Starting phenix.real_space_refine on Sun Jan 19 08:21:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9atb_43829/01_2025/9atb_43829.cif Found real_map, /net/cci-nas-00/data/ceres_data/9atb_43829/01_2025/9atb_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_43829/01_2025/9atb_43829.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9atb_43829/01_2025/9atb_43829.map" model { file = "/net/cci-nas-00/data/ceres_data/9atb_43829/01_2025/9atb_43829.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9atb_43829/01_2025/9atb_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-5571/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: 28.49, per 1000 atoms: 0.45 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: 13.19 Conformation dependent library (CDL) restraints added in 6.6 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: 7.34 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: 21.39 Time building geometry restraints manager: 15.44 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: 0.02 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: 30.210 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: 0.060 Extract box with map and model: 2.210 Check model and map are aligned: 0.430 Set scattering table: 0.470 Process input model: 116.310 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.300 ------------------------------------------------------------------------------- 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 : 5.500 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: 0.5108 time to fit residues: 142.3675 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 : 5.839 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.069236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.055940 restraints weight = 221556.817| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.79 r_work: 0.2959 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 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 : 5.769 Fit side-chains REVERT: A 140 LYS cc_start: 0.8740 (tptp) cc_final: 0.8354 (tppt) REVERT: B 144 MET cc_start: 0.8754 (ptm) cc_final: 0.8525 (ptm) REVERT: b 275 ASP cc_start: 0.8433 (t70) cc_final: 0.8163 (t0) REVERT: D 144 MET cc_start: 0.8817 (ppp) cc_final: 0.8519 (ptm) REVERT: E 140 LYS cc_start: 0.8791 (tptp) cc_final: 0.8374 (tppt) REVERT: f 13 MET cc_start: 0.8176 (tmm) cc_final: 0.7914 (tmm) outliers start: 16 outliers final: 9 residues processed: 190 average time/residue: 0.5386 time to fit residues: 188.9862 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 : 5.613 ------------------------------------------------------------------------------- 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 682 optimal weight: 4.9990 chunk 352 optimal weight: 3.9990 chunk 434 optimal weight: 0.6980 chunk 636 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 256 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 261 optimal weight: 4.9990 chunk 734 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 847 optimal weight: 0.6980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 131 GLN C 6 ASN ** E 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 30 GLN k 147 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.068533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.055254 restraints weight = 221382.144| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.76 r_work: 0.2937 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 63690 Z= 0.264 Angle : 0.509 8.718 86636 Z= 0.297 Chirality : 0.039 0.190 10912 Planarity : 0.003 0.033 11506 Dihedral : 4.528 30.907 9086 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.75 % Allowed : 8.30 % Favored : 90.95 % 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: 1.40 (0.09), residues: 8646 helix: 2.49 (0.07), residues: 4653 sheet: -0.33 (0.16), residues: 946 loop : -1.18 (0.11), residues: 3047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.018 0.002 PHE K 335 TYR 0.010 0.001 TYR E 361 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 191 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 140 time to evaluate : 5.675 Fit side-chains REVERT: A 140 LYS cc_start: 0.8762 (tptp) cc_final: 0.8382 (tppt) REVERT: B 144 MET cc_start: 0.8764 (ptm) cc_final: 0.8481 (ptm) REVERT: b 275 ASP cc_start: 0.8441 (t70) cc_final: 0.8174 (t0) REVERT: C 335 PHE cc_start: 0.8499 (OUTLIER) cc_final: 0.7088 (t80) REVERT: D 144 MET cc_start: 0.8769 (ppp) cc_final: 0.8417 (ptm) REVERT: D 335 PHE cc_start: 0.8930 (OUTLIER) cc_final: 0.8117 (t80) REVERT: E 140 LYS cc_start: 0.8818 (tptp) cc_final: 0.8412 (tppt) REVERT: J 13 MET cc_start: 0.8126 (tmm) cc_final: 0.7892 (tpt) outliers start: 51 outliers final: 31 residues processed: 180 average time/residue: 0.5268 time to fit residues: 175.1987 Evaluate side-chains 160 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 5.602 ------------------------------------------------------------------------------- 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 480 optimal weight: 4.9990 chunk 581 optimal weight: 1.9990 chunk 402 optimal weight: 3.9990 chunk 644 optimal weight: 10.0000 chunk 491 optimal weight: 3.9990 chunk 457 optimal weight: 10.0000 chunk 366 optimal weight: 3.9990 chunk 502 optimal weight: 2.9990 chunk 843 optimal weight: 10.0000 chunk 439 optimal weight: 4.9990 chunk 640 optimal weight: 0.1980 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 ASN E 22 GLN E 48 GLN ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 26 ASN ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 372 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.068146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054846 restraints weight = 222529.226| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 2.77 r_work: 0.2927 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 63690 Z= 0.288 Angle : 0.509 7.604 86636 Z= 0.296 Chirality : 0.039 0.194 10912 Planarity : 0.003 0.034 11506 Dihedral : 4.468 31.080 9086 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.10 % Allowed : 9.81 % Favored : 89.09 % 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: 1.43 (0.09), residues: 8646 helix: 2.52 (0.07), residues: 4642 sheet: -0.32 (0.16), residues: 946 loop : -1.18 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.020 0.002 PHE K 335 TYR 0.012 0.001 TYR A 361 ARG 0.003 0.000 ARG H 370 *********************** 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 209 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 134 time to evaluate : 5.731 Fit side-chains REVERT: A 140 LYS cc_start: 0.8744 (tptp) cc_final: 0.8367 (tppt) REVERT: B 144 MET cc_start: 0.8774 (ptm) cc_final: 0.8469 (ptm) REVERT: b 275 ASP cc_start: 0.8459 (t70) cc_final: 0.8199 (t0) REVERT: C 335 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.7220 (t80) REVERT: D 144 MET cc_start: 0.8714 (ppp) cc_final: 0.8458 (ptm) REVERT: D 335 PHE cc_start: 0.8991 (OUTLIER) cc_final: 0.8281 (t80) REVERT: E 36 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8842 (pp) REVERT: E 140 LYS cc_start: 0.8812 (tptp) cc_final: 0.8405 (tppt) REVERT: E 335 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8288 (t80) REVERT: J 13 MET cc_start: 0.8318 (tmm) cc_final: 0.8039 (tpt) REVERT: J 129 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7673 (mt0) REVERT: j 216 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7947 (ttp-170) REVERT: K 129 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7378 (mp10) outliers start: 75 outliers final: 41 residues processed: 197 average time/residue: 0.5134 time to fit residues: 187.6246 Evaluate side-chains 170 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 5.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 374 LEU 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 175 VAL 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 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 36 LEU 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 e residue 5 ILE 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 29 ILE 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 148 VAL Chi-restraints excluded: chain H residue 393 LEU Chi-restraints excluded: chain h residue 5 ILE 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 i residue 5 ILE Chi-restraints excluded: chain J residue 129 GLN 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 206 THR Chi-restraints excluded: chain j residue 229 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 635 optimal weight: 3.9990 chunk 852 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 477 optimal weight: 2.9990 chunk 307 optimal weight: 0.6980 chunk 646 optimal weight: 20.0000 chunk 366 optimal weight: 3.9990 chunk 687 optimal weight: 10.0000 chunk 349 optimal weight: 0.9980 chunk 666 optimal weight: 5.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 124 ASN ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 332 GLN ** h 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.069276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056028 restraints weight = 221946.803| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.77 r_work: 0.2960 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63690 Z= 0.225 Angle : 0.467 12.095 86636 Z= 0.274 Chirality : 0.038 0.183 10912 Planarity : 0.002 0.033 11506 Dihedral : 4.272 31.039 9086 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.40 % Allowed : 10.53 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.57 (0.09), residues: 8646 helix: 2.66 (0.07), residues: 4708 sheet: -0.32 (0.16), residues: 968 loop : -1.23 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.017 0.001 PHE K 335 TYR 0.011 0.001 TYR A 361 ARG 0.003 0.000 ARG b 370 *********************** 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 248 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 153 time to evaluate : 5.700 Fit side-chains REVERT: A 140 LYS cc_start: 0.8697 (tptp) cc_final: 0.8286 (tppt) REVERT: A 146 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8782 (mm) REVERT: B 101 THR cc_start: 0.8476 (m) cc_final: 0.8132 (t) REVERT: b 275 ASP cc_start: 0.8437 (t70) cc_final: 0.8182 (t0) REVERT: C 335 PHE cc_start: 0.8625 (OUTLIER) cc_final: 0.7295 (t80) REVERT: c 79 GLU cc_start: 0.8098 (tt0) cc_final: 0.7888 (tp30) REVERT: c 335 PHE cc_start: 0.8808 (OUTLIER) cc_final: 0.7746 (t80) REVERT: D 144 MET cc_start: 0.8674 (ppp) cc_final: 0.8473 (ptm) REVERT: D 335 PHE cc_start: 0.8949 (OUTLIER) cc_final: 0.8285 (t80) REVERT: E 36 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8755 (pp) REVERT: E 140 LYS cc_start: 0.8743 (tptp) cc_final: 0.8346 (tppt) REVERT: E 335 PHE cc_start: 0.9255 (OUTLIER) cc_final: 0.8256 (t80) REVERT: e 335 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.7930 (t80) REVERT: h 334 ARG cc_start: 0.9015 (OUTLIER) cc_final: 0.8724 (ttt180) REVERT: J 13 MET cc_start: 0.8347 (tmm) cc_final: 0.8045 (tpt) REVERT: J 129 GLN cc_start: 0.7879 (OUTLIER) cc_final: 0.7460 (mt0) REVERT: j 216 ARG cc_start: 0.8292 (ttp80) cc_final: 0.7886 (ttp-170) REVERT: j 354 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8646 (p) REVERT: K 36 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8858 (pp) REVERT: K 129 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.7431 (mp10) REVERT: K 217 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8453 (tt) outliers start: 95 outliers final: 53 residues processed: 233 average time/residue: 0.5188 time to fit residues: 222.0624 Evaluate side-chains 202 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 136 time to evaluate : 5.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ILE 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 c residue 368 MET 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 36 LEU 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 335 PHE Chi-restraints excluded: chain e residue 5 ILE Chi-restraints excluded: chain e residue 12 LEU 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 200 VAL Chi-restraints excluded: chain G residue 29 ILE Chi-restraints excluded: chain G residue 205 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 g residue 5 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 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 I residue 339 ILE Chi-restraints excluded: chain i residue 5 ILE Chi-restraints excluded: chain i residue 335 PHE Chi-restraints excluded: chain J residue 129 GLN 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 354 SER Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 83 THR 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 217 LEU Chi-restraints excluded: chain K residue 297 ILE 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 Chi-restraints excluded: chain k residue 382 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 807 optimal weight: 0.5980 chunk 746 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 526 optimal weight: 4.9990 chunk 809 optimal weight: 0.6980 chunk 228 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 551 optimal weight: 4.9990 chunk 606 optimal weight: 3.9990 chunk 217 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 86 ASN c 65 GLN ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 30 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.070571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057379 restraints weight = 219809.480| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.77 r_work: 0.2993 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 63690 Z= 0.185 Angle : 0.437 8.575 86636 Z= 0.257 Chirality : 0.037 0.189 10912 Planarity : 0.002 0.041 11506 Dihedral : 4.082 30.143 9086 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.41 % Allowed : 11.46 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.80 (0.09), residues: 8646 helix: 2.86 (0.07), residues: 4708 sheet: -0.21 (0.16), residues: 968 loop : -1.17 (0.11), residues: 2970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP i 238 PHE 0.016 0.001 PHE K 335 TYR 0.008 0.001 TYR b 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 272 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 176 time to evaluate : 5.615 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8653 (tptp) cc_final: 0.8220 (tppt) REVERT: B 101 THR cc_start: 0.8366 (m) cc_final: 0.8045 (t) REVERT: b 275 ASP cc_start: 0.8404 (t70) cc_final: 0.8150 (t0) REVERT: b 335 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.7910 (t80) REVERT: b 358 ASP cc_start: 0.7909 (m-30) cc_final: 0.7683 (m-30) REVERT: C 335 PHE cc_start: 0.8563 (OUTLIER) cc_final: 0.7195 (t80) REVERT: c 79 GLU cc_start: 0.8183 (tt0) cc_final: 0.7905 (tp30) REVERT: c 335 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7740 (t80) REVERT: D 335 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8231 (t80) REVERT: E 36 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8676 (pp) REVERT: E 140 LYS cc_start: 0.8653 (tptp) cc_final: 0.8266 (tppt) REVERT: E 335 PHE cc_start: 0.9233 (OUTLIER) cc_final: 0.8282 (t80) REVERT: e 335 PHE cc_start: 0.8882 (OUTLIER) cc_final: 0.7924 (t80) REVERT: e 390 GLN cc_start: 0.8867 (mm110) cc_final: 0.8553 (mt0) REVERT: F 140 LYS cc_start: 0.9016 (tptp) cc_final: 0.8746 (tppt) REVERT: h 334 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8688 (ttt180) REVERT: I 154 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: i 144 MET cc_start: 0.6670 (tpt) cc_final: 0.6336 (ttt) REVERT: J 13 MET cc_start: 0.8296 (tmm) cc_final: 0.8052 (tpt) REVERT: J 129 GLN cc_start: 0.7832 (OUTLIER) cc_final: 0.7416 (mt0) REVERT: j 216 ARG cc_start: 0.8381 (ttp80) cc_final: 0.8076 (ttp-170) REVERT: j 354 SER cc_start: 0.8907 (OUTLIER) cc_final: 0.8662 (p) REVERT: K 36 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8796 (pp) REVERT: K 129 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7405 (mp10) REVERT: K 217 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8414 (tt) outliers start: 96 outliers final: 55 residues processed: 256 average time/residue: 0.5114 time to fit residues: 240.5863 Evaluate side-chains 217 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 148 time to evaluate : 5.661 ------------------------------------------------------------------------------- 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 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 72 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain d residue 200 VAL Chi-restraints excluded: chain d residue 226 LEU Chi-restraints excluded: chain E residue 36 LEU 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 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 29 ILE Chi-restraints excluded: chain G residue 262 VAL Chi-restraints excluded: chain G residue 315 ASP 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 393 LEU Chi-restraints excluded: chain h residue 5 ILE Chi-restraints excluded: chain h residue 175 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 154 GLU 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 i residue 335 PHE Chi-restraints excluded: chain J residue 129 GLN 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 j residue 354 SER 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 217 LEU Chi-restraints excluded: chain K residue 297 ILE 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 144 MET Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 322 ASP Chi-restraints excluded: chain k residue 382 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 599 optimal weight: 6.9990 chunk 261 optimal weight: 0.1980 chunk 633 optimal weight: 8.9990 chunk 453 optimal weight: 10.0000 chunk 617 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 469 optimal weight: 0.8980 chunk 828 optimal weight: 3.9990 chunk 379 optimal weight: 9.9990 chunk 192 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 overall best weight: 1.4382 ------------------------------------------------------------------------------- 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 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 332 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.070780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.057591 restraints weight = 219950.423| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.78 r_work: 0.2996 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 63690 Z= 0.185 Angle : 0.435 7.887 86636 Z= 0.255 Chirality : 0.037 0.216 10912 Planarity : 0.002 0.037 11506 Dihedral : 4.010 30.278 9086 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.43 % Allowed : 11.89 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.86 (0.09), residues: 8646 helix: 2.90 (0.07), residues: 4719 sheet: -0.17 (0.16), residues: 968 loop : -1.15 (0.11), residues: 2959 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP i 238 PHE 0.016 0.001 PHE K 335 TYR 0.007 0.001 TYR d 194 ARG 0.002 0.000 ARG b 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 259 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 162 time to evaluate : 5.778 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8606 (tptp) cc_final: 0.8196 (tppt) REVERT: B 101 THR cc_start: 0.8334 (m) cc_final: 0.8016 (t) REVERT: b 275 ASP cc_start: 0.8401 (t70) cc_final: 0.8148 (t0) REVERT: b 335 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7898 (t80) REVERT: b 358 ASP cc_start: 0.7982 (m-30) cc_final: 0.7733 (m-30) REVERT: C 335 PHE cc_start: 0.8564 (OUTLIER) cc_final: 0.7197 (t80) REVERT: c 79 GLU cc_start: 0.8145 (tt0) cc_final: 0.7876 (tp30) REVERT: c 335 PHE cc_start: 0.8774 (OUTLIER) cc_final: 0.7780 (t80) REVERT: D 335 PHE cc_start: 0.8929 (OUTLIER) cc_final: 0.8205 (t80) REVERT: E 36 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8652 (pp) REVERT: E 140 LYS cc_start: 0.8624 (tptp) cc_final: 0.8243 (tppt) REVERT: E 335 PHE cc_start: 0.9236 (OUTLIER) cc_final: 0.8284 (t80) REVERT: e 335 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.7934 (t80) REVERT: e 390 GLN cc_start: 0.8927 (mm110) cc_final: 0.8611 (mt0) REVERT: F 140 LYS cc_start: 0.8986 (tptp) cc_final: 0.8737 (tppt) REVERT: h 334 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8691 (ttt180) REVERT: h 375 GLN cc_start: 0.8425 (mm-40) cc_final: 0.8165 (tm-30) REVERT: I 154 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: i 144 MET cc_start: 0.6757 (tpt) cc_final: 0.6420 (ttt) REVERT: J 129 GLN cc_start: 0.7851 (OUTLIER) cc_final: 0.7500 (mt0) REVERT: j 216 ARG cc_start: 0.8359 (ttp80) cc_final: 0.8039 (ttp-170) REVERT: j 354 SER cc_start: 0.8865 (OUTLIER) cc_final: 0.8629 (p) REVERT: K 36 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8752 (pp) REVERT: K 129 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: K 217 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8500 (tt) outliers start: 97 outliers final: 67 residues processed: 240 average time/residue: 0.5202 time to fit residues: 230.2842 Evaluate side-chains 237 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 156 time to evaluate : 5.668 ------------------------------------------------------------------------------- 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 95 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 72 ILE 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 d residue 200 VAL Chi-restraints excluded: chain d residue 226 LEU Chi-restraints excluded: chain E residue 36 LEU 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 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 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 241 THR Chi-restraints excluded: chain H residue 393 LEU 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 154 GLU Chi-restraints excluded: chain I residue 175 VAL Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain i residue 5 ILE Chi-restraints excluded: chain i residue 335 PHE Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 13 MET Chi-restraints excluded: chain j residue 38 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain j residue 206 THR Chi-restraints excluded: chain j residue 229 THR Chi-restraints excluded: chain j residue 324 LEU Chi-restraints excluded: chain j residue 354 SER Chi-restraints excluded: chain K residue 36 LEU Chi-restraints excluded: chain K residue 83 THR 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 217 LEU Chi-restraints excluded: chain K residue 297 ILE 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 144 MET Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 322 ASP Chi-restraints excluded: chain k residue 382 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 798 optimal weight: 9.9990 chunk 436 optimal weight: 0.9990 chunk 593 optimal weight: 1.9990 chunk 333 optimal weight: 0.8980 chunk 788 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 68 optimal weight: 0.0970 chunk 94 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 625 optimal weight: 1.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 30 GLN b 39 ASN F 199 ASN ** F 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 387 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.072807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.059820 restraints weight = 219393.516| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.74 r_work: 0.3049 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2451 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= 0.151 Angle : 0.411 13.869 86636 Z= 0.240 Chirality : 0.036 0.172 10912 Planarity : 0.002 0.035 11506 Dihedral : 3.825 29.112 9086 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.40 % Allowed : 12.33 % Favored : 86.28 % 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: 2.13 (0.09), residues: 8646 helix: 3.21 (0.07), residues: 4642 sheet: -0.08 (0.16), residues: 1023 loop : -1.07 (0.11), residues: 2981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP j 238 PHE 0.014 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 293 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 198 time to evaluate : 5.647 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8443 (tptp) cc_final: 0.8183 (tppt) REVERT: B 101 THR cc_start: 0.8168 (m) cc_final: 0.7879 (t) REVERT: b 275 ASP cc_start: 0.8404 (t70) cc_final: 0.8151 (t0) REVERT: b 335 PHE cc_start: 0.8700 (OUTLIER) cc_final: 0.8023 (t80) REVERT: b 358 ASP cc_start: 0.7779 (m-30) cc_final: 0.7561 (m-30) REVERT: C 335 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.7067 (t80) REVERT: c 79 GLU cc_start: 0.8108 (tt0) cc_final: 0.7858 (tp30) REVERT: c 335 PHE cc_start: 0.8766 (OUTLIER) cc_final: 0.7858 (t80) REVERT: D 335 PHE cc_start: 0.8841 (OUTLIER) cc_final: 0.8119 (t80) REVERT: E 36 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8818 (pt) REVERT: E 140 LYS cc_start: 0.8498 (tptp) cc_final: 0.8187 (tppt) REVERT: E 335 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8339 (t80) REVERT: e 335 PHE cc_start: 0.8847 (OUTLIER) cc_final: 0.7888 (t80) REVERT: e 390 GLN cc_start: 0.8886 (mm110) cc_final: 0.8608 (mt0) REVERT: F 140 LYS cc_start: 0.8888 (tptp) cc_final: 0.8679 (tppt) REVERT: f 13 MET cc_start: 0.9138 (mmm) cc_final: 0.8785 (ttt) REVERT: h 334 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8638 (ttt180) REVERT: h 375 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8033 (tm-30) REVERT: i 144 MET cc_start: 0.6716 (tpt) cc_final: 0.6404 (ttt) REVERT: J 129 GLN cc_start: 0.7859 (OUTLIER) cc_final: 0.7629 (mm-40) REVERT: j 216 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8015 (ttp-170) REVERT: K 36 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8817 (pp) REVERT: K 129 GLN cc_start: 0.8378 (OUTLIER) cc_final: 0.7459 (mp10) REVERT: K 217 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8527 (tt) REVERT: k 335 PHE cc_start: 0.9189 (OUTLIER) cc_final: 0.8912 (t80) outliers start: 95 outliers final: 55 residues processed: 272 average time/residue: 0.5051 time to fit residues: 250.6466 Evaluate side-chains 236 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 5.674 ------------------------------------------------------------------------------- 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 205 VAL Chi-restraints excluded: chain C residue 224 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 72 ILE 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 d residue 200 VAL Chi-restraints excluded: chain E residue 36 LEU 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 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 5 ILE 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 241 THR 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 17 ASN Chi-restraints excluded: chain J residue 129 GLN 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 73 SER Chi-restraints excluded: chain j residue 203 THR Chi-restraints excluded: chain j residue 206 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 217 LEU Chi-restraints excluded: chain K residue 297 ILE Chi-restraints excluded: chain K residue 335 PHE Chi-restraints excluded: chain k residue 101 THR Chi-restraints excluded: chain k residue 148 VAL Chi-restraints excluded: chain k residue 335 PHE Chi-restraints excluded: chain k residue 382 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 239 optimal weight: 0.6980 chunk 124 optimal weight: 0.7980 chunk 224 optimal weight: 0.9980 chunk 442 optimal weight: 3.9990 chunk 694 optimal weight: 0.9980 chunk 783 optimal weight: 8.9990 chunk 734 optimal weight: 0.8980 chunk 633 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 664 optimal weight: 3.9990 chunk 784 optimal weight: 0.6980 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 129 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.073337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.060337 restraints weight = 219907.948| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.78 r_work: 0.3060 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2619 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= 0.145 Angle : 0.408 8.222 86636 Z= 0.238 Chirality : 0.036 0.172 10912 Planarity : 0.002 0.034 11506 Dihedral : 3.737 28.883 9086 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.10 % Allowed : 12.83 % Favored : 86.07 % 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: 2.35 (0.10), residues: 8646 helix: 3.38 (0.07), residues: 4565 sheet: 0.00 (0.16), residues: 1023 loop : -0.82 (0.12), residues: 3058 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 0.015 0.001 TYR d 194 ARG 0.003 0.000 ARG b 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 264 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 189 time to evaluate : 5.855 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8399 (tptp) cc_final: 0.8149 (tppt) REVERT: B 101 THR cc_start: 0.8026 (m) cc_final: 0.7736 (t) REVERT: b 275 ASP cc_start: 0.8325 (t70) cc_final: 0.8067 (t0) REVERT: b 335 PHE cc_start: 0.8716 (OUTLIER) cc_final: 0.8077 (t80) REVERT: b 358 ASP cc_start: 0.7710 (m-30) cc_final: 0.7465 (m-30) REVERT: C 335 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7088 (t80) REVERT: c 79 GLU cc_start: 0.8108 (tt0) cc_final: 0.7846 (tp30) REVERT: c 126 VAL cc_start: 0.9282 (t) cc_final: 0.9033 (p) REVERT: c 335 PHE cc_start: 0.8710 (OUTLIER) cc_final: 0.7771 (t80) REVERT: D 335 PHE cc_start: 0.8817 (OUTLIER) cc_final: 0.8049 (t80) REVERT: E 36 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8757 (pt) REVERT: E 140 LYS cc_start: 0.8481 (tptp) cc_final: 0.8164 (tppt) REVERT: E 335 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8363 (t80) REVERT: e 335 PHE cc_start: 0.8840 (OUTLIER) cc_final: 0.7987 (t80) REVERT: e 390 GLN cc_start: 0.8880 (mm110) cc_final: 0.8578 (mt0) REVERT: F 140 LYS cc_start: 0.8826 (tptp) cc_final: 0.8608 (tppt) REVERT: g 358 ASP cc_start: 0.8584 (m-30) cc_final: 0.8366 (m-30) REVERT: h 334 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8594 (ttt180) REVERT: h 375 GLN cc_start: 0.8327 (mm-40) cc_final: 0.7996 (tm-30) REVERT: i 144 MET cc_start: 0.6695 (tpt) cc_final: 0.6375 (ttt) REVERT: J 129 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7504 (mm-40) REVERT: j 216 ARG cc_start: 0.8303 (ttp80) cc_final: 0.7979 (ttp-170) REVERT: K 36 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8754 (pp) REVERT: K 129 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7296 (mp10) REVERT: K 217 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8525 (tt) REVERT: k 335 PHE cc_start: 0.9198 (OUTLIER) cc_final: 0.8925 (t80) outliers start: 75 outliers final: 50 residues processed: 251 average time/residue: 0.5274 time to fit residues: 244.6317 Evaluate side-chains 231 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 5.739 ------------------------------------------------------------------------------- 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 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 72 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 36 LEU 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 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 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 241 THR Chi-restraints excluded: chain H residue 363 THR 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 205 VAL Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 13 MET 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 K residue 36 LEU Chi-restraints excluded: chain K residue 83 THR 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 217 LEU 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 335 PHE Chi-restraints excluded: chain k residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 756 optimal weight: 8.9990 chunk 628 optimal weight: 6.9990 chunk 517 optimal weight: 8.9990 chunk 313 optimal weight: 0.7980 chunk 828 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 648 optimal weight: 5.9990 chunk 724 optimal weight: 40.0000 chunk 35 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 670 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 235 ASN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.072172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059034 restraints weight = 221042.118| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.79 r_work: 0.3028 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 63690 Z= 0.184 Angle : 0.426 8.902 86636 Z= 0.248 Chirality : 0.037 0.210 10912 Planarity : 0.002 0.034 11506 Dihedral : 3.779 29.352 9086 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.02 % Allowed : 13.09 % Favored : 85.89 % 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: 2.34 (0.09), residues: 8646 helix: 3.36 (0.07), residues: 4554 sheet: -0.01 (0.16), residues: 1023 loop : -0.80 (0.12), residues: 3069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP F 238 PHE 0.016 0.001 PHE K 335 TYR 0.013 0.001 TYR j 239 ARG 0.006 0.000 ARG g 93 ********************** 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 234 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 165 time to evaluate : 5.712 Fit side-chains revert: symmetry clash REVERT: A 140 LYS cc_start: 0.8379 (tptp) cc_final: 0.8158 (tppt) REVERT: A 144 MET cc_start: 0.8407 (tpp) cc_final: 0.8152 (ttt) REVERT: B 101 THR cc_start: 0.8111 (m) cc_final: 0.7843 (t) REVERT: b 275 ASP cc_start: 0.8366 (t70) cc_final: 0.8107 (t0) REVERT: b 358 ASP cc_start: 0.7785 (m-30) cc_final: 0.7552 (m-30) REVERT: C 335 PHE cc_start: 0.8576 (OUTLIER) cc_final: 0.7233 (t80) REVERT: c 79 GLU cc_start: 0.8152 (tt0) cc_final: 0.7891 (tp30) REVERT: c 335 PHE cc_start: 0.8750 (OUTLIER) cc_final: 0.7762 (t80) REVERT: D 335 PHE cc_start: 0.8908 (OUTLIER) cc_final: 0.8192 (t80) REVERT: E 36 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8626 (pp) REVERT: E 140 LYS cc_start: 0.8494 (tptp) cc_final: 0.8171 (tppt) REVERT: E 335 PHE cc_start: 0.9246 (OUTLIER) cc_final: 0.8322 (t80) REVERT: e 335 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.7909 (t80) REVERT: e 390 GLN cc_start: 0.8865 (mm110) cc_final: 0.8565 (mt0) REVERT: F 140 LYS cc_start: 0.8848 (tptp) cc_final: 0.8627 (tppt) REVERT: f 13 MET cc_start: 0.9085 (mmm) cc_final: 0.8714 (ttt) REVERT: h 334 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8620 (ttt180) REVERT: h 375 GLN cc_start: 0.8373 (mm-40) cc_final: 0.8028 (tm-30) REVERT: i 144 MET cc_start: 0.6675 (tpt) cc_final: 0.6367 (ttt) REVERT: J 129 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7542 (mt0) REVERT: j 216 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7920 (ttp-170) REVERT: K 36 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8737 (pp) REVERT: K 129 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: K 217 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8590 (tt) REVERT: k 335 PHE cc_start: 0.9259 (OUTLIER) cc_final: 0.8954 (t80) outliers start: 69 outliers final: 54 residues processed: 220 average time/residue: 0.5288 time to fit residues: 214.7317 Evaluate side-chains 229 residues out of total 6798 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 163 time to evaluate : 5.683 ------------------------------------------------------------------------------- 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 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 72 ILE Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 335 PHE Chi-restraints excluded: chain E residue 36 LEU 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 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 175 VAL 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 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 241 THR Chi-restraints excluded: chain H residue 363 THR 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 205 VAL Chi-restraints excluded: chain J residue 129 GLN Chi-restraints excluded: chain J residue 335 PHE Chi-restraints excluded: chain J residue 393 LEU Chi-restraints excluded: chain j residue 13 MET 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 83 THR 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 217 LEU 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 335 PHE Chi-restraints excluded: chain k residue 382 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 858 random chunks: chunk 634 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 426 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 133 optimal weight: 0.0370 chunk 631 optimal weight: 4.9990 chunk 323 optimal weight: 0.9990 chunk 516 optimal weight: 0.9980 chunk 197 optimal weight: 0.7980 chunk 543 optimal weight: 3.9990 chunk 759 optimal weight: 3.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- 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** g 26 ASN J 16 ASN J 298 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.073296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.060247 restraints weight = 219719.554| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.79 r_work: 0.3056 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 63690 Z= 0.151 Angle : 0.407 7.996 86636 Z= 0.237 Chirality : 0.036 0.190 10912 Planarity : 0.002 0.032 11506 Dihedral : 3.707 28.956 9086 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.02 % Allowed : 13.12 % Favored : 85.86 % 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: 2.41 (0.10), residues: 8646 helix: 3.41 (0.07), residues: 4565 sheet: 0.06 (0.16), residues: 1023 loop : -0.78 (0.12), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 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 E 31 =============================================================================== Job complete usr+sys time: 20676.75 seconds wall clock time: 358 minutes 51.60 seconds (21531.60 seconds total)