96 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.079361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.055686 restraints weight = 115828.397| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 4.53 r_work: 0.2546 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 31401 Z= 0.085 Angle : 0.518 10.651 42409 Z= 0.248 Chirality : 0.042 0.130 4645 Planarity : 0.003 0.034 5390 Dihedral : 3.396 13.641 4263 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.38 % Allowed : 14.49 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.44 (0.13), residues: 3889 helix: 0.41 (0.12), residues: 2017 sheet: 0.09 (0.22), residues: 444 loop : -1.35 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 274 TYR 0.008 0.001 TYR A 217 PHE 0.004 0.001 PHE F 203 TRP 0.017 0.001 TRP F 198 HIS 0.001 0.000 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00202 (31401) covalent geometry : angle 0.51784 (42409) hydrogen bonds : bond 0.03167 ( 1051) hydrogen bonds : angle 3.94616 ( 3063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 327 time to evaluate : 1.278 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8934 (m-40) cc_final: 0.8679 (p0) REVERT: A 178 ILE cc_start: 0.9002 (mm) cc_final: 0.8586 (tp) REVERT: B 25 ASN cc_start: 0.8933 (m-40) cc_final: 0.8680 (p0) REVERT: B 142 GLN cc_start: 0.9500 (mm110) cc_final: 0.8879 (mp10) REVERT: B 178 ILE cc_start: 0.9001 (mm) cc_final: 0.8564 (tp) REVERT: C 25 ASN cc_start: 0.8904 (m-40) cc_final: 0.8672 (p0) REVERT: C 142 GLN cc_start: 0.9496 (mm110) cc_final: 0.8870 (mp10) REVERT: C 178 ILE cc_start: 0.8985 (mm) cc_final: 0.8550 (tp) REVERT: D 25 ASN cc_start: 0.8906 (m-40) cc_final: 0.8675 (p0) REVERT: D 178 ILE cc_start: 0.8993 (mm) cc_final: 0.8559 (tp) REVERT: E 25 ASN cc_start: 0.8931 (m-40) cc_final: 0.8681 (p0) REVERT: E 142 GLN cc_start: 0.9491 (mm110) cc_final: 0.8868 (mp10) REVERT: E 178 ILE cc_start: 0.8995 (mm) cc_final: 0.8583 (tp) REVERT: F 26 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8593 (tp40) REVERT: F 30 GLN cc_start: 0.9177 (mt0) cc_final: 0.8669 (mp10) REVERT: F 178 ILE cc_start: 0.9011 (mm) cc_final: 0.8598 (tp) REVERT: G 25 ASN cc_start: 0.8914 (m-40) cc_final: 0.8675 (p0) REVERT: G 142 GLN cc_start: 0.9495 (mm110) cc_final: 0.8869 (mp10) REVERT: G 178 ILE cc_start: 0.9000 (mm) cc_final: 0.8586 (tp) REVERT: H 25 ASN cc_start: 0.8931 (m-40) cc_final: 0.8682 (p0) REVERT: H 142 GLN cc_start: 0.9411 (mp10) cc_final: 0.8718 (mp10) REVERT: H 178 ILE cc_start: 0.8994 (mm) cc_final: 0.8571 (tp) REVERT: I 25 ASN cc_start: 0.8911 (m-40) cc_final: 0.8673 (p0) REVERT: I 178 ILE cc_start: 0.9006 (mm) cc_final: 0.8587 (tp) REVERT: J 25 ASN cc_start: 0.8932 (m-40) cc_final: 0.8682 (p0) REVERT: J 178 ILE cc_start: 0.9010 (mm) cc_final: 0.8580 (tp) REVERT: K 25 ASN cc_start: 0.8926 (m-40) cc_final: 0.8677 (p0) REVERT: K 142 GLN cc_start: 0.9494 (mm110) cc_final: 0.8872 (mp10) REVERT: K 178 ILE cc_start: 0.8991 (mm) cc_final: 0.8546 (tp) REVERT: L 25 ASN cc_start: 0.8931 (m-40) cc_final: 0.8693 (p0) REVERT: L 178 ILE cc_start: 0.8998 (mm) cc_final: 0.8573 (tp) outliers start: 12 outliers final: 2 residues processed: 339 average time/residue: 0.1895 time to fit residues: 103.7970 Evaluate side-chains 323 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 321 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain D residue 71 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 346 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 19 optimal weight: 0.2980 chunk 233 optimal weight: 1.9990 chunk 322 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.078373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.054207 restraints weight = 140374.870| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 4.95 r_work: 0.2496 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2503 r_free = 0.2503 target_work(ls_wunit_k1) = 0.045 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2503 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31401 Z= 0.117 Angle : 0.526 10.204 42409 Z= 0.255 Chirality : 0.044 0.126 4645 Planarity : 0.003 0.033 5390 Dihedral : 3.333 12.316 4263 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.13 % Allowed : 14.81 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.14), residues: 3889 helix: 0.47 (0.12), residues: 2113 sheet: 0.23 (0.23), residues: 444 loop : -1.34 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 274 TYR 0.010 0.001 TYR F 217 PHE 0.005 0.001 PHE J 113 TRP 0.015 0.001 TRP F 198 HIS 0.001 0.000 HIS I 140 Details of bonding type rmsd covalent geometry : bond 0.00276 (31401) covalent geometry : angle 0.52610 (42409) hydrogen bonds : bond 0.03709 ( 1051) hydrogen bonds : angle 3.94005 ( 3063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 323 time to evaluate : 0.982 Fit side-chains revert: symmetry clash REVERT: A 25 ASN cc_start: 0.8932 (m-40) cc_final: 0.8700 (p0) REVERT: A 178 ILE cc_start: 0.9019 (mm) cc_final: 0.8590 (tp) REVERT: B 25 ASN cc_start: 0.8919 (m-40) cc_final: 0.8693 (p0) REVERT: B 142 GLN cc_start: 0.9481 (mm110) cc_final: 0.8857 (mp10) REVERT: B 178 ILE cc_start: 0.9008 (mm) cc_final: 0.8566 (tp) REVERT: C 25 ASN cc_start: 0.8915 (m-40) cc_final: 0.8692 (p0) REVERT: C 142 GLN cc_start: 0.9480 (mm110) cc_final: 0.8852 (mp10) REVERT: C 178 ILE cc_start: 0.9006 (mm) cc_final: 0.8555 (tp) REVERT: D 25 ASN cc_start: 0.8918 (m-40) cc_final: 0.8680 (p0) REVERT: D 178 ILE cc_start: 0.9018 (mm) cc_final: 0.8579 (tp) REVERT: E 25 ASN cc_start: 0.8928 (m-40) cc_final: 0.8702 (p0) REVERT: E 142 GLN cc_start: 0.9487 (mm110) cc_final: 0.8868 (mp10) REVERT: E 178 ILE cc_start: 0.9023 (mm) cc_final: 0.8593 (tp) REVERT: F 26 GLN cc_start: 0.9464 (mm-40) cc_final: 0.8510 (tp40) REVERT: F 30 GLN cc_start: 0.9166 (mt0) cc_final: 0.8656 (mp10) REVERT: F 178 ILE cc_start: 0.9028 (mm) cc_final: 0.8608 (tp) REVERT: G 25 ASN cc_start: 0.8934 (m-40) cc_final: 0.8705 (p0) REVERT: G 142 GLN cc_start: 0.9482 (mm110) cc_final: 0.8870 (mp10) REVERT: G 178 ILE cc_start: 0.9008 (mm) cc_final: 0.8579 (tp) REVERT: H 25 ASN cc_start: 0.8930 (m-40) cc_final: 0.8700 (p0) REVERT: H 178 ILE cc_start: 0.9028 (mm) cc_final: 0.8591 (tp) REVERT: I 25 ASN cc_start: 0.8919 (m-40) cc_final: 0.8691 (p0) REVERT: I 178 ILE cc_start: 0.9021 (mm) cc_final: 0.8591 (tp) REVERT: J 25 ASN cc_start: 0.8929 (m-40) cc_final: 0.8698 (p0) REVERT: J 178 ILE cc_start: 0.9027 (mm) cc_final: 0.8591 (tp) REVERT: K 25 ASN cc_start: 0.8923 (m-40) cc_final: 0.8697 (p0) REVERT: K 142 GLN cc_start: 0.9468 (mm110) cc_final: 0.8849 (mp10) REVERT: K 178 ILE cc_start: 0.9002 (mm) cc_final: 0.8555 (tp) REVERT: L 25 ASN cc_start: 0.8905 (m-40) cc_final: 0.8695 (p0) REVERT: L 178 ILE cc_start: 0.9014 (mm) cc_final: 0.8564 (tp) outliers start: 4 outliers final: 2 residues processed: 327 average time/residue: 0.1846 time to fit residues: 96.8542 Evaluate side-chains 321 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 319 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 71 SER Chi-restraints excluded: chain L residue 71 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 93 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 283 optimal weight: 0.7980 chunk 16 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 310 optimal weight: 0.0970 chunk 370 optimal weight: 0.9980 chunk 305 optimal weight: 0.4980 chunk 228 optimal weight: 7.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.080139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.056040 restraints weight = 138116.430| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 4.95 r_work: 0.2530 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2530 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31401 Z= 0.085 Angle : 0.516 10.882 42409 Z= 0.246 Chirality : 0.042 0.127 4645 Planarity : 0.003 0.033 5390 Dihedral : 3.199 13.465 4263 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.03 % Allowed : 14.56 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.14), residues: 3889 helix: 0.87 (0.12), residues: 2077 sheet: 0.37 (0.23), residues: 444 loop : -1.32 (0.16), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 274 TYR 0.009 0.001 TYR I 229 PHE 0.003 0.001 PHE F 184 TRP 0.021 0.001 TRP F 198 HIS 0.003 0.000 HIS F 196 Details of bonding type rmsd covalent geometry : bond 0.00202 (31401) covalent geometry : angle 0.51555 (42409) hydrogen bonds : bond 0.02940 ( 1051) hydrogen bonds : angle 3.80598 ( 3063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7778 Ramachandran restraints generated. 3889 Oldfield, 0 Emsley, 3889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 339 time to evaluate : 1.180 Fit side-chains REVERT: A 25 ASN cc_start: 0.8880 (m-40) cc_final: 0.8664 (p0) REVERT: A 142 GLN cc_start: 0.9081 (mp10) cc_final: 0.8614 (mp10) REVERT: A 178 ILE cc_start: 0.8993 (mm) cc_final: 0.8578 (tp) REVERT: B 25 ASN cc_start: 0.8881 (m-40) cc_final: 0.8668 (p0) REVERT: B 142 GLN cc_start: 0.9484 (mm110) cc_final: 0.8882 (mp10) REVERT: B 178 ILE cc_start: 0.8982 (mm) cc_final: 0.8562 (tp) REVERT: C 25 ASN cc_start: 0.8874 (m-40) cc_final: 0.8637 (p0) REVERT: C 142 GLN cc_start: 0.9492 (mm110) cc_final: 0.8883 (mp10) REVERT: C 178 ILE cc_start: 0.8970 (mm) cc_final: 0.8544 (tp) REVERT: D 25 ASN cc_start: 0.8863 (m-40) cc_final: 0.8635 (p0) REVERT: D 178 ILE cc_start: 0.8994 (mm) cc_final: 0.8584 (tp) REVERT: E 25 ASN cc_start: 0.8889 (m-40) cc_final: 0.8672 (p0) REVERT: E 142 GLN cc_start: 0.9482 (mm110) cc_final: 0.8881 (mp10) REVERT: E 178 ILE cc_start: 0.8993 (mm) cc_final: 0.8570 (tp) REVERT: F 26 GLN cc_start: 0.9466 (mm-40) cc_final: 0.8522 (tp40) REVERT: F 30 GLN cc_start: 0.9121 (mt0) cc_final: 0.8667 (mp10) REVERT: F 178 ILE cc_start: 0.8997 (mm) cc_final: 0.8601 (tp) REVERT: G 25 ASN cc_start: 0.8907 (m-40) cc_final: 0.8667 (p0) REVERT: G 142 GLN cc_start: 0.9499 (mm110) cc_final: 0.8902 (mp10) REVERT: G 178 ILE cc_start: 0.8991 (mm) cc_final: 0.8588 (tp) REVERT: H 25 ASN cc_start: 0.8888 (m-40) cc_final: 0.8673 (p0) REVERT: H 142 GLN cc_start: 0.9390 (mp10) cc_final: 0.8720 (mp10) REVERT: H 178 ILE cc_start: 0.8994 (mm) cc_final: 0.8581 (tp) REVERT: I 25 ASN cc_start: 0.8894 (m-40) cc_final: 0.8655 (p0) REVERT: I 178 ILE cc_start: 0.8993 (mm) cc_final: 0.8579 (tp) REVERT: J 25 ASN cc_start: 0.8885 (m-40) cc_final: 0.8672 (p0) REVERT: J 178 ILE cc_start: 0.9003 (mm) cc_final: 0.8596 (tp) REVERT: K 25 ASN cc_start: 0.8878 (m-40) cc_final: 0.8664 (p0) REVERT: K 142 GLN cc_start: 0.9473 (mm110) cc_final: 0.8874 (mp10) REVERT: K 178 ILE cc_start: 0.8972 (mm) cc_final: 0.8549 (tp) REVERT: L 25 ASN cc_start: 0.8880 (m-40) cc_final: 0.8654 (p0) REVERT: L 178 ILE cc_start: 0.8993 (mm) cc_final: 0.8576 (tp) outliers start: 1 outliers final: 0 residues processed: 340 average time/residue: 0.1708 time to fit residues: 92.6394 Evaluate side-chains 319 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 373 optimal weight: 6.9990 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 164 optimal weight: 0.0970 chunk 242 optimal weight: 8.9990 chunk 375 optimal weight: 9.9990 chunk 196 optimal weight: 4.9990 chunk 172 optimal weight: 7.9990 chunk 153 optimal weight: 0.8980 chunk 339 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.077804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.053415 restraints weight = 145039.872| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 5.02 r_work: 0.2483 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2483 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2486 r_free = 0.2486 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31401 Z= 0.144 Angle : 0.545 10.822 42409 Z= 0.264 Chirality : 0.044 0.138 4645 Planarity : 0.003 0.032 5390 Dihedral : 3.261 11.796 4263 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.06 % Allowed : 15.03 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.08 (0.14), residues: 3889 helix: 0.80 (0.12), residues: 2113 sheet: 0.45 (0.23), residues: 444 loop : -1.23 (0.17), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 274 TYR 0.012 0.001 TYR F 217 PHE 0.007 0.001 PHE J 113 TRP 0.016 0.001 TRP D 198 HIS 0.002 0.000 HIS E 196 Details of bonding type rmsd covalent geometry : bond 0.00338 (31401) covalent geometry : angle 0.54467 (42409) hydrogen bonds : bond 0.04127 ( 1051) hydrogen bonds : angle 3.95077 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7809.10 seconds wall clock time: 133 minutes 56.26 seconds (8036.26 seconds total)