Starting phenix.real_space_refine on Mon Dec 30 08:36:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atb_43829/12_2024/9atb_43829.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atb_43829/12_2024/9atb_43829.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9atb_43829/12_2024/9atb_43829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atb_43829/12_2024/9atb_43829.map" model { file = "/net/cci-nas-00/data/ceres_data/9atb_43829/12_2024/9atb_43829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atb_43829/12_2024/9atb_43829.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.004 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 38456 2.51 5 N 11286 2.21 5 O 13508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 216 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 63316 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "a" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "B" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "b" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "C" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "c" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "D" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "d" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "E" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "e" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "F" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "f" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "G" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "g" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "H" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "h" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "I" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "i" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "J" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "j" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "K" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Chain: "k" Number of atoms: 2878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 2878 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 4, 'TRANS': 390} Time building chain proxies: 27.24, per 1000 atoms: 0.43 Number of scatterers: 63316 At special positions: 0 Unit cell: (184.26, 184.26, 429.57, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 13508 8.00 N 11286 7.00 C 38456 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: 12.77 Conformation dependent library (CDL) restraints added in 6.7 seconds 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16236 Finding SS restraints... Secondary structure from input PDB file: 243 helices and 94 sheets defined 58.7% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.32 Creating SS restraints... Processing helix chain 'A' and resid 8 through 35 removed outlier: 4.290A pdb=" N LEU A 12 " --> pdb=" O ASN A 8 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASN A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR A 20 " --> pdb=" O ASN A 16 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER A 21 " --> pdb=" O ASN A 17 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 99 removed outlier: 3.705A pdb=" N GLN A 48 " --> pdb=" O ASP A 44 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA A 49 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLN A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ARG A 66 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 69 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLU A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY A 80 " --> pdb=" O GLN A 76 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLU A 94 " --> pdb=" O GLN A 90 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 130 removed outlier: 3.793A pdb=" N GLU A 115 " --> pdb=" O SER A 111 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 123 " --> pdb=" O ARG A 119 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASN A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 140 removed outlier: 3.831A pdb=" N ALA A 139 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LYS A 140 " --> pdb=" O VAL A 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 136 through 140' Processing helix chain 'A' and resid 186 through 195 removed outlier: 4.241A pdb=" N TYR A 190 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 218 removed outlier: 3.632A pdb=" N GLY A 215 " --> pdb=" O ASN A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 259 removed outlier: 3.903A pdb=" N SER A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N THR A 254 " --> pdb=" O THR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.672A pdb=" N ALA A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 305 removed outlier: 4.071A pdb=" N ILE A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 303 " --> pdb=" O LEU A 299 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 358 removed outlier: 3.966A pdb=" N ALA A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 324 " --> pdb=" O ASP A 320 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG A 334 " --> pdb=" O ALA A 330 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ILE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR A 344 " --> pdb=" O SER A 340 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASP A 358 " --> pdb=" O SER A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 388 removed outlier: 3.884A pdb=" N SER A 366 " --> pdb=" O ALA A 362 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR A 379 " --> pdb=" O GLN A 375 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 380 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A 381 " --> pdb=" O ALA A 377 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 394 removed outlier: 4.378A pdb=" N LEU A 393 " --> pdb=" O THR A 389 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER A 394 " --> pdb=" O GLN A 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 389 through 394' Processing helix chain 'a' and resid 8 through 35 removed outlier: 4.438A pdb=" N LEU a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N MET a 13 " --> pdb=" O SER a 9 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN a 17 " --> pdb=" O MET a 13 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU a 18 " --> pdb=" O THR a 14 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N SER a 23 " --> pdb=" O ASN a 19 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA a 24 " --> pdb=" O THR a 20 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ASN a 26 " --> pdb=" O GLN a 22 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 99 removed outlier: 3.633A pdb=" N GLN a 48 " --> pdb=" O ASP a 44 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA a 49 " --> pdb=" O ALA a 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS a 59 " --> pdb=" O THR a 55 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY a 60 " --> pdb=" O ALA a 56 " (cutoff:3.500A) Processing helix chain 'a' and resid 107 through 130 removed outlier: 4.310A pdb=" N SER a 111 " --> pdb=" O SER a 107 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE a 112 " --> pdb=" O ASP a 108 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE a 123 " --> pdb=" O ARG a 119 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN a 124 " --> pdb=" O LEU a 120 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR a 130 " --> pdb=" O VAL a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 195 removed outlier: 3.502A pdb=" N TYR a 190 " --> pdb=" O VAL a 186 " (cutoff:3.500A) Processing helix chain 'a' and resid 212 through 218 Processing helix chain 'a' and resid 248 through 258 Processing helix chain 'a' and resid 309 through 358 removed outlier: 3.759A pdb=" N LYS a 313 " --> pdb=" O ASN a 309 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N SER a 337 " --> pdb=" O ASN a 333 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL a 338 " --> pdb=" O ARG a 334 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE a 339 " --> pdb=" O PHE a 335 " (cutoff:3.500A) Processing helix chain 'a' and resid 361 through 387 removed outlier: 3.526A pdb=" N LEU a 374 " --> pdb=" O ARG a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 388 through 396 Processing helix chain 'B' and resid 8 through 35 removed outlier: 3.859A pdb=" N LEU B 12 " --> pdb=" O ASN B 8 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET B 13 " --> pdb=" O SER B 9 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N THR B 20 " --> pdb=" O ASN B 16 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ALA B 24 " --> pdb=" O THR B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 99 removed outlier: 4.027A pdb=" N GLN B 48 " --> pdb=" O ASP B 44 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B 49 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 57 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN B 63 " --> pdb=" O LYS B 59 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG B 66 " --> pdb=" O THR B 62 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN B 69 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLY B 80 " --> pdb=" O GLN B 76 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA B 81 " --> pdb=" O THR B 77 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLU B 84 " --> pdb=" O GLY B 80 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG B 91 " --> pdb=" O ASN B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 130 removed outlier: 3.650A pdb=" N GLU B 115 " --> pdb=" O SER B 111 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 123 " --> pdb=" O ARG B 119 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 128 " --> pdb=" O ASN B 124 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR B 130 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 140 removed outlier: 3.775A pdb=" N ALA B 139 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS B 140 " --> pdb=" O VAL B 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 136 through 140' Processing helix chain 'B' and resid 186 through 195 removed outlier: 4.055A pdb=" N TYR B 190 " --> pdb=" O VAL B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 218 Processing helix chain 'B' and resid 220 through 222 No H-bonds generated for 'chain 'B' and resid 220 through 222' Processing helix chain 'B' and resid 248 through 259 removed outlier: 3.950A pdb=" N SER B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR B 254 " --> pdb=" O THR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 279 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.884A pdb=" N ILE B 302 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N THR B 303 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N SER B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 355 removed outlier: 4.111A pdb=" N ASP B 315 " --> pdb=" O LEU B 311 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA B 316 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ALA B 317 " --> pdb=" O LYS B 313 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 324 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE B 339 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR B 344 " --> pdb=" O SER B 340 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 387 removed outlier: 4.032A pdb=" N SER B 366 " --> pdb=" O ALA B 362 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 380 " --> pdb=" O GLN B 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 381 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN B 386 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLN B 387 " --> pdb=" O ALA B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 396 removed outlier: 3.517A pdb=" N LEU B 396 " --> pdb=" O LEU B 393 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 35 removed outlier: 3.981A pdb=" N LEU b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET b 13 " --> pdb=" O SER b 9 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASN b 17 " --> pdb=" O MET b 13 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU b 18 " --> pdb=" O THR b 14 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN b 19 " --> pdb=" O GLN b 15 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER b 23 " --> pdb=" O ASN b 19 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA b 24 " --> pdb=" O THR b 20 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 99 removed outlier: 3.772A pdb=" N GLN b 48 " --> pdb=" O ASP b 44 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA b 49 " --> pdb=" O ALA b 45 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS b 59 " --> pdb=" O THR b 55 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY b 60 " --> pdb=" O ALA b 56 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU b 61 " --> pdb=" O ASN b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 130 removed outlier: 3.825A pdb=" N ILE b 112 " --> pdb=" O ASP b 108 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN b 124 " --> pdb=" O LEU b 120 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR b 130 " --> pdb=" O VAL b 126 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 195 removed outlier: 3.687A pdb=" N TYR b 190 " --> pdb=" O VAL b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 211 through 217 Processing helix chain 'b' and resid 248 through 259 Processing helix chain 'b' and resid 298 through 302 Processing helix chain 'b' and resid 309 through 358 removed outlier: 4.149A pdb=" N LYS b 313 " --> pdb=" O ASN b 309 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER b 337 " --> pdb=" O ASN b 333 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N VAL b 338 " --> pdb=" O ARG b 334 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE b 339 " --> pdb=" O PHE b 335 " (cutoff:3.500A) Processing helix chain 'b' and resid 360 through 387 removed outlier: 4.038A pdb=" N GLU b 364 " --> pdb=" O ASP b 360 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU b 374 " --> pdb=" O ARG b 370 " (cutoff:3.500A) Processing helix chain 'b' and resid 389 through 394 removed outlier: 4.440A pdb=" N LEU b 393 " --> pdb=" O THR b 389 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER b 394 " --> pdb=" O GLN b 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 389 through 394' Processing helix chain 'C' and resid 8 through 35 removed outlier: 3.750A pdb=" N LEU C 12 " --> pdb=" O ASN C 8 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 13 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ASN C 19 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N THR C 20 " --> pdb=" O ASN C 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N SER C 21 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 100 removed outlier: 3.755A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG C 66 " --> pdb=" O THR C 62 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ASN C 69 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLU C 79 " --> pdb=" O ALA C 75 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N GLU C 84 " --> pdb=" O GLY C 80 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N VAL C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 98 " --> pdb=" O GLU C 94 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C 99 " --> pdb=" O LEU C 95 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 130 removed outlier: 4.240A pdb=" N GLU C 115 " --> pdb=" O SER C 111 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 123 " --> pdb=" O ARG C 119 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 124 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR C 130 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 195 removed outlier: 4.224A pdb=" N TYR C 190 " --> pdb=" O VAL C 186 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 218 Processing helix chain 'C' and resid 248 through 259 removed outlier: 3.730A pdb=" N SER C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR C 254 " --> pdb=" O THR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.872A pdb=" N ILE C 302 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N THR C 303 " --> pdb=" O LEU C 299 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 304 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 358 removed outlier: 3.545A pdb=" N LYS C 313 " --> pdb=" O ASN C 309 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA C 316 " --> pdb=" O ALA C 312 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ALA C 317 " --> pdb=" O LYS C 313 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C 334 " --> pdb=" O ALA C 330 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE C 339 " --> pdb=" O PHE C 335 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 344 " --> pdb=" O SER C 340 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE C 356 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP C 358 " --> pdb=" O SER C 354 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 386 removed outlier: 3.759A pdb=" N SER C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 379 " --> pdb=" O GLN C 375 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER C 380 " --> pdb=" O GLN C 376 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 381 " --> pdb=" O ALA C 377 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 386 " --> pdb=" O LEU C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 389 through 394 removed outlier: 4.230A pdb=" N LEU C 393 " --> pdb=" O THR C 389 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER C 394 " --> pdb=" O GLN C 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 389 through 394' Processing helix chain 'c' and resid 8 through 35 removed outlier: 4.299A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET c 13 " --> pdb=" O SER c 9 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN c 17 " --> pdb=" O MET c 13 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU c 18 " --> pdb=" O THR c 14 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER c 23 " --> pdb=" O ASN c 19 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA c 24 " --> pdb=" O THR c 20 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN c 26 " --> pdb=" O GLN c 22 " (cutoff:3.500A) Processing helix chain 'c' and resid 44 through 99 removed outlier: 3.899A pdb=" N GLN c 48 " --> pdb=" O ASP c 44 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS c 59 " --> pdb=" O THR c 55 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N GLY c 60 " --> pdb=" O ALA c 56 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU c 61 " --> pdb=" O ASN c 57 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 130 removed outlier: 3.710A pdb=" N ILE c 112 " --> pdb=" O ASP c 108 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE c 123 " --> pdb=" O ARG c 119 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN c 124 " --> pdb=" O LEU c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 195 removed outlier: 3.712A pdb=" N TYR c 190 " --> pdb=" O VAL c 186 " (cutoff:3.500A) Processing helix chain 'c' and resid 212 through 218 Processing helix chain 'c' and resid 248 through 258 Processing helix chain 'c' and resid 298 through 302 Processing helix chain 'c' and resid 309 through 358 removed outlier: 3.844A pdb=" N LYS c 313 " --> pdb=" O ASN c 309 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER c 337 " --> pdb=" O ASN c 333 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N VAL c 338 " --> pdb=" O ARG c 334 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE c 339 " --> pdb=" O PHE c 335 " (cutoff:3.500A) Processing helix chain 'c' and resid 361 through 387 removed outlier: 3.715A pdb=" N LEU c 374 " --> pdb=" O ARG c 370 " (cutoff:3.500A) Processing helix chain 'c' and resid 389 through 395 removed outlier: 4.401A pdb=" N LEU c 393 " --> pdb=" O THR c 389 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER c 394 " --> pdb=" O GLN c 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 35 removed outlier: 4.158A pdb=" N LEU D 12 " --> pdb=" O ASN D 8 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 13 " --> pdb=" O SER D 9 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR D 20 " --> pdb=" O ASN D 16 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER D 21 " --> pdb=" O ASN D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 99 removed outlier: 3.575A pdb=" N GLN D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN D 57 " --> pdb=" O ARG D 53 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA D 68 " --> pdb=" O ALA D 64 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN D 69 " --> pdb=" O GLN D 65 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 79 " --> pdb=" O ALA D 75 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA D 81 " --> pdb=" O THR D 77 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLU D 84 " --> pdb=" O GLY D 80 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 94 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLN D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 130 removed outlier: 3.695A pdb=" N GLU D 115 " --> pdb=" O SER D 111 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE D 123 " --> pdb=" O ARG D 119 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASN D 124 " --> pdb=" O LEU D 120 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU D 128 " --> pdb=" O ASN D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 140 removed outlier: 3.896A pdb=" N ALA D 139 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LYS D 140 " --> pdb=" O VAL D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 136 through 140' Processing helix chain 'D' and resid 186 through 195 removed outlier: 4.062A pdb=" N TYR D 190 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLN D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 218 removed outlier: 3.813A pdb=" N GLY D 215 " --> pdb=" O ASN D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 259 removed outlier: 3.709A pdb=" N SER D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 254 " --> pdb=" O THR D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 removed outlier: 3.514A pdb=" N ALA D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 305 removed outlier: 3.998A pdb=" N ILE D 302 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR D 303 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 304 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 358 removed outlier: 3.611A pdb=" N ASP D 315 " --> pdb=" O LEU D 311 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA D 316 " --> pdb=" O ALA D 312 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ALA D 317 " --> pdb=" O LYS D 313 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU D 324 " --> pdb=" O ASP D 320 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 334 " --> pdb=" O ALA D 330 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE D 339 " --> pdb=" O PHE D 335 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER D 340 " --> pdb=" O ASP D 336 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR D 344 " --> pdb=" O SER D 340 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL D 346 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE D 356 " --> pdb=" O SER D 352 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN D 357 " --> pdb=" O ARG D 353 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP D 358 " --> pdb=" O SER D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 386 removed outlier: 3.832A pdb=" N SER D 366 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE D 373 " --> pdb=" O THR D 369 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER D 380 " --> pdb=" O GLN D 376 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL D 381 " --> pdb=" O ALA D 377 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 396 removed outlier: 3.920A pdb=" N ASN D 391 " --> pdb=" O THR D 388 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 396 " --> pdb=" O LEU D 393 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 35 removed outlier: 4.416A pdb=" N LEU d 12 " --> pdb=" O ASN d 8 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN d 17 " --> pdb=" O MET d 13 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU d 18 " --> pdb=" O THR d 14 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN d 19 " --> pdb=" O GLN d 15 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER d 23 " --> pdb=" O ASN d 19 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA d 24 " --> pdb=" O THR d 20 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ASN d 26 " --> pdb=" O GLN d 22 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 99 removed outlier: 4.047A pdb=" N ALA d 49 " --> pdb=" O ALA d 45 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS d 59 " --> pdb=" O THR d 55 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY d 60 " --> pdb=" O ALA d 56 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU d 61 " --> pdb=" O ASN d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 105 through 130 removed outlier: 3.618A pdb=" N LEU d 109 " --> pdb=" O SER d 105 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLN d 110 " --> pdb=" O ALA d 106 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N SER d 111 " --> pdb=" O SER d 107 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE d 112 " --> pdb=" O ASP d 108 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE d 123 " --> pdb=" O ARG d 119 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASN d 124 " --> pdb=" O LEU d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 195 removed outlier: 3.571A pdb=" N TYR d 190 " --> pdb=" O VAL d 186 " (cutoff:3.500A) Processing helix chain 'd' and resid 211 through 218 removed outlier: 3.521A pdb=" N GLY d 215 " --> pdb=" O ASN d 211 " (cutoff:3.500A) Processing helix chain 'd' and resid 248 through 258 Processing helix chain 'd' and resid 275 through 279 removed outlier: 3.564A pdb=" N SER d 278 " --> pdb=" O ASP d 275 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA d 279 " --> pdb=" O PRO d 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 275 through 279' Processing helix chain 'd' and resid 298 through 302 removed outlier: 3.726A pdb=" N ILE d 302 " --> pdb=" O LEU d 299 " (cutoff:3.500A) Processing helix chain 'd' and resid 309 through 358 removed outlier: 3.791A pdb=" N LYS d 313 " --> pdb=" O ASN d 309 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER d 337 " --> pdb=" O ASN d 333 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL d 338 " --> pdb=" O ARG d 334 " (cutoff:3.500A) Processing helix chain 'd' and resid 361 through 387 removed outlier: 3.751A pdb=" N LEU d 374 " --> pdb=" O ARG d 370 " (cutoff:3.500A) Processing helix chain 'd' and resid 388 through 396 removed outlier: 3.704A pdb=" N ASN d 391 " --> pdb=" O THR d 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 35 removed outlier: 3.971A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN E 19 " --> pdb=" O GLN E 15 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N THR E 20 " --> pdb=" O ASN E 16 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER E 21 " --> pdb=" O ASN E 17 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA E 24 " --> pdb=" O THR E 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER E 33 " --> pdb=" O ILE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 99 removed outlier: 3.704A pdb=" N GLN E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA E 49 " --> pdb=" O ALA E 45 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN E 63 " --> pdb=" O LYS E 59 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA E 68 " --> pdb=" O ALA E 64 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN E 69 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N GLY E 80 " --> pdb=" O GLN E 76 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU E 84 " --> pdb=" O GLY E 80 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU E 94 " --> pdb=" O GLN E 90 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 130 removed outlier: 4.086A pdb=" N GLU E 115 " --> pdb=" O SER E 111 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE E 123 " --> pdb=" O ARG E 119 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN E 124 " --> pdb=" O LEU E 120 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU E 128 " --> pdb=" O ASN E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 195 removed outlier: 4.107A pdb=" N TYR E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 218 removed outlier: 4.043A pdb=" N GLY E 215 " --> pdb=" O ASN E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 259 removed outlier: 3.552A pdb=" N VAL E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N SER E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR E 254 " --> pdb=" O THR E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 275 through 279 removed outlier: 4.005A pdb=" N ALA E 279 " --> pdb=" O PRO E 276 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 305 removed outlier: 4.024A pdb=" N ILE E 302 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER E 304 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 358 removed outlier: 4.064A pdb=" N ALA E 316 " --> pdb=" O ALA E 312 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA E 317 " --> pdb=" O LYS E 313 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU E 324 " --> pdb=" O ASP E 320 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG E 334 " --> pdb=" O ALA E 330 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE E 339 " --> pdb=" O PHE E 335 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER E 340 " --> pdb=" O ASP E 336 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR E 344 " --> pdb=" O SER E 340 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL E 346 " --> pdb=" O LEU E 342 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE E 356 " --> pdb=" O SER E 352 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN E 357 " --> pdb=" O ARG E 353 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP E 358 " --> pdb=" O SER E 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 387 removed outlier: 3.832A pdb=" N THR E 379 " --> pdb=" O GLN E 375 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER E 380 " --> pdb=" O GLN E 376 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL E 381 " --> pdb=" O ALA E 377 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 386 " --> pdb=" O LEU E 382 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 396 Processing helix chain 'e' and resid 9 through 35 removed outlier: 3.510A pdb=" N MET e 13 " --> pdb=" O SER e 9 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN e 17 " --> pdb=" O MET e 13 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU e 18 " --> pdb=" O THR e 14 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER e 23 " --> pdb=" O ASN e 19 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA e 24 " --> pdb=" O THR e 20 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN e 26 " --> pdb=" O GLN e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 100 removed outlier: 3.630A pdb=" N GLN e 48 " --> pdb=" O ASP e 44 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA e 49 " --> pdb=" O ALA e 45 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS e 59 " --> pdb=" O THR e 55 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLY e 60 " --> pdb=" O ALA e 56 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU e 61 " --> pdb=" O ASN e 57 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA e 100 " --> pdb=" O SER e 96 " (cutoff:3.500A) Processing helix chain 'e' and resid 105 through 130 removed outlier: 3.658A pdb=" N LEU e 109 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN e 110 " --> pdb=" O ALA e 106 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER e 111 " --> pdb=" O SER e 107 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE e 112 " --> pdb=" O ASP e 108 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ILE e 123 " --> pdb=" O ARG e 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN e 124 " --> pdb=" O LEU e 120 " (cutoff:3.500A) Processing helix chain 'e' and resid 186 through 195 Processing helix chain 'e' and resid 212 through 218 Processing helix chain 'e' and resid 248 through 258 Processing helix chain 'e' and resid 275 through 279 removed outlier: 3.672A pdb=" N ALA e 279 " --> pdb=" O PRO e 276 " (cutoff:3.500A) Processing helix chain 'e' and resid 298 through 302 removed outlier: 3.708A pdb=" N ILE e 302 " --> pdb=" O LEU e 299 " (cutoff:3.500A) Processing helix chain 'e' and resid 309 through 358 removed outlier: 3.811A pdb=" N LYS e 313 " --> pdb=" O ASN e 309 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER e 337 " --> pdb=" O ASN e 333 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL e 338 " --> pdb=" O ARG e 334 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE e 339 " --> pdb=" O PHE e 335 " (cutoff:3.500A) Processing helix chain 'e' and resid 361 through 387 removed outlier: 3.966A pdb=" N LEU e 374 " --> pdb=" O ARG e 370 " (cutoff:3.500A) Processing helix chain 'e' and resid 388 through 395 removed outlier: 3.559A pdb=" N ASN e 391 " --> pdb=" O THR e 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 35 removed outlier: 3.841A pdb=" N LEU F 12 " --> pdb=" O ASN F 8 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ASN F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR F 20 " --> pdb=" O ASN F 16 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER F 21 " --> pdb=" O ASN F 17 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 99 removed outlier: 3.942A pdb=" N GLN F 48 " --> pdb=" O ASP F 44 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA F 49 " --> pdb=" O ALA F 45 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLN F 63 " --> pdb=" O LYS F 59 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG F 66 " --> pdb=" O THR F 62 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA F 68 " --> pdb=" O ALA F 64 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN F 69 " --> pdb=" O GLN F 65 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU F 79 " --> pdb=" O ALA F 75 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY F 80 " --> pdb=" O GLN F 76 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA F 81 " --> pdb=" O THR F 77 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N GLU F 84 " --> pdb=" O GLY F 80 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N VAL F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLU F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 130 removed outlier: 3.864A pdb=" N LEU F 109 " --> pdb=" O SER F 105 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU F 115 " --> pdb=" O SER F 111 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE F 123 " --> pdb=" O ARG F 119 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN F 124 " --> pdb=" O LEU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 186 through 195 removed outlier: 4.207A pdb=" N TYR F 190 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 218 removed outlier: 3.551A pdb=" N GLY F 215 " --> pdb=" O ASN F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 222 No H-bonds generated for 'chain 'F' and resid 220 through 222' Processing helix chain 'F' and resid 249 through 259 removed outlier: 3.978A pdb=" N SER F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 305 removed outlier: 3.759A pdb=" N ILE F 302 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR F 303 " --> pdb=" O LEU F 299 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N SER F 304 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 309 through 358 removed outlier: 4.417A pdb=" N ASP F 315 " --> pdb=" O LEU F 311 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA F 316 " --> pdb=" O ALA F 312 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA F 317 " --> pdb=" O LYS F 313 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU F 324 " --> pdb=" O ASP F 320 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG F 334 " --> pdb=" O ALA F 330 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE F 339 " --> pdb=" O PHE F 335 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 340 " --> pdb=" O ASP F 336 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR F 344 " --> pdb=" O SER F 340 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL F 346 " --> pdb=" O LEU F 342 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR F 347 " --> pdb=" O GLY F 343 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ILE F 356 " --> pdb=" O SER F 352 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLN F 357 " --> pdb=" O ARG F 353 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP F 358 " --> pdb=" O SER F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 363 through 387 removed outlier: 3.823A pdb=" N THR F 379 " --> pdb=" O GLN F 375 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N SER F 380 " --> pdb=" O GLN F 376 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL F 381 " --> pdb=" O ALA F 377 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN F 387 " --> pdb=" O ALA F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 394 removed outlier: 4.102A pdb=" N LEU F 393 " --> pdb=" O THR F 389 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER F 394 " --> pdb=" O GLN F 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 389 through 394' Processing helix chain 'f' and resid 8 through 35 removed outlier: 3.950A pdb=" N LEU f 12 " --> pdb=" O ASN f 8 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN f 17 " --> pdb=" O MET f 13 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU f 18 " --> pdb=" O THR f 14 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN f 19 " --> pdb=" O GLN f 15 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER f 23 " --> pdb=" O ASN f 19 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA f 24 " --> pdb=" O THR f 20 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN f 26 " --> pdb=" O GLN f 22 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 99 removed outlier: 4.005A pdb=" N ALA f 49 " --> pdb=" O ALA f 45 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS f 59 " --> pdb=" O THR f 55 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLY f 60 " --> pdb=" O ALA f 56 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU f 61 " --> pdb=" O ASN f 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 105 through 130 removed outlier: 4.181A pdb=" N GLN f 110 " --> pdb=" O ALA f 106 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N SER f 111 " --> pdb=" O SER f 107 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE f 112 " --> pdb=" O ASP f 108 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE f 123 " --> pdb=" O ARG f 119 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ASN f 124 " --> pdb=" O LEU f 120 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR f 130 " --> pdb=" O VAL f 126 " (cutoff:3.500A) Processing helix chain 'f' and resid 186 through 195 removed outlier: 3.572A pdb=" N TYR f 190 " --> pdb=" O VAL f 186 " (cutoff:3.500A) Processing helix chain 'f' and resid 211 through 218 removed outlier: 3.662A pdb=" N GLY f 215 " --> pdb=" O ASN f 211 " (cutoff:3.500A) Processing helix chain 'f' and resid 248 through 258 Processing helix chain 'f' and resid 275 through 279 removed outlier: 3.704A pdb=" N ALA f 279 " --> pdb=" O PRO f 276 " (cutoff:3.500A) Processing helix chain 'f' and resid 298 through 302 removed outlier: 3.537A pdb=" N ILE f 302 " --> pdb=" O LEU f 299 " (cutoff:3.500A) Processing helix chain 'f' and resid 309 through 358 removed outlier: 3.725A pdb=" N LYS f 313 " --> pdb=" O ASN f 309 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER f 337 " --> pdb=" O ASN f 333 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL f 338 " --> pdb=" O ARG f 334 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE f 339 " --> pdb=" O PHE f 335 " (cutoff:3.500A) Processing helix chain 'f' and resid 361 through 387 Processing helix chain 'f' and resid 389 through 394 removed outlier: 3.967A pdb=" N LEU f 393 " --> pdb=" O THR f 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 35 removed outlier: 3.850A pdb=" N ASN G 19 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR G 20 " --> pdb=" O ASN G 16 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER G 21 " --> pdb=" O ASN G 17 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU G 32 " --> pdb=" O ALA G 28 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 99 removed outlier: 4.000A pdb=" N ALA G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN G 57 " --> pdb=" O ARG G 53 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG G 66 " --> pdb=" O THR G 62 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASN G 69 " --> pdb=" O GLN G 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY G 80 " --> pdb=" O GLN G 76 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA G 81 " --> pdb=" O THR G 77 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU G 84 " --> pdb=" O GLY G 80 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU G 94 " --> pdb=" O GLN G 90 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 130 removed outlier: 4.262A pdb=" N GLU G 115 " --> pdb=" O SER G 111 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE G 123 " --> pdb=" O ARG G 119 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN G 124 " --> pdb=" O LEU G 120 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR G 130 " --> pdb=" O VAL G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 195 removed outlier: 4.147A pdb=" N TYR G 190 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN G 191 " --> pdb=" O ALA G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 218 removed outlier: 3.801A pdb=" N GLY G 215 " --> pdb=" O ASN G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 259 removed outlier: 3.505A pdb=" N VAL G 252 " --> pdb=" O SER G 248 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR G 254 " --> pdb=" O THR G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 275 through 279 removed outlier: 3.799A pdb=" N ALA G 279 " --> pdb=" O PRO G 276 " (cutoff:3.500A) Processing helix chain 'G' and resid 299 through 305 removed outlier: 3.732A pdb=" N THR G 303 " --> pdb=" O LEU G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 309 through 358 removed outlier: 4.055A pdb=" N ASP G 315 " --> pdb=" O LEU G 311 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA G 316 " --> pdb=" O ALA G 312 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA G 317 " --> pdb=" O LYS G 313 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU G 324 " --> pdb=" O ASP G 320 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG G 334 " --> pdb=" O ALA G 330 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 339 " --> pdb=" O PHE G 335 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER G 340 " --> pdb=" O ASP G 336 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR G 344 " --> pdb=" O SER G 340 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL G 346 " --> pdb=" O LEU G 342 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR G 347 " --> pdb=" O GLY G 343 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE G 356 " --> pdb=" O SER G 352 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP G 358 " --> pdb=" O SER G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 362 through 386 removed outlier: 4.220A pdb=" N SER G 366 " --> pdb=" O ALA G 362 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR G 379 " --> pdb=" O GLN G 375 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER G 380 " --> pdb=" O GLN G 376 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL G 381 " --> pdb=" O ALA G 377 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN G 386 " --> pdb=" O LEU G 382 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 396 removed outlier: 3.878A pdb=" N ASN G 391 " --> pdb=" O THR G 388 " (cutoff:3.500A) Processing helix chain 'g' and resid 9 through 35 removed outlier: 3.569A pdb=" N ASN g 17 " --> pdb=" O MET g 13 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER g 23 " --> pdb=" O ASN g 19 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA g 24 " --> pdb=" O THR g 20 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN g 26 " --> pdb=" O GLN g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 44 through 99 removed outlier: 3.693A pdb=" N GLN g 48 " --> pdb=" O ASP g 44 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ALA g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS g 59 " --> pdb=" O THR g 55 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY g 60 " --> pdb=" O ALA g 56 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU g 61 " --> pdb=" O ASN g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 107 through 130 removed outlier: 4.327A pdb=" N SER g 111 " --> pdb=" O SER g 107 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE g 112 " --> pdb=" O ASP g 108 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE g 123 " --> pdb=" O ARG g 119 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASN g 124 " --> pdb=" O LEU g 120 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR g 130 " --> pdb=" O VAL g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 186 through 195 Processing helix chain 'g' and resid 212 through 218 Processing helix chain 'g' and resid 248 through 259 Processing helix chain 'g' and resid 275 through 279 removed outlier: 3.789A pdb=" N ALA g 279 " --> pdb=" O PRO g 276 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 302 removed outlier: 3.637A pdb=" N ILE g 302 " --> pdb=" O LEU g 299 " (cutoff:3.500A) Processing helix chain 'g' and resid 309 through 358 removed outlier: 3.764A pdb=" N LYS g 313 " --> pdb=" O ASN g 309 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER g 337 " --> pdb=" O ASN g 333 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL g 338 " --> pdb=" O ARG g 334 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE g 339 " --> pdb=" O PHE g 335 " (cutoff:3.500A) Processing helix chain 'g' and resid 361 through 387 removed outlier: 3.550A pdb=" N LEU g 374 " --> pdb=" O ARG g 370 " (cutoff:3.500A) Processing helix chain 'g' and resid 390 through 395 removed outlier: 4.145A pdb=" N SER g 394 " --> pdb=" O GLN g 390 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU g 395 " --> pdb=" O ASN g 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 390 through 395' Processing helix chain 'H' and resid 8 through 35 removed outlier: 4.102A pdb=" N LEU H 12 " --> pdb=" O ASN H 8 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASN H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR H 20 " --> pdb=" O ASN H 16 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER H 21 " --> pdb=" O ASN H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 99 removed outlier: 3.804A pdb=" N GLN H 48 " --> pdb=" O ASP H 44 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLN H 63 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN H 69 " --> pdb=" O GLN H 65 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU H 79 " --> pdb=" O ALA H 75 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY H 80 " --> pdb=" O GLN H 76 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA H 81 " --> pdb=" O THR H 77 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU H 84 " --> pdb=" O GLY H 80 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU H 94 " --> pdb=" O GLN H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 130 removed outlier: 3.652A pdb=" N ARG H 119 " --> pdb=" O GLU H 115 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN H 124 " --> pdb=" O LEU H 120 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU H 128 " --> pdb=" O ASN H 124 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR H 130 " --> pdb=" O VAL H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 195 removed outlier: 4.113A pdb=" N GLN H 191 " --> pdb=" O ALA H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 217 removed outlier: 3.687A pdb=" N GLY H 215 " --> pdb=" O ASN H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 259 removed outlier: 3.505A pdb=" N VAL H 252 " --> pdb=" O SER H 248 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SER H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR H 254 " --> pdb=" O THR H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 303 removed outlier: 3.723A pdb=" N ILE H 302 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR H 303 " --> pdb=" O LEU H 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 298 through 303' Processing helix chain 'H' and resid 309 through 358 removed outlier: 4.032A pdb=" N ASP H 315 " --> pdb=" O LEU H 311 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA H 316 " --> pdb=" O ALA H 312 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA H 317 " --> pdb=" O LYS H 313 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU H 324 " --> pdb=" O ASP H 320 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE H 339 " --> pdb=" O PHE H 335 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N SER H 340 " --> pdb=" O ASP H 336 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR H 344 " --> pdb=" O SER H 340 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL H 346 " --> pdb=" O LEU H 342 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR H 347 " --> pdb=" O GLY H 343 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE H 356 " --> pdb=" O SER H 352 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN H 357 " --> pdb=" O ARG H 353 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP H 358 " --> pdb=" O SER H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 362 through 386 removed outlier: 4.055A pdb=" N SER H 366 " --> pdb=" O ALA H 362 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER H 380 " --> pdb=" O GLN H 376 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN H 386 " --> pdb=" O LEU H 382 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 396 removed outlier: 3.731A pdb=" N ASN H 391 " --> pdb=" O THR H 388 " (cutoff:3.500A) Processing helix chain 'h' and resid 9 through 35 removed outlier: 3.648A pdb=" N ASN h 17 " --> pdb=" O MET h 13 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER h 23 " --> pdb=" O ASN h 19 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA h 24 " --> pdb=" O THR h 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASN h 26 " --> pdb=" O GLN h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 44 through 99 removed outlier: 4.018A pdb=" N ALA h 49 " --> pdb=" O ALA h 45 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS h 59 " --> pdb=" O THR h 55 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY h 60 " --> pdb=" O ALA h 56 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU h 61 " --> pdb=" O ASN h 57 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 130 removed outlier: 3.699A pdb=" N ILE h 112 " --> pdb=" O ASP h 108 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE h 123 " --> pdb=" O ARG h 119 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN h 124 " --> pdb=" O LEU h 120 " (cutoff:3.500A) Processing helix chain 'h' and resid 186 through 195 removed outlier: 3.677A pdb=" N TYR h 190 " --> pdb=" O VAL h 186 " (cutoff:3.500A) Processing helix chain 'h' and resid 212 through 218 Processing helix chain 'h' and resid 248 through 258 Processing helix chain 'h' and resid 298 through 302 Processing helix chain 'h' and resid 309 through 358 removed outlier: 3.738A pdb=" N LYS h 313 " --> pdb=" O ASN h 309 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER h 337 " --> pdb=" O ASN h 333 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N VAL h 338 " --> pdb=" O ARG h 334 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE h 339 " --> pdb=" O PHE h 335 " (cutoff:3.500A) Processing helix chain 'h' and resid 361 through 387 Processing helix chain 'h' and resid 390 through 395 removed outlier: 4.305A pdb=" N SER h 394 " --> pdb=" O GLN h 390 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU h 395 " --> pdb=" O ASN h 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 390 through 395' Processing helix chain 'I' and resid 9 through 35 removed outlier: 3.511A pdb=" N MET I 13 " --> pdb=" O SER I 9 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN I 19 " --> pdb=" O GLN I 15 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR I 20 " --> pdb=" O ASN I 16 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N SER I 21 " --> pdb=" O ASN I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 100 removed outlier: 3.993A pdb=" N GLN I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ALA I 49 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE I 50 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN I 63 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG I 66 " --> pdb=" O THR I 62 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 68 " --> pdb=" O ALA I 64 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN I 69 " --> pdb=" O GLN I 65 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY I 80 " --> pdb=" O GLN I 76 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU I 84 " --> pdb=" O GLY I 80 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL I 85 " --> pdb=" O ALA I 81 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU I 94 " --> pdb=" O GLN I 90 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA I 99 " --> pdb=" O LEU I 95 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA I 100 " --> pdb=" O SER I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 130 removed outlier: 4.438A pdb=" N GLU I 115 " --> pdb=" O SER I 111 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE I 123 " --> pdb=" O ARG I 119 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ASN I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 186 through 195 removed outlier: 4.247A pdb=" N TYR I 190 " --> pdb=" O VAL I 186 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLN I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA I 192 " --> pdb=" O ALA I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 217 Processing helix chain 'I' and resid 220 through 222 No H-bonds generated for 'chain 'I' and resid 220 through 222' Processing helix chain 'I' and resid 248 through 259 removed outlier: 3.687A pdb=" N SER I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR I 254 " --> pdb=" O THR I 250 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 305 removed outlier: 3.654A pdb=" N ILE I 302 " --> pdb=" O GLN I 298 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR I 303 " --> pdb=" O LEU I 299 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER I 304 " --> pdb=" O SER I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 358 removed outlier: 4.016A pdb=" N ASP I 315 " --> pdb=" O LEU I 311 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ALA I 316 " --> pdb=" O ALA I 312 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA I 317 " --> pdb=" O LYS I 313 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU I 324 " --> pdb=" O ASP I 320 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE I 339 " --> pdb=" O PHE I 335 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER I 340 " --> pdb=" O ASP I 336 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR I 344 " --> pdb=" O SER I 340 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR I 347 " --> pdb=" O GLY I 343 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ILE I 356 " --> pdb=" O SER I 352 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN I 357 " --> pdb=" O ARG I 353 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASP I 358 " --> pdb=" O SER I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 386 removed outlier: 4.238A pdb=" N SER I 366 " --> pdb=" O ALA I 362 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR I 379 " --> pdb=" O GLN I 375 " (cutoff:3.500A) Processing helix chain 'I' and resid 387 through 388 No H-bonds generated for 'chain 'I' and resid 387 through 388' Processing helix chain 'I' and resid 389 through 396 Processing helix chain 'i' and resid 9 through 35 removed outlier: 3.585A pdb=" N MET i 13 " --> pdb=" O SER i 9 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASN i 17 " --> pdb=" O MET i 13 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU i 18 " --> pdb=" O THR i 14 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER i 23 " --> pdb=" O ASN i 19 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ALA i 24 " --> pdb=" O THR i 20 " (cutoff:3.500A) Processing helix chain 'i' and resid 45 through 99 removed outlier: 4.289A pdb=" N ALA i 49 " --> pdb=" O ALA i 45 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS i 59 " --> pdb=" O THR i 55 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLY i 60 " --> pdb=" O ALA i 56 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU i 61 " --> pdb=" O ASN i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 130 removed outlier: 3.681A pdb=" N ILE i 112 " --> pdb=" O ASP i 108 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN i 124 " --> pdb=" O LEU i 120 " (cutoff:3.500A) Processing helix chain 'i' and resid 186 through 195 removed outlier: 3.542A pdb=" N TYR i 190 " --> pdb=" O VAL i 186 " (cutoff:3.500A) Processing helix chain 'i' and resid 211 through 218 Processing helix chain 'i' and resid 248 through 258 Processing helix chain 'i' and resid 275 through 279 removed outlier: 3.517A pdb=" N SER i 278 " --> pdb=" O ASP i 275 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ALA i 279 " --> pdb=" O PRO i 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 275 through 279' Processing helix chain 'i' and resid 298 through 302 removed outlier: 3.629A pdb=" N ILE i 302 " --> pdb=" O LEU i 299 " (cutoff:3.500A) Processing helix chain 'i' and resid 309 through 358 removed outlier: 3.885A pdb=" N LYS i 313 " --> pdb=" O ASN i 309 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER i 337 " --> pdb=" O ASN i 333 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL i 338 " --> pdb=" O ARG i 334 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE i 339 " --> pdb=" O PHE i 335 " (cutoff:3.500A) Processing helix chain 'i' and resid 361 through 387 Processing helix chain 'i' and resid 390 through 396 removed outlier: 4.260A pdb=" N SER i 394 " --> pdb=" O GLN i 390 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU i 395 " --> pdb=" O ASN i 391 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU i 396 " --> pdb=" O VAL i 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 390 through 396' Processing helix chain 'J' and resid 9 through 35 removed outlier: 3.966A pdb=" N ASN J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N THR J 20 " --> pdb=" O ASN J 16 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER J 21 " --> pdb=" O ASN J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 100 removed outlier: 4.259A pdb=" N ALA J 49 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN J 57 " --> pdb=" O ARG J 53 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN J 63 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA J 68 " --> pdb=" O ALA J 64 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN J 69 " --> pdb=" O GLN J 65 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU J 79 " --> pdb=" O ALA J 75 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY J 80 " --> pdb=" O GLN J 76 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA J 81 " --> pdb=" O THR J 77 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU J 84 " --> pdb=" O GLY J 80 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL J 85 " --> pdb=" O ALA J 81 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU J 94 " --> pdb=" O GLN J 90 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA J 99 " --> pdb=" O LEU J 95 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 130 removed outlier: 3.648A pdb=" N GLU J 115 " --> pdb=" O SER J 111 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE J 123 " --> pdb=" O ARG J 119 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASN J 124 " --> pdb=" O LEU J 120 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR J 130 " --> pdb=" O VAL J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 195 removed outlier: 4.004A pdb=" N GLN J 191 " --> pdb=" O ALA J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 218 Processing helix chain 'J' and resid 220 through 222 No H-bonds generated for 'chain 'J' and resid 220 through 222' Processing helix chain 'J' and resid 248 through 259 removed outlier: 3.727A pdb=" N SER J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR J 254 " --> pdb=" O THR J 250 " (cutoff:3.500A) Processing helix chain 'J' and resid 275 through 279 Processing helix chain 'J' and resid 298 through 305 removed outlier: 3.578A pdb=" N ILE J 302 " --> pdb=" O GLN J 298 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR J 303 " --> pdb=" O LEU J 299 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 358 removed outlier: 4.086A pdb=" N ASP J 315 " --> pdb=" O LEU J 311 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA J 316 " --> pdb=" O ALA J 312 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA J 317 " --> pdb=" O LYS J 313 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG J 334 " --> pdb=" O ALA J 330 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE J 339 " --> pdb=" O PHE J 335 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER J 340 " --> pdb=" O ASP J 336 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N THR J 347 " --> pdb=" O GLY J 343 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ILE J 356 " --> pdb=" O SER J 352 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN J 357 " --> pdb=" O ARG J 353 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP J 358 " --> pdb=" O SER J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 362 through 386 removed outlier: 3.671A pdb=" N SER J 366 " --> pdb=" O ALA J 362 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR J 379 " --> pdb=" O GLN J 375 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER J 380 " --> pdb=" O GLN J 376 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL J 381 " --> pdb=" O ALA J 377 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN J 386 " --> pdb=" O LEU J 382 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 396 removed outlier: 3.562A pdb=" N LEU J 393 " --> pdb=" O GLN J 390 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 35 removed outlier: 4.213A pdb=" N LEU j 12 " --> pdb=" O ASN j 8 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET j 13 " --> pdb=" O SER j 9 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN j 17 " --> pdb=" O MET j 13 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU j 18 " --> pdb=" O THR j 14 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN j 19 " --> pdb=" O GLN j 15 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER j 23 " --> pdb=" O ASN j 19 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ALA j 24 " --> pdb=" O THR j 20 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 100 removed outlier: 3.827A pdb=" N LYS j 59 " --> pdb=" O THR j 55 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLY j 60 " --> pdb=" O ALA j 56 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU j 61 " --> pdb=" O ASN j 57 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ALA j 100 " --> pdb=" O SER j 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 105 through 130 removed outlier: 3.843A pdb=" N LEU j 109 " --> pdb=" O SER j 105 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N GLN j 110 " --> pdb=" O ALA j 106 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER j 111 " --> pdb=" O SER j 107 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE j 112 " --> pdb=" O ASP j 108 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE j 123 " --> pdb=" O ARG j 119 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN j 124 " --> pdb=" O LEU j 120 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR j 130 " --> pdb=" O VAL j 126 " (cutoff:3.500A) Processing helix chain 'j' and resid 186 through 195 removed outlier: 3.611A pdb=" N TYR j 190 " --> pdb=" O VAL j 186 " (cutoff:3.500A) Processing helix chain 'j' and resid 211 through 218 removed outlier: 3.632A pdb=" N GLY j 218 " --> pdb=" O ALA j 214 " (cutoff:3.500A) Processing helix chain 'j' and resid 248 through 258 Processing helix chain 'j' and resid 275 through 279 removed outlier: 3.798A pdb=" N ALA j 279 " --> pdb=" O PRO j 276 " (cutoff:3.500A) Processing helix chain 'j' and resid 298 through 302 removed outlier: 3.558A pdb=" N ILE j 302 " --> pdb=" O LEU j 299 " (cutoff:3.500A) Processing helix chain 'j' and resid 309 through 358 removed outlier: 3.898A pdb=" N LYS j 313 " --> pdb=" O ASN j 309 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER j 337 " --> pdb=" O ASN j 333 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL j 338 " --> pdb=" O ARG j 334 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ILE j 339 " --> pdb=" O PHE j 335 " (cutoff:3.500A) Processing helix chain 'j' and resid 360 through 387 removed outlier: 3.994A pdb=" N GLU j 364 " --> pdb=" O ASP j 360 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU j 374 " --> pdb=" O ARG j 370 " (cutoff:3.500A) Processing helix chain 'j' and resid 389 through 394 removed outlier: 4.266A pdb=" N LEU j 393 " --> pdb=" O THR j 389 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER j 394 " --> pdb=" O GLN j 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 389 through 394' Processing helix chain 'K' and resid 8 through 35 removed outlier: 3.819A pdb=" N LEU K 12 " --> pdb=" O ASN K 8 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N MET K 13 " --> pdb=" O SER K 9 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN K 19 " --> pdb=" O GLN K 15 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR K 20 " --> pdb=" O ASN K 16 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER K 21 " --> pdb=" O ASN K 17 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER K 33 " --> pdb=" O ILE K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 99 removed outlier: 3.769A pdb=" N GLN K 48 " --> pdb=" O ASP K 44 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN K 63 " --> pdb=" O LYS K 59 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ARG K 66 " --> pdb=" O THR K 62 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA K 68 " --> pdb=" O ALA K 64 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY K 80 " --> pdb=" O GLN K 76 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA K 81 " --> pdb=" O THR K 77 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLU K 84 " --> pdb=" O GLY K 80 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N VAL K 85 " --> pdb=" O ALA K 81 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG K 91 " --> pdb=" O ASN K 87 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU K 94 " --> pdb=" O GLN K 90 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLN K 98 " --> pdb=" O GLU K 94 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 130 removed outlier: 3.763A pdb=" N GLU K 115 " --> pdb=" O SER K 111 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN K 124 " --> pdb=" O LEU K 120 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR K 130 " --> pdb=" O VAL K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 195 removed outlier: 4.242A pdb=" N TYR K 190 " --> pdb=" O VAL K 186 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 211 through 217 Processing helix chain 'K' and resid 220 through 222 No H-bonds generated for 'chain 'K' and resid 220 through 222' Processing helix chain 'K' and resid 249 through 259 removed outlier: 4.217A pdb=" N SER K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR K 254 " --> pdb=" O THR K 250 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 279 removed outlier: 3.521A pdb=" N ALA K 279 " --> pdb=" O PRO K 276 " (cutoff:3.500A) Processing helix chain 'K' and resid 298 through 303 removed outlier: 3.888A pdb=" N ILE K 302 " --> pdb=" O GLN K 298 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR K 303 " --> pdb=" O LEU K 299 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 298 through 303' Processing helix chain 'K' and resid 309 through 358 removed outlier: 3.627A pdb=" N ASP K 315 " --> pdb=" O LEU K 311 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA K 316 " --> pdb=" O ALA K 312 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA K 317 " --> pdb=" O LYS K 313 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU K 324 " --> pdb=" O ASP K 320 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ARG K 334 " --> pdb=" O ALA K 330 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE K 339 " --> pdb=" O PHE K 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER K 340 " --> pdb=" O ASP K 336 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL K 346 " --> pdb=" O LEU K 342 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR K 347 " --> pdb=" O GLY K 343 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE K 356 " --> pdb=" O SER K 352 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN K 357 " --> pdb=" O ARG K 353 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP K 358 " --> pdb=" O SER K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 362 through 387 removed outlier: 3.815A pdb=" N SER K 366 " --> pdb=" O ALA K 362 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR K 379 " --> pdb=" O GLN K 375 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N SER K 380 " --> pdb=" O GLN K 376 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL K 381 " --> pdb=" O ALA K 377 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLN K 387 " --> pdb=" O ALA K 383 " (cutoff:3.500A) Processing helix chain 'K' and resid 389 through 394 removed outlier: 3.600A pdb=" N LEU K 393 " --> pdb=" O THR K 389 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER K 394 " --> pdb=" O GLN K 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 389 through 394' Processing helix chain 'k' and resid 8 through 35 removed outlier: 4.063A pdb=" N LEU k 12 " --> pdb=" O ASN k 8 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET k 13 " --> pdb=" O SER k 9 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN k 17 " --> pdb=" O MET k 13 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU k 18 " --> pdb=" O THR k 14 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER k 23 " --> pdb=" O ASN k 19 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA k 24 " --> pdb=" O THR k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 99 removed outlier: 4.154A pdb=" N LYS k 59 " --> pdb=" O THR k 55 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY k 60 " --> pdb=" O ALA k 56 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU k 61 " --> pdb=" O ASN k 57 " (cutoff:3.500A) Processing helix chain 'k' and resid 105 through 130 removed outlier: 3.654A pdb=" N LEU k 109 " --> pdb=" O SER k 105 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLN k 110 " --> pdb=" O ALA k 106 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER k 111 " --> pdb=" O SER k 107 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ILE k 112 " --> pdb=" O ASP k 108 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE k 123 " --> pdb=" O ARG k 119 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN k 124 " --> pdb=" O LEU k 120 " (cutoff:3.500A) Processing helix chain 'k' and resid 186 through 195 removed outlier: 3.683A pdb=" N TYR k 190 " --> pdb=" O VAL k 186 " (cutoff:3.500A) Processing helix chain 'k' and resid 212 through 218 Processing helix chain 'k' and resid 248 through 258 Processing helix chain 'k' and resid 275 through 279 removed outlier: 3.566A pdb=" N ALA k 279 " --> pdb=" O PRO k 276 " (cutoff:3.500A) Processing helix chain 'k' and resid 298 through 302 Processing helix chain 'k' and resid 309 through 358 removed outlier: 3.796A pdb=" N LYS k 313 " --> pdb=" O ASN k 309 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N SER k 337 " --> pdb=" O ASN k 333 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL k 338 " --> pdb=" O ARG k 334 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE k 339 " --> pdb=" O PHE k 335 " (cutoff:3.500A) Processing helix chain 'k' and resid 361 through 387 Processing helix chain 'k' and resid 389 through 394 removed outlier: 4.078A pdb=" N LEU k 393 " --> pdb=" O THR k 389 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER k 394 " --> pdb=" O GLN k 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 389 through 394' Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 147 Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 207 removed outlier: 3.532A pdb=" N ALA A 204 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA4, first strand: chain 'A' and resid 224 through 226 Processing sheet with id=AA5, first strand: chain 'a' and resid 143 through 147 Processing sheet with id=AA6, first strand: chain 'a' and resid 202 through 207 removed outlier: 6.988A pdb=" N THR a 202 " --> pdb=" O ALA a 288 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N PHE a 290 " --> pdb=" O THR a 202 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ALA a 204 " --> pdb=" O PHE a 290 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU a 292 " --> pdb=" O ALA a 204 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N THR a 206 " --> pdb=" O LEU a 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'a' and resid 224 through 226 Processing sheet with id=AA8, first strand: chain 'a' and resid 224 through 226 Processing sheet with id=AA9, first strand: chain 'B' and resid 144 through 147 Processing sheet with id=AB1, first strand: chain 'B' and resid 205 through 207 Processing sheet with id=AB2, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.640A pdb=" N ALA B 225 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 243 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 224 through 226 removed outlier: 3.640A pdb=" N ALA B 225 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 243 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 131 through 132 Processing sheet with id=AB5, first strand: chain 'b' and resid 143 through 144 Processing sheet with id=AB6, first strand: chain 'b' and resid 202 through 207 removed outlier: 6.808A pdb=" N THR b 202 " --> pdb=" O ALA b 288 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N PHE b 290 " --> pdb=" O THR b 202 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA b 204 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU b 292 " --> pdb=" O ALA b 204 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR b 206 " --> pdb=" O LEU b 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'b' and resid 224 through 226 removed outlier: 3.622A pdb=" N ALA b 225 " --> pdb=" O THR b 243 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'b' and resid 224 through 226 removed outlier: 3.622A pdb=" N ALA b 225 " --> pdb=" O THR b 243 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 144 through 147 Processing sheet with id=AC1, first strand: chain 'C' and resid 202 through 207 removed outlier: 6.730A pdb=" N THR C 202 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE C 290 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ALA C 204 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N LEU C 292 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N THR C 206 " --> pdb=" O LEU C 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AC3, first strand: chain 'C' and resid 224 through 226 Processing sheet with id=AC4, first strand: chain 'c' and resid 143 through 147 Processing sheet with id=AC5, first strand: chain 'c' and resid 202 through 207 Processing sheet with id=AC6, first strand: chain 'c' and resid 224 through 226 Processing sheet with id=AC7, first strand: chain 'c' and resid 224 through 226 Processing sheet with id=AC8, first strand: chain 'D' and resid 144 through 147 Processing sheet with id=AC9, first strand: chain 'D' and resid 202 through 207 removed outlier: 6.719A pdb=" N THR D 202 " --> pdb=" O ALA D 288 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N PHE D 290 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA D 204 " --> pdb=" O PHE D 290 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU D 292 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR D 206 " --> pdb=" O LEU D 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'D' and resid 224 through 226 Processing sheet with id=AD2, first strand: chain 'D' and resid 224 through 226 removed outlier: 3.525A pdb=" N LYS D 268 " --> pdb=" O ILE D 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'd' and resid 131 through 132 Processing sheet with id=AD4, first strand: chain 'd' and resid 143 through 147 Processing sheet with id=AD5, first strand: chain 'd' and resid 202 through 206 removed outlier: 6.796A pdb=" N THR d 202 " --> pdb=" O ALA d 288 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N PHE d 290 " --> pdb=" O THR d 202 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA d 204 " --> pdb=" O PHE d 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'd' and resid 224 through 226 Processing sheet with id=AD7, first strand: chain 'd' and resid 224 through 226 Processing sheet with id=AD8, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'E' and resid 144 through 147 removed outlier: 3.537A pdb=" N MET E 144 " --> pdb=" O ILE E 158 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 202 through 205 removed outlier: 6.867A pdb=" N THR E 202 " --> pdb=" O ALA E 288 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N PHE E 290 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA E 204 " --> pdb=" O PHE E 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AE3, first strand: chain 'E' and resid 224 through 226 Processing sheet with id=AE4, first strand: chain 'e' and resid 131 through 132 Processing sheet with id=AE5, first strand: chain 'e' and resid 143 through 147 Processing sheet with id=AE6, first strand: chain 'e' and resid 202 through 207 removed outlier: 6.651A pdb=" N THR e 202 " --> pdb=" O ALA e 288 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N PHE e 290 " --> pdb=" O THR e 202 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ALA e 204 " --> pdb=" O PHE e 290 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU e 292 " --> pdb=" O ALA e 204 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N THR e 206 " --> pdb=" O LEU e 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'e' and resid 224 through 226 Processing sheet with id=AE8, first strand: chain 'e' and resid 224 through 226 removed outlier: 3.636A pdb=" N LYS e 268 " --> pdb=" O ILE e 244 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 146 through 147 Processing sheet with id=AF1, first strand: chain 'F' and resid 202 through 207 removed outlier: 7.014A pdb=" N THR F 202 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N PHE F 290 " --> pdb=" O THR F 202 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA F 204 " --> pdb=" O PHE F 290 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N LEU F 292 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N THR F 206 " --> pdb=" O LEU F 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 224 through 226 Processing sheet with id=AF3, first strand: chain 'F' and resid 224 through 226 Processing sheet with id=AF4, first strand: chain 'f' and resid 143 through 147 Processing sheet with id=AF5, first strand: chain 'f' and resid 202 through 207 Processing sheet with id=AF6, first strand: chain 'f' and resid 224 through 226 Processing sheet with id=AF7, first strand: chain 'f' and resid 224 through 226 removed outlier: 4.658A pdb=" N TRP f 238 " --> pdb=" O LEU f 274 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'G' and resid 144 through 147 Processing sheet with id=AF9, first strand: chain 'G' and resid 202 through 207 removed outlier: 6.987A pdb=" N THR G 202 " --> pdb=" O ALA G 288 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N PHE G 290 " --> pdb=" O THR G 202 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ALA G 204 " --> pdb=" O PHE G 290 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU G 292 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N THR G 206 " --> pdb=" O LEU G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'G' and resid 224 through 226 Processing sheet with id=AG2, first strand: chain 'G' and resid 224 through 226 Processing sheet with id=AG3, first strand: chain 'g' and resid 131 through 132 Processing sheet with id=AG4, first strand: chain 'g' and resid 143 through 147 Processing sheet with id=AG5, first strand: chain 'g' and resid 202 through 207 removed outlier: 6.622A pdb=" N THR g 202 " --> pdb=" O ALA g 288 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N PHE g 290 " --> pdb=" O THR g 202 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ALA g 204 " --> pdb=" O PHE g 290 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU g 292 " --> pdb=" O ALA g 204 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR g 206 " --> pdb=" O LEU g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG5 Processing sheet with id=AG6, first strand: chain 'g' and resid 224 through 226 Processing sheet with id=AG7, first strand: chain 'g' and resid 224 through 226 Processing sheet with id=AG8, first strand: chain 'H' and resid 144 through 147 Processing sheet with id=AG9, first strand: chain 'H' and resid 202 through 207 Processing sheet with id=AH1, first strand: chain 'H' and resid 224 through 226 Processing sheet with id=AH2, first strand: chain 'H' and resid 224 through 226 Processing sheet with id=AH3, first strand: chain 'h' and resid 143 through 147 removed outlier: 3.534A pdb=" N ILE h 156 " --> pdb=" O ILE h 146 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 203 through 207 removed outlier: 6.477A pdb=" N ALA h 204 " --> pdb=" O PHE h 290 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU h 292 " --> pdb=" O ALA h 204 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N THR h 206 " --> pdb=" O LEU h 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'h' and resid 224 through 226 Processing sheet with id=AH6, first strand: chain 'h' and resid 224 through 226 Processing sheet with id=AH7, first strand: chain 'I' and resid 144 through 147 removed outlier: 3.887A pdb=" N MET I 144 " --> pdb=" O ILE I 158 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'I' and resid 202 through 207 Processing sheet with id=AH9, first strand: chain 'I' and resid 224 through 226 removed outlier: 3.620A pdb=" N ALA I 225 " --> pdb=" O THR I 243 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR I 243 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'I' and resid 224 through 226 removed outlier: 3.620A pdb=" N ALA I 225 " --> pdb=" O THR I 243 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR I 243 " --> pdb=" O ALA I 225 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'i' and resid 143 through 147 Processing sheet with id=AI3, first strand: chain 'i' and resid 202 through 207 removed outlier: 7.060A pdb=" N THR i 202 " --> pdb=" O ALA i 288 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N PHE i 290 " --> pdb=" O THR i 202 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA i 204 " --> pdb=" O PHE i 290 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU i 292 " --> pdb=" O ALA i 204 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N THR i 206 " --> pdb=" O LEU i 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI3 Processing sheet with id=AI4, first strand: chain 'i' and resid 224 through 226 Processing sheet with id=AI5, first strand: chain 'i' and resid 224 through 226 Processing sheet with id=AI6, first strand: chain 'J' and resid 144 through 147 Processing sheet with id=AI7, first strand: chain 'J' and resid 202 through 207 removed outlier: 6.821A pdb=" N THR J 202 " --> pdb=" O ALA J 288 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N PHE J 290 " --> pdb=" O THR J 202 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ALA J 204 " --> pdb=" O PHE J 290 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N LEU J 292 " --> pdb=" O ALA J 204 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR J 206 " --> pdb=" O LEU J 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'J' and resid 224 through 226 Processing sheet with id=AI9, first strand: chain 'J' and resid 231 through 232 Processing sheet with id=AJ1, first strand: chain 'j' and resid 143 through 147 Processing sheet with id=AJ2, first strand: chain 'j' and resid 202 through 207 removed outlier: 3.897A pdb=" N THR j 206 " --> pdb=" O PHE j 290 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'j' and resid 224 through 226 Processing sheet with id=AJ4, first strand: chain 'j' and resid 224 through 226 Processing sheet with id=AJ5, first strand: chain 'K' and resid 131 through 132 Processing sheet with id=AJ6, first strand: chain 'K' and resid 144 through 147 removed outlier: 3.751A pdb=" N MET K 144 " --> pdb=" O ILE K 158 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'K' and resid 202 through 207 removed outlier: 6.813A pdb=" N THR K 202 " --> pdb=" O ALA K 288 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N PHE K 290 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA K 204 " --> pdb=" O PHE K 290 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU K 292 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N THR K 206 " --> pdb=" O LEU K 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'K' and resid 224 through 226 Processing sheet with id=AJ9, first strand: chain 'K' and resid 224 through 226 Processing sheet with id=AK1, first strand: chain 'k' and resid 143 through 147 removed outlier: 3.514A pdb=" N ILE k 146 " --> pdb=" O ILE k 156 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'k' and resid 183 through 184 Processing sheet with id=AK3, first strand: chain 'k' and resid 183 through 184 Processing sheet with id=AK4, first strand: chain 'k' and resid 202 through 207 removed outlier: 7.095A pdb=" N THR k 202 " --> pdb=" O ALA k 288 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N PHE k 290 " --> pdb=" O THR k 202 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA k 204 " --> pdb=" O PHE k 290 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU k 292 " --> pdb=" O ALA k 204 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N THR k 206 " --> pdb=" O LEU k 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK4 3747 hydrogen bonds defined for protein. 10836 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: 25.70 Time building geometry restraints manager: 15.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16147 1.33 - 1.45: 10423 1.45 - 1.57: 36988 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 63690 Sorted by residual: bond pdb=" CG GLN G 129 " pdb=" CD GLN G 129 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.17e+00 bond pdb=" CB ASN E 17 " pdb=" CG ASN E 17 " ideal model delta sigma weight residual 1.516 1.471 0.045 2.50e-02 1.60e+03 3.21e+00 bond pdb=" C GLY d 80 " pdb=" O GLY d 80 " ideal model delta sigma weight residual 1.234 1.255 -0.021 1.21e-02 6.83e+03 3.12e+00 bond pdb=" C GLY k 80 " pdb=" O GLY k 80 " ideal model delta sigma weight residual 1.234 1.255 -0.021 1.21e-02 6.83e+03 3.12e+00 bond pdb=" CB PHE E 335 " pdb=" CG PHE E 335 " ideal model delta sigma weight residual 1.502 1.461 0.041 2.30e-02 1.89e+03 3.11e+00 ... (remaining 63685 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 83645 1.89 - 3.78: 2714 3.78 - 5.67: 238 5.67 - 7.56: 32 7.56 - 9.44: 7 Bond angle restraints: 86636 Sorted by residual: angle pdb=" N ILE f 58 " pdb=" CA ILE f 58 " pdb=" C ILE f 58 " ideal model delta sigma weight residual 110.42 115.51 -5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" C ALA g 139 " pdb=" N LYS g 140 " pdb=" CA LYS g 140 " ideal model delta sigma weight residual 121.54 130.70 -9.16 1.91e+00 2.74e-01 2.30e+01 angle pdb=" N ILE e 58 " pdb=" CA ILE e 58 " pdb=" C ILE e 58 " ideal model delta sigma weight residual 110.42 114.89 -4.47 9.60e-01 1.09e+00 2.17e+01 angle pdb=" N ILE h 58 " pdb=" CA ILE h 58 " pdb=" C ILE h 58 " ideal model delta sigma weight residual 110.42 114.69 -4.27 9.60e-01 1.09e+00 1.98e+01 angle pdb=" N ILE b 58 " pdb=" CA ILE b 58 " pdb=" C ILE b 58 " ideal model delta sigma weight residual 110.42 114.57 -4.15 9.60e-01 1.09e+00 1.87e+01 ... (remaining 86631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 35764 17.93 - 35.87: 2646 35.87 - 53.80: 380 53.80 - 71.73: 108 71.73 - 89.66: 64 Dihedral angle restraints: 38962 sinusoidal: 13948 harmonic: 25014 Sorted by residual: dihedral pdb=" CA ALA K 306 " pdb=" C ALA K 306 " pdb=" N SER K 307 " pdb=" CA SER K 307 " ideal model delta harmonic sigma weight residual 180.00 151.89 28.11 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ALA G 306 " pdb=" C ALA G 306 " pdb=" N SER G 307 " pdb=" CA SER G 307 " ideal model delta harmonic sigma weight residual 180.00 152.51 27.49 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA PHE k 335 " pdb=" C PHE k 335 " pdb=" N ASP k 336 " pdb=" CA ASP k 336 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 ... (remaining 38959 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 8435 0.051 - 0.101: 2026 0.101 - 0.152: 410 0.152 - 0.203: 35 0.203 - 0.254: 6 Chirality restraints: 10912 Sorted by residual: chirality pdb=" CB VAL c 148 " pdb=" CA VAL c 148 " pdb=" CG1 VAL c 148 " pdb=" CG2 VAL c 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB VAL h 148 " pdb=" CA VAL h 148 " pdb=" CG1 VAL h 148 " pdb=" CG2 VAL h 148 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CG LEU K 61 " pdb=" CB LEU K 61 " pdb=" CD1 LEU K 61 " pdb=" CD2 LEU K 61 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 10909 not shown) Planarity restraints: 11506 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR h 361 " -0.028 2.00e-02 2.50e+03 1.80e-02 6.47e+00 pdb=" CG TYR h 361 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR h 361 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR h 361 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR h 361 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR h 361 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR h 361 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR h 361 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP b 322 " 0.012 2.00e-02 2.50e+03 2.48e-02 6.16e+00 pdb=" CG ASP b 322 " -0.043 2.00e-02 2.50e+03 pdb=" OD1 ASP b 322 " 0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP b 322 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 335 " -0.018 2.00e-02 2.50e+03 1.54e-02 4.13e+00 pdb=" CG PHE K 335 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE K 335 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE K 335 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE K 335 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE K 335 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE K 335 " -0.003 2.00e-02 2.50e+03 ... (remaining 11503 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 454 2.59 - 3.17: 58182 3.17 - 3.74: 89086 3.74 - 4.32: 116621 4.32 - 4.90: 197635 Nonbonded interactions: 461978 Sorted by model distance: nonbonded pdb=" OG SER i 354 " pdb=" OD2 ASP i 358 " model vdw 2.010 3.040 nonbonded pdb=" OG SER C 354 " pdb=" OD2 ASP C 358 " model vdw 2.094 3.040 nonbonded pdb=" O GLN J 298 " pdb=" OG SER J 301 " model vdw 2.095 3.040 nonbonded pdb=" O GLY f 195 " pdb=" OG1 THR f 198 " model vdw 2.146 3.040 nonbonded pdb=" O ASN K 391 " pdb=" OG SER K 394 " model vdw 2.153 3.040 ... (remaining 461973 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.180 Check model and map are aligned: 0.390 Set scattering table: 0.450 Process input model: 116.020 Find NCS groups from input model: 2.430 Set up NCS constraints: 0.520 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 145.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 63690 Z= 0.547 Angle : 0.787 9.445 86636 Z= 0.477 Chirality : 0.046 0.254 10912 Planarity : 0.003 0.040 11506 Dihedral : 13.578 89.665 22726 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.04 % Allowed : 0.49 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.09), residues: 8646 helix: 1.32 (0.07), residues: 4719 sheet: -0.88 (0.16), residues: 935 loop : -1.37 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP i 238 PHE 0.036 0.003 PHE K 335 TYR 0.041 0.002 TYR h 361 ARG 0.007 0.001 ARG a 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 146 time to evaluate : 5.597 Fit side-chains REVERT: B 194 TYR cc_start: 0.8023 (m-80) cc_final: 0.7810 (m-80) REVERT: B 361 TYR cc_start: 0.8483 (m-80) cc_final: 0.8227 (m-80) REVERT: b 275 ASP cc_start: 0.8343 (t70) cc_final: 0.8037 (t0) REVERT: d 144 MET cc_start: 0.8084 (mmm) cc_final: 0.7809 (mtp) REVERT: j 198 THR cc_start: 0.7783 (t) cc_final: 0.7566 (t) outliers start: 3 outliers final: 0 residues processed: 149 average time/residue: 0.5104 time to fit residues: 142.5981 Evaluate side-chains 110 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 5.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 724 optimal weight: 6.9990 chunk 650 optimal weight: 9.9990 chunk 360 optimal weight: 0.8980 chunk 222 optimal weight: 0.9990 chunk 438 optimal weight: 0.9990 chunk 347 optimal weight: 1.9990 chunk 672 optimal weight: 3.9990 chunk 260 optimal weight: 2.9990 chunk 408 optimal weight: 4.9990 chunk 500 optimal weight: 0.8980 chunk 779 optimal weight: 2.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 86 ASN a 86 ASN b 30 GLN b 39 ASN b 211 ASN C 199 ASN ** D 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 GLN d 48 GLN d 86 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** E 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 52 ASN e 86 ASN e 386 ASN ** F 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN f 22 GLN f 48 GLN G 63 GLN g 22 GLN g 26 ASN H 30 GLN H 67 ASN H 145 ASN h 86 ASN I 86 ASN i 86 ASN i 387 GLN i 390 GLN j 65 GLN j 86 ASN j 386 ASN K 52 ASN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN k 86 ASN k 90 GLN k 372 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 63690 Z= 0.203 Angle : 0.517 7.769 86636 Z= 0.304 Chirality : 0.039 0.190 10912 Planarity : 0.003 0.045 11506 Dihedral : 4.736 33.597 9086 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.24 % Allowed : 5.18 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.09), residues: 8646 helix: 2.32 (0.07), residues: 4642 sheet: -0.39 (0.16), residues: 946 loop : -1.17 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP i 238 PHE 0.014 0.001 PHE K 335 TYR 0.015 0.001 TYR h 361 ARG 0.005 0.000 ARG f 370 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 5.571 Fit side-chains REVERT: A 140 LYS cc_start: 0.8482 (tptp) cc_final: 0.8188 (tppt) REVERT: B 144 MET cc_start: 0.8551 (ptm) cc_final: 0.8305 (ptm) REVERT: b 275 ASP cc_start: 0.8213 (t70) cc_final: 0.7938 (t0) REVERT: D 144 MET cc_start: 0.8595 (ppp) cc_final: 0.8266 (ptm) REVERT: E 140 LYS cc_start: 0.8426 (tptp) cc_final: 0.8071 (tppt) REVERT: f 13 MET cc_start: 0.7992 (tmm) cc_final: 0.7751 (tmm) outliers start: 16 outliers final: 9 residues processed: 190 average time/residue: 0.5159 time to fit residues: 181.1054 Evaluate side-chains 138 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 5.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 126 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 433 optimal weight: 8.9990 chunk 241 optimal weight: 2.9990 chunk 648 optimal weight: 9.9990 chunk 530 optimal weight: 0.9980 chunk 214 optimal weight: 0.7980 chunk 780 optimal weight: 8.9990 chunk 843 optimal weight: 8.9990 chunk 695 optimal weight: 1.9990 chunk 774 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 626 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 131 GLN E 76 GLN E 129 GLN E 375 GLN ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN g 26 ASN h 22 GLN ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 147 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 63690 Z= 0.240 Angle : 0.493 8.278 86636 Z= 0.288 Chirality : 0.038 0.187 10912 Planarity : 0.002 0.032 11506 Dihedral : 4.479 30.738 9086 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.81 % Allowed : 8.08 % Favored : 91.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.09), residues: 8646 helix: 2.54 (0.07), residues: 4664 sheet: -0.30 (0.16), residues: 946 loop : -1.18 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.017 0.002 PHE K 335 TYR 0.010 0.001 TYR a 239 ARG 0.005 0.000 ARG b 370 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 144 time to evaluate : 5.641 Fit side-chains REVERT: A 140 LYS cc_start: 0.8454 (tptp) cc_final: 0.8179 (tppt) REVERT: B 144 MET cc_start: 0.8568 (ptm) cc_final: 0.8260 (ptm) REVERT: b 275 ASP cc_start: 0.8219 (t70) cc_final: 0.7939 (t0) REVERT: C 335 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7017 (t80) REVERT: D 144 MET cc_start: 0.8514 (ppp) cc_final: 0.8153 (ptm) REVERT: D 335 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7971 (t80) REVERT: E 140 LYS cc_start: 0.8422 (tptp) cc_final: 0.8097 (tppt) outliers start: 55 outliers final: 31 residues processed: 186 average time/residue: 0.5338 time to fit residues: 183.8619 Evaluate side-chains 164 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 5.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain c residue 368 MET Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 339 ILE Chi-restraints excluded: chain i residue 5 ILE Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 229 THR Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 101 THR Chi-restraints excluded: chain k residue 126 VAL Chi-restraints excluded: chain k residue 322 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 771 optimal weight: 0.0470 chunk 586 optimal weight: 0.8980 chunk 405 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 372 optimal weight: 6.9990 chunk 524 optimal weight: 0.1980 chunk 783 optimal weight: 4.9990 chunk 829 optimal weight: 0.8980 chunk 409 optimal weight: 6.9990 chunk 742 optimal weight: 1.9990 chunk 223 optimal weight: 9.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN b 22 GLN b 26 ASN b 86 ASN c 65 GLN d 22 GLN ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 22 GLN g 26 ASN ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 332 GLN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 372 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 63690 Z= 0.154 Angle : 0.425 6.129 86636 Z= 0.252 Chirality : 0.036 0.161 10912 Planarity : 0.002 0.031 11506 Dihedral : 4.135 29.764 9086 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.85 % Allowed : 9.19 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.09), residues: 8646 helix: 2.84 (0.07), residues: 4730 sheet: -0.02 (0.16), residues: 946 loop : -1.20 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.012 0.001 PHE A 335 TYR 0.008 0.001 TYR g 361 ARG 0.003 0.000 ARG B 325 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 5.570 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8278 (tptp) cc_final: 0.7978 (tppt) REVERT: B 101 THR cc_start: 0.8106 (m) cc_final: 0.7792 (t) REVERT: b 275 ASP cc_start: 0.8177 (t70) cc_final: 0.7896 (t0) REVERT: C 335 PHE cc_start: 0.8313 (OUTLIER) cc_final: 0.6788 (t80) REVERT: D 144 MET cc_start: 0.8370 (ppp) cc_final: 0.8166 (ptm) REVERT: D 335 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7942 (t80) REVERT: E 140 LYS cc_start: 0.8243 (tptp) cc_final: 0.7946 (tppt) REVERT: E 335 PHE cc_start: 0.9060 (OUTLIER) cc_final: 0.8144 (t80) REVERT: F 140 LYS cc_start: 0.8772 (tptp) cc_final: 0.8558 (tppt) REVERT: j 216 ARG cc_start: 0.8245 (ttp80) cc_final: 0.7915 (ttp-170) REVERT: K 129 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7161 (mp10) REVERT: K 217 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8312 (tt) outliers start: 58 outliers final: 29 residues processed: 245 average time/residue: 0.5080 time to fit residues: 229.5571 Evaluate side-chains 181 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 5.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain d residue 92 ILE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 339 ILE Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 217 LEU Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 101 THR Chi-restraints excluded: chain k residue 322 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 690 optimal weight: 4.9990 chunk 470 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 617 optimal weight: 1.9990 chunk 342 optimal weight: 0.0770 chunk 707 optimal weight: 4.9990 chunk 573 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 423 optimal weight: 0.9980 chunk 744 optimal weight: 0.0370 chunk 209 optimal weight: 5.9990 overall best weight: 0.8018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 26 ASN F 129 GLN ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 129 GLN I 332 GLN ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 63690 Z= 0.151 Angle : 0.412 7.553 86636 Z= 0.243 Chirality : 0.036 0.162 10912 Planarity : 0.002 0.038 11506 Dihedral : 3.919 29.261 9086 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.16 % Allowed : 10.06 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.09), residues: 8646 helix: 3.01 (0.07), residues: 4730 sheet: 0.13 (0.16), residues: 946 loop : -1.14 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP j 238 PHE 0.013 0.001 PHE K 335 TYR 0.009 0.001 TYR j 361 ARG 0.005 0.000 ARG g 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 185 time to evaluate : 5.627 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.7852 (tpp) cc_final: 0.7643 (ttt) REVERT: B 101 THR cc_start: 0.7865 (m) cc_final: 0.7590 (t) REVERT: b 275 ASP cc_start: 0.8164 (t70) cc_final: 0.7883 (t0) REVERT: C 335 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.6780 (t80) REVERT: c 335 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7802 (t80) REVERT: D 335 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7924 (t80) REVERT: E 140 LYS cc_start: 0.8167 (tptp) cc_final: 0.7897 (tppt) REVERT: E 335 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8150 (t80) REVERT: e 335 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7949 (t80) REVERT: h 375 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7547 (tm-30) REVERT: K 36 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8821 (pp) REVERT: K 129 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7137 (mp10) outliers start: 79 outliers final: 38 residues processed: 247 average time/residue: 0.5291 time to fit residues: 239.7793 Evaluate side-chains 202 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 5.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain c residue 335 PHE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain e residue 335 PHE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 363 THR Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 324 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 101 THR Chi-restraints excluded: chain k residue 322 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 279 optimal weight: 0.7980 chunk 746 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 486 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 830 optimal weight: 0.8980 chunk 689 optimal weight: 0.6980 chunk 384 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 274 optimal weight: 3.9990 chunk 435 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 GLN ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 63690 Z= 0.147 Angle : 0.408 15.475 86636 Z= 0.238 Chirality : 0.036 0.169 10912 Planarity : 0.002 0.036 11506 Dihedral : 3.803 29.031 9086 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.97 % Allowed : 10.66 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.34 (0.09), residues: 8646 helix: 3.36 (0.07), residues: 4554 sheet: 0.03 (0.16), residues: 1023 loop : -0.81 (0.12), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP i 238 PHE 0.013 0.001 PHE K 335 TYR 0.017 0.001 TYR d 194 ARG 0.003 0.000 ARG b 370 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 183 time to evaluate : 5.556 Fit side-chains revert: symmetry clash REVERT: B 101 THR cc_start: 0.7717 (m) cc_final: 0.7424 (t) REVERT: b 275 ASP cc_start: 0.8148 (t70) cc_final: 0.7868 (t0) REVERT: b 335 PHE cc_start: 0.8611 (OUTLIER) cc_final: 0.7855 (t80) REVERT: C 335 PHE cc_start: 0.8334 (OUTLIER) cc_final: 0.6767 (t80) REVERT: c 335 PHE cc_start: 0.8658 (OUTLIER) cc_final: 0.7791 (t80) REVERT: D 335 PHE cc_start: 0.8686 (OUTLIER) cc_final: 0.7917 (t80) REVERT: E 140 LYS cc_start: 0.8068 (tptp) cc_final: 0.7866 (tppt) REVERT: E 335 PHE cc_start: 0.9081 (OUTLIER) cc_final: 0.8174 (t80) REVERT: e 335 PHE cc_start: 0.8722 (OUTLIER) cc_final: 0.7949 (t80) REVERT: e 390 GLN cc_start: 0.8913 (mm110) cc_final: 0.8551 (mt0) REVERT: h 334 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8495 (ttt180) REVERT: h 375 GLN cc_start: 0.7726 (mm-40) cc_final: 0.7415 (tm-30) REVERT: i 144 MET cc_start: 0.6543 (tpt) cc_final: 0.6303 (ttt) REVERT: K 36 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8754 (pp) REVERT: K 129 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7215 (mp10) outliers start: 66 outliers final: 42 residues processed: 233 average time/residue: 0.5117 time to fit residues: 218.8455 Evaluate side-chains 217 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 166 time to evaluate : 5.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 335 PHE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain c residue 335 PHE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain e residue 335 PHE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 92 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 126 VAL Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 334 ARG Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 229 THR Chi-restraints excluded: chain j residue 324 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 800 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 chunk 472 optimal weight: 1.9990 chunk 606 optimal weight: 4.9990 chunk 469 optimal weight: 5.9990 chunk 698 optimal weight: 3.9990 chunk 463 optimal weight: 2.9990 chunk 826 optimal weight: 9.9990 chunk 517 optimal weight: 0.0970 chunk 504 optimal weight: 0.4980 chunk 381 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 17 ASN ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 63690 Z= 0.220 Angle : 0.445 11.215 86636 Z= 0.257 Chirality : 0.037 0.222 10912 Planarity : 0.002 0.034 11506 Dihedral : 3.873 29.659 9086 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.19 % Allowed : 10.91 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.09), residues: 8646 helix: 3.27 (0.07), residues: 4554 sheet: -0.04 (0.16), residues: 1023 loop : -0.83 (0.12), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 238 PHE 0.017 0.001 PHE K 335 TYR 0.012 0.001 TYR j 239 ARG 0.003 0.000 ARG H 370 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 167 time to evaluate : 5.597 Fit side-chains revert: symmetry clash REVERT: B 101 THR cc_start: 0.7956 (m) cc_final: 0.7627 (t) REVERT: b 275 ASP cc_start: 0.8183 (t70) cc_final: 0.7912 (t0) REVERT: C 335 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7197 (t80) REVERT: c 335 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.7775 (t80) REVERT: D 335 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8003 (t80) REVERT: E 140 LYS cc_start: 0.8174 (tptp) cc_final: 0.7929 (tppt) REVERT: E 335 PHE cc_start: 0.9138 (OUTLIER) cc_final: 0.8147 (t80) REVERT: e 335 PHE cc_start: 0.8844 (OUTLIER) cc_final: 0.7896 (t80) REVERT: e 390 GLN cc_start: 0.8912 (mm110) cc_final: 0.8549 (mt0) REVERT: F 140 LYS cc_start: 0.8927 (tppt) cc_final: 0.8632 (tptp) REVERT: h 334 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8547 (ttt180) REVERT: h 375 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7453 (tm-30) REVERT: i 144 MET cc_start: 0.6540 (tpt) cc_final: 0.6318 (ttt) REVERT: K 36 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8754 (pp) REVERT: K 129 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7246 (mp10) outliers start: 81 outliers final: 56 residues processed: 231 average time/residue: 0.5614 time to fit residues: 238.4012 Evaluate side-chains 227 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 163 time to evaluate : 5.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain c residue 335 PHE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 144 MET Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 335 PHE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 92 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 144 MET Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 363 THR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 144 MET Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 334 ARG Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 229 THR Chi-restraints excluded: chain j residue 324 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 101 THR Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 322 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 511 optimal weight: 0.9990 chunk 330 optimal weight: 7.9990 chunk 493 optimal weight: 1.9990 chunk 249 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 525 optimal weight: 1.9990 chunk 563 optimal weight: 0.0000 chunk 408 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 650 optimal weight: 9.9990 overall best weight: 1.0128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN J 17 ASN ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 63690 Z= 0.152 Angle : 0.408 10.001 86636 Z= 0.239 Chirality : 0.036 0.179 10912 Planarity : 0.002 0.032 11506 Dihedral : 3.780 29.516 9086 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.07 % Allowed : 11.28 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.09), residues: 8646 helix: 3.39 (0.07), residues: 4554 sheet: 0.06 (0.16), residues: 1023 loop : -0.78 (0.12), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.013 0.001 PHE K 335 TYR 0.013 0.001 TYR j 239 ARG 0.003 0.000 ARG b 370 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 179 time to evaluate : 5.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 THR cc_start: 0.7780 (m) cc_final: 0.7470 (t) REVERT: b 275 ASP cc_start: 0.8155 (t70) cc_final: 0.7880 (t0) REVERT: b 335 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7861 (t80) REVERT: C 335 PHE cc_start: 0.8403 (OUTLIER) cc_final: 0.7018 (t80) REVERT: c 335 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7848 (t80) REVERT: D 335 PHE cc_start: 0.8762 (OUTLIER) cc_final: 0.7972 (t80) REVERT: E 140 LYS cc_start: 0.8063 (tptp) cc_final: 0.7852 (tppt) REVERT: E 335 PHE cc_start: 0.9089 (OUTLIER) cc_final: 0.8148 (t80) REVERT: e 335 PHE cc_start: 0.8787 (OUTLIER) cc_final: 0.7842 (t80) REVERT: e 390 GLN cc_start: 0.8886 (mm110) cc_final: 0.8530 (mt0) REVERT: h 334 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8478 (ttt180) REVERT: h 375 GLN cc_start: 0.7815 (mm-40) cc_final: 0.7486 (tm-30) REVERT: i 144 MET cc_start: 0.6591 (tpt) cc_final: 0.6389 (ttt) REVERT: J 13 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.7462 (tpp) REVERT: K 36 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8766 (pp) REVERT: K 129 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7121 (mp10) outliers start: 73 outliers final: 52 residues processed: 233 average time/residue: 0.5141 time to fit residues: 220.3137 Evaluate side-chains 236 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 174 time to evaluate : 5.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 335 PHE Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain c residue 335 PHE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain e residue 335 PHE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 92 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 339 ILE Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 126 VAL Chi-restraints excluded: chain g residue 363 THR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 334 ARG Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 175 VAL Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 229 THR Chi-restraints excluded: chain j residue 324 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 101 THR Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 322 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 752 optimal weight: 1.9990 chunk 792 optimal weight: 0.8980 chunk 722 optimal weight: 20.0000 chunk 770 optimal weight: 10.0000 chunk 463 optimal weight: 0.7980 chunk 335 optimal weight: 4.9990 chunk 605 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 696 optimal weight: 4.9990 chunk 728 optimal weight: 7.9990 chunk 767 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 26 ASN ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 387 GLN ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 63690 Z= 0.221 Angle : 0.448 9.112 86636 Z= 0.259 Chirality : 0.037 0.220 10912 Planarity : 0.002 0.031 11506 Dihedral : 3.874 29.825 9086 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.06 % Allowed : 11.43 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.09), residues: 8646 helix: 3.27 (0.07), residues: 4554 sheet: 0.09 (0.16), residues: 1001 loop : -0.84 (0.12), residues: 3091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 238 PHE 0.017 0.001 PHE K 335 TYR 0.012 0.001 TYR j 239 ARG 0.003 0.000 ARG H 370 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 165 time to evaluate : 5.496 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8047 (tpp) cc_final: 0.7733 (ttt) REVERT: B 101 THR cc_start: 0.7973 (m) cc_final: 0.7670 (t) REVERT: b 275 ASP cc_start: 0.8181 (t70) cc_final: 0.7911 (t0) REVERT: C 335 PHE cc_start: 0.8516 (OUTLIER) cc_final: 0.7190 (t80) REVERT: c 335 PHE cc_start: 0.8738 (OUTLIER) cc_final: 0.7735 (t80) REVERT: D 335 PHE cc_start: 0.8835 (OUTLIER) cc_final: 0.8048 (t80) REVERT: E 140 LYS cc_start: 0.8121 (tptp) cc_final: 0.7900 (tppt) REVERT: E 335 PHE cc_start: 0.9155 (OUTLIER) cc_final: 0.8144 (t80) REVERT: e 390 GLN cc_start: 0.8902 (mm110) cc_final: 0.8553 (mt0) REVERT: F 140 LYS cc_start: 0.8725 (tppt) cc_final: 0.8476 (tptp) REVERT: h 334 ARG cc_start: 0.8857 (OUTLIER) cc_final: 0.8553 (ttt180) REVERT: h 375 GLN cc_start: 0.7809 (mm-40) cc_final: 0.7489 (tm-30) REVERT: K 36 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8772 (pp) REVERT: K 129 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7159 (mp10) outliers start: 72 outliers final: 55 residues processed: 223 average time/residue: 0.4968 time to fit residues: 204.1758 Evaluate side-chains 222 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 160 time to evaluate : 5.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain C residue 50 ILE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain c residue 335 PHE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain e residue 335 PHE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain f residue 5 ILE Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 92 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 205 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 126 VAL Chi-restraints excluded: chain g residue 363 THR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 334 ARG Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain J residue 144 MET Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 82 LEU Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 229 THR Chi-restraints excluded: chain j residue 324 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 114 ASP Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 205 VAL Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 95 LEU Chi-restraints excluded: chain k residue 101 THR Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 322 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 506 optimal weight: 0.8980 chunk 814 optimal weight: 4.9990 chunk 497 optimal weight: 0.9990 chunk 386 optimal weight: 0.4980 chunk 566 optimal weight: 4.9990 chunk 854 optimal weight: 9.9990 chunk 786 optimal weight: 1.9990 chunk 680 optimal weight: 0.1980 chunk 70 optimal weight: 0.8980 chunk 525 optimal weight: 0.9980 chunk 417 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 199 ASN e 22 GLN e 26 ASN ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 63690 Z= 0.144 Angle : 0.402 8.425 86636 Z= 0.235 Chirality : 0.036 0.190 10912 Planarity : 0.002 0.029 11506 Dihedral : 3.718 29.215 9086 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.81 % Allowed : 11.64 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.47 (0.10), residues: 8646 helix: 3.41 (0.07), residues: 4576 sheet: 0.14 (0.16), residues: 1023 loop : -0.72 (0.12), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.012 0.001 PHE K 335 TYR 0.014 0.001 TYR j 239 ARG 0.007 0.000 ARG E 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17292 Ramachandran restraints generated. 8646 Oldfield, 0 Emsley, 8646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 195 time to evaluate : 5.592 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 144 MET cc_start: 0.7924 (tpp) cc_final: 0.7640 (ttt) REVERT: B 101 THR cc_start: 0.7658 (m) cc_final: 0.7378 (t) REVERT: B 271 TYR cc_start: 0.7349 (m-80) cc_final: 0.7137 (m-80) REVERT: b 275 ASP cc_start: 0.8127 (t70) cc_final: 0.7851 (t0) REVERT: b 335 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.7894 (t80) REVERT: C 335 PHE cc_start: 0.8368 (OUTLIER) cc_final: 0.6855 (t80) REVERT: c 335 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.7834 (t80) REVERT: D 335 PHE cc_start: 0.8677 (OUTLIER) cc_final: 0.7867 (t80) REVERT: E 140 LYS cc_start: 0.8026 (tptp) cc_final: 0.7796 (tppt) REVERT: E 335 PHE cc_start: 0.9065 (OUTLIER) cc_final: 0.8177 (t80) REVERT: e 335 PHE cc_start: 0.8795 (OUTLIER) cc_final: 0.7888 (t80) REVERT: e 390 GLN cc_start: 0.8854 (mm110) cc_final: 0.8440 (mt0) REVERT: f 13 MET cc_start: 0.8930 (mmm) cc_final: 0.8574 (ttt) REVERT: h 334 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8464 (ttt180) REVERT: h 375 GLN cc_start: 0.7781 (mm-40) cc_final: 0.7441 (tm-30) REVERT: K 36 LEU cc_start: 0.9047 (OUTLIER) cc_final: 0.8761 (pp) REVERT: K 129 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7152 (mp10) outliers start: 55 outliers final: 40 residues processed: 239 average time/residue: 0.5187 time to fit residues: 227.3791 Evaluate side-chains 225 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 176 time to evaluate : 5.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain B residue 159 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain b residue 12 LEU Chi-restraints excluded: chain b residue 335 PHE Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain c residue 148 VAL Chi-restraints excluded: chain c residue 175 VAL Chi-restraints excluded: chain c residue 200 VAL Chi-restraints excluded: chain c residue 335 PHE Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 335 PHE Chi-restraints excluded: chain e residue 335 PHE Chi-restraints excluded: chain e residue 395 LEU Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 297 ILE Chi-restraints excluded: chain f residue 74 LEU Chi-restraints excluded: chain f residue 92 ILE Chi-restraints excluded: chain f residue 200 VAL Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 361 TYR Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 126 VAL Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 148 VAL Chi-restraints excluded: chain h residue 200 VAL Chi-restraints excluded: chain h residue 334 ARG Chi-restraints excluded: chain h residue 374 LEU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 229 THR Chi-restraints excluded: chain j residue 324 LEU Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 129 GLN Chi-restraints excluded: chain K residue 144 MET Chi-restraints excluded: chain K residue 206 THR Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 331 VAL Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 540 optimal weight: 3.9990 chunk 725 optimal weight: 9.9990 chunk 208 optimal weight: 6.9990 chunk 627 optimal weight: 0.1980 chunk 100 optimal weight: 0.0970 chunk 189 optimal weight: 1.9990 chunk 681 optimal weight: 2.9990 chunk 285 optimal weight: 0.9980 chunk 700 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.074039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.061066 restraints weight = 219199.552| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.78 r_work: 0.3074 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 63690 Z= 0.146 Angle : 0.403 8.410 86636 Z= 0.235 Chirality : 0.036 0.197 10912 Planarity : 0.002 0.029 11506 Dihedral : 3.656 28.530 9086 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.81 % Allowed : 11.77 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.10), residues: 8646 helix: 3.41 (0.07), residues: 4609 sheet: 0.19 (0.16), residues: 1023 loop : -0.80 (0.12), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP i 238 PHE 0.014 0.001 PHE K 335 TYR 0.013 0.001 TYR j 239 ARG 0.005 0.000 ARG d 355 =============================================================================== Job complete usr+sys time: 8213.01 seconds wall clock time: 148 minutes 21.02 seconds (8901.02 seconds total)