Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 17:10:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogz_20060/04_2023/6ogz_20060_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 94 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 41 5.49 5 S 399 5.16 5 C 47522 2.51 5 N 12848 2.21 5 O 14152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A GLU 33": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A GLU 67": "OE1" <-> "OE2" Residue "A GLU 86": "OE1" <-> "OE2" Residue "A ARG 87": "NH1" <-> "NH2" Residue "A GLU 99": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 221": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A GLU 266": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A ARG 335": "NH1" <-> "NH2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A GLU 390": "OE1" <-> "OE2" Residue "A GLU 404": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 432": "NH1" <-> "NH2" Residue "A GLU 468": "OE1" <-> "OE2" Residue "A GLU 489": "OE1" <-> "OE2" Residue "A ARG 627": "NH1" <-> "NH2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A GLU 769": "OE1" <-> "OE2" Residue "A GLU 774": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A ARG 829": "NH1" <-> "NH2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A ARG 879": "NH1" <-> "NH2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A GLU 957": "OE1" <-> "OE2" Residue "A ARG 987": "NH1" <-> "NH2" Residue "A ARG 1019": "NH1" <-> "NH2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "E ARG 236": "NH1" <-> "NH2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E GLU 429": "OE1" <-> "OE2" Residue "E ARG 455": "NH1" <-> "NH2" Residue "E ARG 488": "NH1" <-> "NH2" Residue "E ARG 522": "NH1" <-> "NH2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "E GLU 581": "OE1" <-> "OE2" Residue "E ARG 624": "NH1" <-> "NH2" Residue "E ARG 663": "NH1" <-> "NH2" Residue "E ARG 671": "NH1" <-> "NH2" Residue "E GLU 682": "OE1" <-> "OE2" Residue "E ARG 684": "NH1" <-> "NH2" Residue "E GLU 697": "OE1" <-> "OE2" Residue "E GLU 700": "OE1" <-> "OE2" Residue "E ARG 701": "NH1" <-> "NH2" Residue "E GLU 720": "OE1" <-> "OE2" Residue "E ARG 721": "NH1" <-> "NH2" Residue "E ARG 732": "NH1" <-> "NH2" Residue "E ARG 747": "NH1" <-> "NH2" Residue "E TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 886": "OE1" <-> "OE2" Residue "F GLU 87": "OE1" <-> "OE2" Residue "F GLU 96": "OE1" <-> "OE2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F ARG 243": "NH1" <-> "NH2" Residue "F GLU 261": "OE1" <-> "OE2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "F ARG 397": "NH1" <-> "NH2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F ARG 455": "NH1" <-> "NH2" Residue "F ARG 522": "NH1" <-> "NH2" Residue "F GLU 562": "OE1" <-> "OE2" Residue "F GLU 581": "OE1" <-> "OE2" Residue "F ARG 624": "NH1" <-> "NH2" Residue "F ARG 637": "NH1" <-> "NH2" Residue "F GLU 650": "OE1" <-> "OE2" Residue "F GLU 682": "OE1" <-> "OE2" Residue "F GLU 700": "OE1" <-> "OE2" Residue "F ARG 701": "NH1" <-> "NH2" Residue "F GLU 720": "OE1" <-> "OE2" Residue "F ARG 732": "NH1" <-> "NH2" Residue "F ARG 797": "NH1" <-> "NH2" Residue "F GLU 871": "OE1" <-> "OE2" Residue "F GLU 886": "OE1" <-> "OE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G GLU 183": "OE1" <-> "OE2" Residue "G GLU 222": "OE1" <-> "OE2" Residue "G ARG 238": "NH1" <-> "NH2" Residue "G GLU 261": "OE1" <-> "OE2" Residue "G GLU 270": "OE1" <-> "OE2" Residue "G ARG 284": "NH1" <-> "NH2" Residue "G ARG 307": "NH1" <-> "NH2" Residue "G ARG 314": "NH1" <-> "NH2" Residue "G GLU 350": "OE1" <-> "OE2" Residue "G ARG 488": "NH1" <-> "NH2" Residue "G GLU 515": "OE1" <-> "OE2" Residue "G ARG 522": "NH1" <-> "NH2" Residue "G ARG 534": "NH1" <-> "NH2" Residue "G ARG 555": "NH1" <-> "NH2" Residue "G ARG 624": "NH1" <-> "NH2" Residue "G TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 650": "OE1" <-> "OE2" Residue "G ARG 655": "NH1" <-> "NH2" Residue "G ARG 663": "NH1" <-> "NH2" Residue "G ARG 671": "NH1" <-> "NH2" Residue "G GLU 682": "OE1" <-> "OE2" Residue "G ARG 684": "NH1" <-> "NH2" Residue "G ARG 701": "NH1" <-> "NH2" Residue "G ARG 721": "NH1" <-> "NH2" Residue "G ARG 732": "NH1" <-> "NH2" Residue "G GLU 743": "OE1" <-> "OE2" Residue "G GLU 886": "OE1" <-> "OE2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I GLU 116": "OE1" <-> "OE2" Residue "I ARG 136": "NH1" <-> "NH2" Residue "I ARG 142": "NH1" <-> "NH2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I ARG 150": "NH1" <-> "NH2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "I GLU 210": "OE1" <-> "OE2" Residue "I GLU 225": "OE1" <-> "OE2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I ARG 238": "NH1" <-> "NH2" Residue "I GLU 283": "OE1" <-> "OE2" Residue "I ARG 307": "NH1" <-> "NH2" Residue "I ARG 314": "NH1" <-> "NH2" Residue "I GLU 429": "OE1" <-> "OE2" Residue "I ARG 488": "NH1" <-> "NH2" Residue "I ARG 522": "NH1" <-> "NH2" Residue "I ARG 555": "NH1" <-> "NH2" Residue "I GLU 581": "OE1" <-> "OE2" Residue "I ARG 624": "NH1" <-> "NH2" Residue "I GLU 650": "OE1" <-> "OE2" Residue "I ARG 655": "NH1" <-> "NH2" Residue "I ASP 667": "OD1" <-> "OD2" Residue "I ARG 671": "NH1" <-> "NH2" Residue "I GLU 682": "OE1" <-> "OE2" Residue "I ARG 684": "NH1" <-> "NH2" Residue "I ARG 685": "NH1" <-> "NH2" Residue "I GLU 697": "OE1" <-> "OE2" Residue "I GLU 700": "OE1" <-> "OE2" Residue "I ARG 701": "NH1" <-> "NH2" Residue "I GLU 720": "OE1" <-> "OE2" Residue "I ARG 721": "NH1" <-> "NH2" Residue "I GLU 723": "OE1" <-> "OE2" Residue "I ARG 732": "NH1" <-> "NH2" Residue "I GLU 743": "OE1" <-> "OE2" Residue "I GLU 744": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "H GLU 121": "OE1" <-> "OE2" Residue "H GLU 134": "OE1" <-> "OE2" Residue "H ARG 142": "NH1" <-> "NH2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ARG 150": "NH1" <-> "NH2" Residue "H GLU 171": "OE1" <-> "OE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "H ARG 236": "NH1" <-> "NH2" Residue "H GLU 283": "OE1" <-> "OE2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 314": "NH1" <-> "NH2" Residue "H GLU 350": "OE1" <-> "OE2" Residue "H GLU 370": "OE1" <-> "OE2" Residue "H ARG 397": "NH1" <-> "NH2" Residue "H ARG 451": "NH1" <-> "NH2" Residue "H ARG 522": "NH1" <-> "NH2" Residue "H GLU 562": "OE1" <-> "OE2" Residue "H GLU 581": "OE1" <-> "OE2" Residue "H GLU 623": "OE1" <-> "OE2" Residue "H ARG 624": "NH1" <-> "NH2" Residue "H ARG 637": "NH1" <-> "NH2" Residue "H GLU 682": "OE1" <-> "OE2" Residue "H GLU 700": "OE1" <-> "OE2" Residue "H ARG 701": "NH1" <-> "NH2" Residue "H ARG 732": "NH1" <-> "NH2" Residue "H GLU 743": "OE1" <-> "OE2" Residue "H ARG 797": "NH1" <-> "NH2" Residue "H GLU 871": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 96": "OE1" <-> "OE2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J GLU 121": "OE1" <-> "OE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ARG 150": "NH1" <-> "NH2" Residue "J GLU 171": "OE1" <-> "OE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "J GLU 222": "OE1" <-> "OE2" Residue "J GLU 225": "OE1" <-> "OE2" Residue "J ARG 230": "NH1" <-> "NH2" Residue "J GLU 234": "OE1" <-> "OE2" Residue "J ARG 236": "NH1" <-> "NH2" Residue "J GLU 261": "OE1" <-> "OE2" Residue "J GLU 270": "OE1" <-> "OE2" Residue "J GLU 283": "OE1" <-> "OE2" Residue "J ARG 307": "NH1" <-> "NH2" Residue "J ARG 314": "NH1" <-> "NH2" Residue "J GLU 322": "OE1" <-> "OE2" Residue "J GLU 345": "OE1" <-> "OE2" Residue "J ARG 397": "NH1" <-> "NH2" Residue "J ARG 451": "NH1" <-> "NH2" Residue "J ARG 522": "NH1" <-> "NH2" Residue "J GLU 581": "OE1" <-> "OE2" Residue "J ARG 624": "NH1" <-> "NH2" Residue "J ARG 637": "NH1" <-> "NH2" Residue "J GLU 697": "OE1" <-> "OE2" Residue "J ARG 701": "NH1" <-> "NH2" Residue "J GLU 720": "OE1" <-> "OE2" Residue "J GLU 723": "OE1" <-> "OE2" Residue "J ARG 732": "NH1" <-> "NH2" Residue "J GLU 743": "OE1" <-> "OE2" Residue "J ARG 797": "NH1" <-> "NH2" Residue "K GLU 134": "OE1" <-> "OE2" Residue "K ARG 136": "NH1" <-> "NH2" Residue "K ARG 142": "NH1" <-> "NH2" Residue "K GLU 148": "OE1" <-> "OE2" Residue "K ARG 150": "NH1" <-> "NH2" Residue "K GLU 171": "OE1" <-> "OE2" Residue "K GLU 210": "OE1" <-> "OE2" Residue "K ARG 238": "NH1" <-> "NH2" Residue "K GLU 261": "OE1" <-> "OE2" Residue "K GLU 270": "OE1" <-> "OE2" Residue "K ARG 284": "NH1" <-> "NH2" Residue "K ARG 307": "NH1" <-> "NH2" Residue "K ARG 314": "NH1" <-> "NH2" Residue "K GLU 345": "OE1" <-> "OE2" Residue "K GLU 363": "OE1" <-> "OE2" Residue "K GLU 429": "OE1" <-> "OE2" Residue "K ARG 488": "NH1" <-> "NH2" Residue "K ARG 522": "NH1" <-> "NH2" Residue "K ARG 555": "NH1" <-> "NH2" Residue "K ARG 624": "NH1" <-> "NH2" Residue "K GLU 650": "OE1" <-> "OE2" Residue "K ARG 655": "NH1" <-> "NH2" Residue "K ARG 663": "NH1" <-> "NH2" Residue "K ARG 671": "NH1" <-> "NH2" Residue "K GLU 682": "OE1" <-> "OE2" Residue "K ARG 684": "NH1" <-> "NH2" Residue "K GLU 700": "OE1" <-> "OE2" Residue "K ARG 701": "NH1" <-> "NH2" Residue "K ARG 721": "NH1" <-> "NH2" Residue "K ARG 732": "NH1" <-> "NH2" Residue "K GLU 743": "OE1" <-> "OE2" Residue "K GLU 744": "OE1" <-> "OE2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "L ARG 142": "NH1" <-> "NH2" Residue "L ARG 150": "NH1" <-> "NH2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 223": "OE1" <-> "OE2" Residue "L GLU 225": "OE1" <-> "OE2" Residue "L GLU 234": "OE1" <-> "OE2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L GLU 270": "OE1" <-> "OE2" Residue "L ARG 307": "NH1" <-> "NH2" Residue "L ARG 314": "NH1" <-> "NH2" Residue "L GLU 322": "OE1" <-> "OE2" Residue "L GLU 370": "OE1" <-> "OE2" Residue "L ARG 397": "NH1" <-> "NH2" Residue "L ARG 451": "NH1" <-> "NH2" Residue "L ARG 522": "NH1" <-> "NH2" Residue "L ARG 624": "NH1" <-> "NH2" Residue "L ARG 637": "NH1" <-> "NH2" Residue "L GLU 697": "OE1" <-> "OE2" Residue "L ARG 701": "NH1" <-> "NH2" Residue "L GLU 720": "OE1" <-> "OE2" Residue "L GLU 723": "OE1" <-> "OE2" Residue "L ARG 732": "NH1" <-> "NH2" Residue "L GLU 744": "OE1" <-> "OE2" Residue "L ARG 797": "NH1" <-> "NH2" Residue "L GLU 886": "OE1" <-> "OE2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "M GLU 87": "OE1" <-> "OE2" Residue "M GLU 88": "OE1" <-> "OE2" Residue "M GLU 96": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M GLU 116": "OE1" <-> "OE2" Residue "M ARG 136": "NH1" <-> "NH2" Residue "M ARG 142": "NH1" <-> "NH2" Residue "M GLU 148": "OE1" <-> "OE2" Residue "M ARG 150": "NH1" <-> "NH2" Residue "M GLU 171": "OE1" <-> "OE2" Residue "M GLU 210": "OE1" <-> "OE2" Residue "M ARG 238": "NH1" <-> "NH2" Residue "M ARG 243": "NH1" <-> "NH2" Residue "M GLU 270": "OE1" <-> "OE2" Residue "M GLU 283": "OE1" <-> "OE2" Residue "M ARG 284": "NH1" <-> "NH2" Residue "M ARG 307": "NH1" <-> "NH2" Residue "M ARG 314": "NH1" <-> "NH2" Residue "M GLU 345": "OE1" <-> "OE2" Residue "M ARG 488": "NH1" <-> "NH2" Residue "M ARG 522": "NH1" <-> "NH2" Residue "M ARG 555": "NH1" <-> "NH2" Residue "M ARG 624": "NH1" <-> "NH2" Residue "M ARG 655": "NH1" <-> "NH2" Residue "M ARG 663": "NH1" <-> "NH2" Residue "M ARG 671": "NH1" <-> "NH2" Residue "M ARG 684": "NH1" <-> "NH2" Residue "M ARG 701": "NH1" <-> "NH2" Residue "M ARG 721": "NH1" <-> "NH2" Residue "M ARG 732": "NH1" <-> "NH2" Residue "M GLU 744": "OE1" <-> "OE2" Residue "M GLU 871": "OE1" <-> "OE2" Residue "N GLU 87": "OE1" <-> "OE2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N GLU 109": "OE1" <-> "OE2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 142": "NH1" <-> "NH2" Residue "N ARG 152": "NH1" <-> "NH2" Residue "N GLU 183": "OE1" <-> "OE2" Residue "N ARG 201": "NH1" <-> "NH2" Residue "N GLU 210": "OE1" <-> "OE2" Residue "N GLU 222": "OE1" <-> "OE2" Residue "N GLU 223": "OE1" <-> "OE2" Residue "N ARG 236": "NH1" <-> "NH2" Residue "N GLU 261": "OE1" <-> "OE2" Residue "N GLU 270": "OE1" <-> "OE2" Residue "N GLU 283": "OE1" <-> "OE2" Residue "N ARG 307": "NH1" <-> "NH2" Residue "N ARG 314": "NH1" <-> "NH2" Residue "N GLU 322": "OE1" <-> "OE2" Residue "N GLU 370": "OE1" <-> "OE2" Residue "N ARG 397": "NH1" <-> "NH2" Residue "N ARG 451": "NH1" <-> "NH2" Residue "N ARG 522": "NH1" <-> "NH2" Residue "N GLU 562": "OE1" <-> "OE2" Residue "N GLU 623": "OE1" <-> "OE2" Residue "N ARG 624": "NH1" <-> "NH2" Residue "N ARG 637": "NH1" <-> "NH2" Residue "N GLU 682": "OE1" <-> "OE2" Residue "N ARG 701": "NH1" <-> "NH2" Residue "N GLU 720": "OE1" <-> "OE2" Residue "N ARG 732": "NH1" <-> "NH2" Residue "N GLU 743": "OE1" <-> "OE2" Residue "N GLU 744": "OE1" <-> "OE2" Residue "N ARG 797": "NH1" <-> "NH2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 74962 Number of models: 1 Model: "" Number of chains: 14 Chain: "B" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 378 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 2, 'rna3p': 15} Chain: "C" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 358 Classifications: {'RNA': 17} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 7, 'rna3p_pyr': 7} Link IDs: {'rna2p': 2, 'rna3p': 14} Chain: "A" Number of atoms: 8754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8754 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 34, 'TRANS': 1047} Chain: "E" Number of atoms: 6492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6492 Classifications: {'peptide': 794} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 763} Chain: "F" Number of atoms: 6570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 803, 6570 Classifications: {'peptide': 803} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 772} Chain: "G" Number of atoms: 6487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 6487 Classifications: {'peptide': 794} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 764} Chain breaks: 1 Chain: "I" Number of atoms: 6379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6379 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 752} Chain: "H" Number of atoms: 6587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6587 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain: "J" Number of atoms: 6587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6587 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain: "K" Number of atoms: 6379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6379 Classifications: {'peptide': 781} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 752} Chain: "L" Number of atoms: 6587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6587 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain: "M" Number of atoms: 6756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 826, 6756 Classifications: {'peptide': 826} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 795} Chain: "N" Number of atoms: 6587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6587 Classifications: {'peptide': 805} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 774} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'GTP': 1, 'UTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 28.56, per 1000 atoms: 0.38 Number of scatterers: 74962 At special positions: 0 Unit cell: (332.32, 326.96, 119.26, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 399 16.00 P 41 15.00 O 14152 8.00 N 12848 7.00 C 47522 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 - 3.50 Amino acid : False - 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: 24.34 Conformation dependent library (CDL) restraints added in 8.4 seconds 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17726 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 412 helices and 81 sheets defined 37.7% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.91 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.602A pdb=" N GLU A 10 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 48 removed outlier: 3.723A pdb=" N ASN A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE A 41 " --> pdb=" O ARG A 37 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 46 " --> pdb=" O HIS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 66 No H-bonds generated for 'chain 'A' and resid 63 through 66' Processing helix chain 'A' and resid 115 through 118 No H-bonds generated for 'chain 'A' and resid 115 through 118' Processing helix chain 'A' and resid 127 through 129 No H-bonds generated for 'chain 'A' and resid 127 through 129' Processing helix chain 'A' and resid 138 through 151 removed outlier: 3.638A pdb=" N ASN A 143 " --> pdb=" O SER A 139 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TRP A 148 " --> pdb=" O ALA A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.799A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N PHE A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.576A pdb=" N SER A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 213 " --> pdb=" O SER A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 230 removed outlier: 3.520A pdb=" N LEU A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 244 removed outlier: 3.580A pdb=" N VAL A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 240 through 244' Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 282 through 285 No H-bonds generated for 'chain 'A' and resid 282 through 285' Processing helix chain 'A' and resid 289 through 293 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 319 through 331 removed outlier: 4.255A pdb=" N PHE A 330 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N HIS A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 344 Processing helix chain 'A' and resid 357 through 375 removed outlier: 3.546A pdb=" N ARG A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N MET A 365 " --> pdb=" O ARG A 361 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS A 373 " --> pdb=" O ASP A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 389 through 395 removed outlier: 3.561A pdb=" N LEU A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 427 Processing helix chain 'A' and resid 467 through 471 removed outlier: 4.072A pdb=" N ILE A 471 " --> pdb=" O GLU A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 485 removed outlier: 3.873A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 502 No H-bonds generated for 'chain 'A' and resid 499 through 502' Processing helix chain 'A' and resid 506 through 508 No H-bonds generated for 'chain 'A' and resid 506 through 508' Processing helix chain 'A' and resid 528 through 530 No H-bonds generated for 'chain 'A' and resid 528 through 530' Processing helix chain 'A' and resid 532 through 543 removed outlier: 3.777A pdb=" N GLY A 537 " --> pdb=" O PRO A 533 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 540 " --> pdb=" O LYS A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 566 No H-bonds generated for 'chain 'A' and resid 563 through 566' Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 602 through 617 removed outlier: 3.571A pdb=" N LEU A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ILE A 615 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N SER A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ASN A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 removed outlier: 3.690A pdb=" N ASP A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 656 " --> pdb=" O SER A 652 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU A 657 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N THR A 658 " --> pdb=" O ASP A 654 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 709 No H-bonds generated for 'chain 'A' and resid 706 through 709' Processing helix chain 'A' and resid 711 through 722 removed outlier: 3.644A pdb=" N VAL A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN A 720 " --> pdb=" O ASN A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 739 removed outlier: 3.696A pdb=" N GLN A 738 " --> pdb=" O THR A 734 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET A 739 " --> pdb=" O LYS A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 754 through 757 No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 779 through 788 removed outlier: 3.620A pdb=" N TYR A 783 " --> pdb=" O ASP A 779 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A 784 " --> pdb=" O ASP A 780 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG A 786 " --> pdb=" O VAL A 782 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA A 787 " --> pdb=" O TYR A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 802 Processing helix chain 'A' and resid 808 through 819 removed outlier: 3.554A pdb=" N ARG A 814 " --> pdb=" O ASN A 810 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 841 removed outlier: 3.792A pdb=" N GLY A 830 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEU A 833 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN A 840 " --> pdb=" O LYS A 836 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N SER A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 861 removed outlier: 3.505A pdb=" N GLU A 848 " --> pdb=" O PRO A 844 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA A 856 " --> pdb=" O ALA A 852 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N THR A 859 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N MET A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 884 removed outlier: 3.738A pdb=" N ARG A 879 " --> pdb=" O ASN A 875 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASP A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Proline residue: A 883 - end of helix Processing helix chain 'A' and resid 905 through 914 removed outlier: 4.591A pdb=" N ILE A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 934 No H-bonds generated for 'chain 'A' and resid 931 through 934' Processing helix chain 'A' and resid 944 through 951 removed outlier: 3.603A pdb=" N TYR A 948 " --> pdb=" O ILE A 944 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 965 removed outlier: 3.580A pdb=" N GLN A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 Processing helix chain 'A' and resid 983 through 988 removed outlier: 3.762A pdb=" N ARG A 987 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A 988 " --> pdb=" O LYS A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1047 removed outlier: 3.508A pdb=" N ILE A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS A1038 " --> pdb=" O HIS A1034 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS A1047 " --> pdb=" O ASN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1070 removed outlier: 3.729A pdb=" N ILE A1064 " --> pdb=" O LYS A1060 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 183 removed outlier: 3.979A pdb=" N ARG E 170 " --> pdb=" O ASP E 166 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU E 181 " --> pdb=" O TYR E 177 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N THR E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU E 183 " --> pdb=" O GLN E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 219 removed outlier: 3.711A pdb=" N CYS E 215 " --> pdb=" O THR E 211 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE E 219 " --> pdb=" O CYS E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.643A pdb=" N PHE E 231 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE E 232 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.649A pdb=" N TYR E 262 " --> pdb=" O ALA E 258 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE E 263 " --> pdb=" O PHE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 277 No H-bonds generated for 'chain 'E' and resid 274 through 277' Processing helix chain 'E' and resid 283 through 286 No H-bonds generated for 'chain 'E' and resid 283 through 286' Processing helix chain 'E' and resid 324 through 339 removed outlier: 3.622A pdb=" N SER E 331 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN E 332 " --> pdb=" O ILE E 328 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE E 334 " --> pdb=" O THR E 330 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 338 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL E 339 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 357 removed outlier: 3.721A pdb=" N GLN E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 379 through 385 Processing helix chain 'E' and resid 387 through 394 removed outlier: 4.266A pdb=" N ALA E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 420 removed outlier: 3.708A pdb=" N ILE E 412 " --> pdb=" O TYR E 408 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET E 415 " --> pdb=" O LEU E 411 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N TRP E 416 " --> pdb=" O ILE E 412 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR E 419 " --> pdb=" O MET E 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 441 removed outlier: 4.272A pdb=" N ALA E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS E 434 " --> pdb=" O SER E 430 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 447 No H-bonds generated for 'chain 'E' and resid 444 through 447' Processing helix chain 'E' and resid 475 through 483 removed outlier: 3.646A pdb=" N LEU E 479 " --> pdb=" O VAL E 475 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N HIS E 480 " --> pdb=" O ALA E 476 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE E 481 " --> pdb=" O ASN E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 506 Processing helix chain 'E' and resid 508 through 513 Processing helix chain 'E' and resid 516 through 519 No H-bonds generated for 'chain 'E' and resid 516 through 519' Processing helix chain 'E' and resid 530 through 537 Processing helix chain 'E' and resid 541 through 544 No H-bonds generated for 'chain 'E' and resid 541 through 544' Processing helix chain 'E' and resid 547 through 550 No H-bonds generated for 'chain 'E' and resid 547 through 550' Processing helix chain 'E' and resid 553 through 567 removed outlier: 3.528A pdb=" N TYR E 561 " --> pdb=" O LEU E 557 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU E 562 " --> pdb=" O ALA E 558 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA E 566 " --> pdb=" O GLU E 562 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N CYS E 567 " --> pdb=" O THR E 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 589 through 592 No H-bonds generated for 'chain 'E' and resid 589 through 592' Processing helix chain 'E' and resid 608 through 614 removed outlier: 3.520A pdb=" N ASN E 614 " --> pdb=" O TYR E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 637 removed outlier: 3.613A pdb=" N ASN E 626 " --> pdb=" O ASN E 622 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP E 627 " --> pdb=" O GLU E 623 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 630 " --> pdb=" O ASN E 626 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE E 631 " --> pdb=" O ASP E 627 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE E 632 " --> pdb=" O ALA E 628 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E 634 " --> pdb=" O ALA E 630 " (cutoff:3.500A) Processing helix chain 'E' and resid 647 through 650 No H-bonds generated for 'chain 'E' and resid 647 through 650' Processing helix chain 'E' and resid 652 through 655 No H-bonds generated for 'chain 'E' and resid 652 through 655' Processing helix chain 'E' and resid 667 through 676 removed outlier: 4.842A pdb=" N LEU E 672 " --> pdb=" O GLN E 668 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 673 " --> pdb=" O MET E 669 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP E 674 " --> pdb=" O TYR E 670 " (cutoff:3.500A) Processing helix chain 'E' and resid 683 through 693 removed outlier: 3.597A pdb=" N ILE E 688 " --> pdb=" O ARG E 684 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU E 691 " --> pdb=" O ASP E 687 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 692 " --> pdb=" O ILE E 688 " (cutoff:3.500A) Processing helix chain 'E' and resid 698 through 701 No H-bonds generated for 'chain 'E' and resid 698 through 701' Processing helix chain 'E' and resid 742 through 747 removed outlier: 3.590A pdb=" N MET E 746 " --> pdb=" O LEU E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 754 through 757 No H-bonds generated for 'chain 'E' and resid 754 through 757' Processing helix chain 'E' and resid 779 through 782 No H-bonds generated for 'chain 'E' and resid 779 through 782' Processing helix chain 'E' and resid 785 through 787 No H-bonds generated for 'chain 'E' and resid 785 through 787' Processing helix chain 'E' and resid 790 through 793 Processing helix chain 'E' and resid 816 through 821 removed outlier: 4.242A pdb=" N ASN E 821 " --> pdb=" O LEU E 818 " (cutoff:3.500A) Processing helix chain 'E' and resid 872 through 874 No H-bonds generated for 'chain 'E' and resid 872 through 874' Processing helix chain 'F' and resid 90 through 94 removed outlier: 3.605A pdb=" N GLN F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 90 through 94' Processing helix chain 'F' and resid 96 through 101 removed outlier: 4.405A pdb=" N THR F 101 " --> pdb=" O ILE F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 116 removed outlier: 3.946A pdb=" N LYS F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU F 115 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 182 removed outlier: 3.833A pdb=" N ARG F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR F 177 " --> pdb=" O PHE F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.881A pdb=" N ALA F 217 " --> pdb=" O ALA F 213 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN F 220 " --> pdb=" O ASP F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 3.593A pdb=" N ILE F 232 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU F 234 " --> pdb=" O ARG F 230 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 265 removed outlier: 3.968A pdb=" N ALA F 258 " --> pdb=" O PRO F 254 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N PHE F 259 " --> pdb=" O ILE F 255 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 283 through 286 No H-bonds generated for 'chain 'F' and resid 283 through 286' Processing helix chain 'F' and resid 324 through 337 removed outlier: 4.115A pdb=" N ILE F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN F 332 " --> pdb=" O ILE F 328 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU F 335 " --> pdb=" O SER F 331 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA F 336 " --> pdb=" O ASN F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 359 removed outlier: 3.982A pdb=" N GLN F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 358 " --> pdb=" O GLN F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 382 through 394 removed outlier: 3.573A pdb=" N PHE F 386 " --> pdb=" O ALA F 382 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET F 393 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 420 removed outlier: 3.923A pdb=" N SER F 413 " --> pdb=" O MET F 409 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLY F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TRP F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 420 " --> pdb=" O TRP F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 439 removed outlier: 3.854A pdb=" N ALA F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 447 Processing helix chain 'F' and resid 462 through 465 No H-bonds generated for 'chain 'F' and resid 462 through 465' Processing helix chain 'F' and resid 476 through 482 removed outlier: 4.018A pdb=" N PHE F 481 " --> pdb=" O ASN F 477 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 505 No H-bonds generated for 'chain 'F' and resid 502 through 505' Processing helix chain 'F' and resid 509 through 521 removed outlier: 3.591A pdb=" N GLN F 519 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 537 removed outlier: 3.793A pdb=" N SER F 535 " --> pdb=" O ASP F 531 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE F 536 " --> pdb=" O TYR F 532 " (cutoff:3.500A) Processing helix chain 'F' and resid 551 through 557 removed outlier: 3.931A pdb=" N LEU F 556 " --> pdb=" O ASP F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 567 No H-bonds generated for 'chain 'F' and resid 565 through 567' Processing helix chain 'F' and resid 588 through 591 No H-bonds generated for 'chain 'F' and resid 588 through 591' Processing helix chain 'F' and resid 604 through 632 removed outlier: 3.936A pdb=" N TYR F 610 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR F 611 " --> pdb=" O LEU F 607 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN F 616 " --> pdb=" O ASN F 612 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU F 623 " --> pdb=" O SER F 619 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASP F 627 " --> pdb=" O GLU F 623 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 630 " --> pdb=" O ASN F 626 " (cutoff:3.500A) Processing helix chain 'F' and resid 634 through 637 No H-bonds generated for 'chain 'F' and resid 634 through 637' Processing helix chain 'F' and resid 652 through 655 No H-bonds generated for 'chain 'F' and resid 652 through 655' Processing helix chain 'F' and resid 668 through 675 removed outlier: 3.702A pdb=" N LEU F 672 " --> pdb=" O GLN F 668 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG F 673 " --> pdb=" O MET F 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 683 through 693 removed outlier: 4.360A pdb=" N ILE F 688 " --> pdb=" O ARG F 684 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE F 692 " --> pdb=" O ILE F 688 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 702 removed outlier: 3.765A pdb=" N GLU F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 748 Processing helix chain 'F' and resid 752 through 758 removed outlier: 3.705A pdb=" N ASN F 756 " --> pdb=" O ALA F 752 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET F 757 " --> pdb=" O GLN F 753 " (cutoff:3.500A) Processing helix chain 'F' and resid 779 through 782 No H-bonds generated for 'chain 'F' and resid 779 through 782' Processing helix chain 'F' and resid 787 through 789 No H-bonds generated for 'chain 'F' and resid 787 through 789' Processing helix chain 'F' and resid 791 through 795 removed outlier: 3.757A pdb=" N LYS F 795 " --> pdb=" O ALA F 791 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 791 through 795' Processing helix chain 'F' and resid 816 through 820 removed outlier: 3.533A pdb=" N ALA F 820 " --> pdb=" O TYR F 817 " (cutoff:3.500A) Processing helix chain 'F' and resid 842 through 845 No H-bonds generated for 'chain 'F' and resid 842 through 845' Processing helix chain 'G' and resid 74 through 83 removed outlier: 3.726A pdb=" N GLN G 78 " --> pdb=" O GLU G 74 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU G 81 " --> pdb=" O LYS G 77 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL G 82 " --> pdb=" O GLN G 78 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU G 83 " --> pdb=" O LEU G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 116 removed outlier: 3.777A pdb=" N LEU G 115 " --> pdb=" O ILE G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 180 removed outlier: 3.762A pdb=" N ARG G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 218 removed outlier: 3.567A pdb=" N ILE G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 233 removed outlier: 3.726A pdb=" N ILE G 232 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA G 233 " --> pdb=" O ARG G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 260 removed outlier: 3.593A pdb=" N PHE G 259 " --> pdb=" O ILE G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 265 No H-bonds generated for 'chain 'G' and resid 262 through 265' Processing helix chain 'G' and resid 274 through 277 No H-bonds generated for 'chain 'G' and resid 274 through 277' Processing helix chain 'G' and resid 283 through 286 No H-bonds generated for 'chain 'G' and resid 283 through 286' Processing helix chain 'G' and resid 324 through 329 Processing helix chain 'G' and resid 331 through 337 removed outlier: 3.579A pdb=" N ALA G 336 " --> pdb=" O ASN G 332 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 360 removed outlier: 4.307A pdb=" N LYS G 355 " --> pdb=" O ALA G 351 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN G 358 " --> pdb=" O GLN G 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 380 through 395 removed outlier: 4.152A pdb=" N CYS G 385 " --> pdb=" O ALA G 381 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA G 392 " --> pdb=" O THR G 388 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N MET G 393 " --> pdb=" O LEU G 389 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 395 " --> pdb=" O ALA G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 418 removed outlier: 4.112A pdb=" N TRP G 416 " --> pdb=" O ILE G 412 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU G 417 " --> pdb=" O SER G 413 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LEU G 418 " --> pdb=" O GLY G 414 " (cutoff:3.500A) Processing helix chain 'G' and resid 428 through 439 removed outlier: 4.268A pdb=" N ALA G 433 " --> pdb=" O GLU G 429 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS G 434 " --> pdb=" O SER G 430 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 437 " --> pdb=" O ALA G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 465 No H-bonds generated for 'chain 'G' and resid 462 through 465' Processing helix chain 'G' and resid 474 through 483 removed outlier: 3.517A pdb=" N TRP G 478 " --> pdb=" O GLN G 474 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LEU G 479 " --> pdb=" O VAL G 475 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N HIS G 480 " --> pdb=" O ALA G 476 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE G 481 " --> pdb=" O ASN G 477 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN G 483 " --> pdb=" O LEU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 505 No H-bonds generated for 'chain 'G' and resid 502 through 505' Processing helix chain 'G' and resid 508 through 511 No H-bonds generated for 'chain 'G' and resid 508 through 511' Processing helix chain 'G' and resid 516 through 522 removed outlier: 3.793A pdb=" N SER G 521 " --> pdb=" O LEU G 517 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG G 522 " --> pdb=" O MET G 518 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 539 removed outlier: 3.594A pdb=" N ILE G 536 " --> pdb=" O TYR G 532 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG G 538 " --> pdb=" O ARG G 534 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 544 No H-bonds generated for 'chain 'G' and resid 541 through 544' Processing helix chain 'G' and resid 547 through 567 removed outlier: 3.707A pdb=" N ASP G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG G 555 " --> pdb=" O VAL G 551 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU G 564 " --> pdb=" O ASN G 560 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N CYS G 567 " --> pdb=" O THR G 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 592 removed outlier: 3.638A pdb=" N THR G 589 " --> pdb=" O LEU G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 604 through 614 removed outlier: 4.136A pdb=" N HIS G 609 " --> pdb=" O GLN G 605 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN G 614 " --> pdb=" O TYR G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 616 through 636 removed outlier: 3.974A pdb=" N ASP G 627 " --> pdb=" O GLU G 623 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE G 631 " --> pdb=" O ASP G 627 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 634 " --> pdb=" O ALA G 630 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 650 No H-bonds generated for 'chain 'G' and resid 647 through 650' Processing helix chain 'G' and resid 652 through 655 No H-bonds generated for 'chain 'G' and resid 652 through 655' Processing helix chain 'G' and resid 661 through 663 No H-bonds generated for 'chain 'G' and resid 661 through 663' Processing helix chain 'G' and resid 670 through 678 removed outlier: 3.712A pdb=" N ARG G 675 " --> pdb=" O ARG G 671 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU G 678 " --> pdb=" O ASP G 674 " (cutoff:3.500A) Processing helix chain 'G' and resid 683 through 693 removed outlier: 4.065A pdb=" N ILE G 688 " --> pdb=" O ARG G 684 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU G 691 " --> pdb=" O ASP G 687 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE G 692 " --> pdb=" O ILE G 688 " (cutoff:3.500A) Processing helix chain 'G' and resid 696 through 701 removed outlier: 3.841A pdb=" N GLU G 700 " --> pdb=" O MET G 696 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG G 701 " --> pdb=" O GLU G 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 696 through 701' Processing helix chain 'G' and resid 742 through 747 Processing helix chain 'G' and resid 752 through 758 removed outlier: 3.674A pdb=" N ASN G 756 " --> pdb=" O ALA G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 778 through 782 Processing helix chain 'G' and resid 787 through 795 removed outlier: 3.935A pdb=" N PHE G 790 " --> pdb=" O ALA G 787 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ALA G 791 " --> pdb=" O THR G 788 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N GLN G 792 " --> pdb=" O VAL G 789 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE G 793 " --> pdb=" O PHE G 790 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS G 795 " --> pdb=" O GLN G 792 " (cutoff:3.500A) Processing helix chain 'G' and resid 816 through 821 removed outlier: 4.445A pdb=" N ASN G 821 " --> pdb=" O LEU G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 872 through 874 No H-bonds generated for 'chain 'G' and resid 872 through 874' Processing helix chain 'I' and resid 113 through 116 No H-bonds generated for 'chain 'I' and resid 113 through 116' Processing helix chain 'I' and resid 166 through 183 removed outlier: 3.655A pdb=" N ARG I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN I 175 " --> pdb=" O GLU I 171 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU I 181 " --> pdb=" O TYR I 177 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 213 Processing helix chain 'I' and resid 216 through 219 No H-bonds generated for 'chain 'I' and resid 216 through 219' Processing helix chain 'I' and resid 226 through 233 removed outlier: 3.830A pdb=" N ALA I 233 " --> pdb=" O ARG I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 265 removed outlier: 3.541A pdb=" N TYR I 262 " --> pdb=" O ALA I 258 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE I 263 " --> pdb=" O PHE I 259 " (cutoff:3.500A) Processing helix chain 'I' and resid 274 through 277 No H-bonds generated for 'chain 'I' and resid 274 through 277' Processing helix chain 'I' and resid 283 through 286 No H-bonds generated for 'chain 'I' and resid 283 through 286' Processing helix chain 'I' and resid 322 through 337 removed outlier: 4.125A pdb=" N THR I 327 " --> pdb=" O SER I 323 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER I 331 " --> pdb=" O THR I 327 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN I 332 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE I 334 " --> pdb=" O THR I 330 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU I 335 " --> pdb=" O SER I 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA I 336 " --> pdb=" O ASN I 332 " (cutoff:3.500A) Processing helix chain 'I' and resid 349 through 359 removed outlier: 3.913A pdb=" N ILE I 353 " --> pdb=" O THR I 349 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN I 354 " --> pdb=" O GLU I 350 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS I 355 " --> pdb=" O ALA I 351 " (cutoff:3.500A) Processing helix chain 'I' and resid 371 through 374 removed outlier: 3.736A pdb=" N LEU I 374 " --> pdb=" O THR I 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 371 through 374' Processing helix chain 'I' and resid 382 through 393 removed outlier: 4.010A pdb=" N LYS I 387 " --> pdb=" O ASN I 383 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 390 " --> pdb=" O PHE I 386 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA I 392 " --> pdb=" O THR I 388 " (cutoff:3.500A) Processing helix chain 'I' and resid 408 through 420 removed outlier: 3.543A pdb=" N MET I 415 " --> pdb=" O LEU I 411 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TRP I 416 " --> pdb=" O ILE I 412 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU I 417 " --> pdb=" O SER I 413 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU I 418 " --> pdb=" O GLY I 414 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR I 419 " --> pdb=" O MET I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 439 removed outlier: 3.591A pdb=" N VAL I 432 " --> pdb=" O ARG I 428 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA I 433 " --> pdb=" O GLU I 429 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 462 through 465 No H-bonds generated for 'chain 'I' and resid 462 through 465' Processing helix chain 'I' and resid 478 through 483 removed outlier: 3.802A pdb=" N ASN I 483 " --> pdb=" O LEU I 479 " (cutoff:3.500A) Processing helix chain 'I' and resid 502 through 506 Processing helix chain 'I' and resid 510 through 513 No H-bonds generated for 'chain 'I' and resid 510 through 513' Processing helix chain 'I' and resid 516 through 519 No H-bonds generated for 'chain 'I' and resid 516 through 519' Processing helix chain 'I' and resid 530 through 536 removed outlier: 3.612A pdb=" N ARG I 534 " --> pdb=" O VAL I 530 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER I 535 " --> pdb=" O ASP I 531 " (cutoff:3.500A) Processing helix chain 'I' and resid 541 through 546 removed outlier: 4.467A pdb=" N ARG I 546 " --> pdb=" O LEU I 542 " (cutoff:3.500A) Processing helix chain 'I' and resid 551 through 560 removed outlier: 3.781A pdb=" N ARG I 555 " --> pdb=" O VAL I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 562 through 567 removed outlier: 3.802A pdb=" N CYS I 567 " --> pdb=" O THR I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 589 through 592 No H-bonds generated for 'chain 'I' and resid 589 through 592' Processing helix chain 'I' and resid 604 through 637 removed outlier: 3.638A pdb=" N HIS I 609 " --> pdb=" O GLN I 605 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN I 612 " --> pdb=" O PHE I 608 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN I 614 " --> pdb=" O TYR I 610 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG I 624 " --> pdb=" O ASN I 620 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP I 627 " --> pdb=" O GLU I 623 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA I 630 " --> pdb=" O ASN I 626 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE I 631 " --> pdb=" O ASP I 627 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA I 634 " --> pdb=" O ALA I 630 " (cutoff:3.500A) Processing helix chain 'I' and resid 647 through 650 No H-bonds generated for 'chain 'I' and resid 647 through 650' Processing helix chain 'I' and resid 652 through 655 No H-bonds generated for 'chain 'I' and resid 652 through 655' Processing helix chain 'I' and resid 672 through 678 removed outlier: 4.523A pdb=" N LEU I 678 " --> pdb=" O ASP I 674 " (cutoff:3.500A) Processing helix chain 'I' and resid 683 through 693 removed outlier: 3.615A pdb=" N ILE I 688 " --> pdb=" O ARG I 684 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU I 691 " --> pdb=" O ASP I 687 " (cutoff:3.500A) Processing helix chain 'I' and resid 696 through 699 No H-bonds generated for 'chain 'I' and resid 696 through 699' Processing helix chain 'I' and resid 742 through 748 removed outlier: 3.567A pdb=" N MET I 746 " --> pdb=" O LEU I 742 " (cutoff:3.500A) Processing helix chain 'I' and resid 754 through 757 No H-bonds generated for 'chain 'I' and resid 754 through 757' Processing helix chain 'I' and resid 779 through 782 No H-bonds generated for 'chain 'I' and resid 779 through 782' Processing helix chain 'I' and resid 786 through 788 No H-bonds generated for 'chain 'I' and resid 786 through 788' Processing helix chain 'I' and resid 792 through 795 No H-bonds generated for 'chain 'I' and resid 792 through 795' Processing helix chain 'I' and resid 816 through 821 removed outlier: 4.248A pdb=" N ASN I 821 " --> pdb=" O LEU I 818 " (cutoff:3.500A) Processing helix chain 'I' and resid 872 through 874 No H-bonds generated for 'chain 'I' and resid 872 through 874' Processing helix chain 'H' and resid 84 through 101 removed outlier: 3.870A pdb=" N GLU H 88 " --> pdb=" O LYS H 84 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N HIS H 89 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS H 91 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL H 93 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN H 94 " --> pdb=" O GLN H 90 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR H 101 " --> pdb=" O ILE H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 116 removed outlier: 3.823A pdb=" N LYS H 113 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU H 115 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 183 removed outlier: 3.711A pdb=" N ARG H 170 " --> pdb=" O ASP H 166 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR H 177 " --> pdb=" O PHE H 173 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU H 183 " --> pdb=" O GLN H 179 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 212 No H-bonds generated for 'chain 'H' and resid 209 through 212' Processing helix chain 'H' and resid 217 through 220 No H-bonds generated for 'chain 'H' and resid 217 through 220' Processing helix chain 'H' and resid 226 through 231 Processing helix chain 'H' and resid 254 through 260 removed outlier: 3.609A pdb=" N ALA H 258 " --> pdb=" O PRO H 254 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE H 259 " --> pdb=" O ILE H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 262 through 265 No H-bonds generated for 'chain 'H' and resid 262 through 265' Processing helix chain 'H' and resid 274 through 280 removed outlier: 3.642A pdb=" N ASN H 279 " --> pdb=" O ASP H 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 286 No H-bonds generated for 'chain 'H' and resid 283 through 286' Processing helix chain 'H' and resid 325 through 338 removed outlier: 3.937A pdb=" N THR H 330 " --> pdb=" O ASP H 326 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN H 332 " --> pdb=" O ILE H 328 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR H 333 " --> pdb=" O THR H 329 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER H 338 " --> pdb=" O ILE H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 359 removed outlier: 4.191A pdb=" N GLN H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LYS H 355 " --> pdb=" O ALA H 351 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN H 358 " --> pdb=" O GLN H 354 " (cutoff:3.500A) Processing helix chain 'H' and resid 379 through 382 No H-bonds generated for 'chain 'H' and resid 379 through 382' Processing helix chain 'H' and resid 384 through 394 removed outlier: 4.055A pdb=" N LEU H 389 " --> pdb=" O CYS H 385 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE H 390 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET H 393 " --> pdb=" O LEU H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 408 through 420 removed outlier: 3.583A pdb=" N SER H 413 " --> pdb=" O MET H 409 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TRP H 416 " --> pdb=" O ILE H 412 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU H 417 " --> pdb=" O SER H 413 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR H 419 " --> pdb=" O MET H 415 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 439 removed outlier: 3.738A pdb=" N ALA H 433 " --> pdb=" O GLU H 429 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA H 437 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 447 No H-bonds generated for 'chain 'H' and resid 444 through 447' Processing helix chain 'H' and resid 462 through 465 No H-bonds generated for 'chain 'H' and resid 462 through 465' Processing helix chain 'H' and resid 474 through 477 No H-bonds generated for 'chain 'H' and resid 474 through 477' Processing helix chain 'H' and resid 479 through 483 removed outlier: 3.534A pdb=" N ASN H 483 " --> pdb=" O LEU H 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 479 through 483' Processing helix chain 'H' and resid 509 through 522 removed outlier: 3.804A pdb=" N MET H 518 " --> pdb=" O MET H 514 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN H 519 " --> pdb=" O GLU H 515 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU H 520 " --> pdb=" O ALA H 516 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 537 removed outlier: 3.622A pdb=" N ARG H 534 " --> pdb=" O VAL H 530 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE H 536 " --> pdb=" O TYR H 532 " (cutoff:3.500A) Processing helix chain 'H' and resid 547 through 550 No H-bonds generated for 'chain 'H' and resid 547 through 550' Processing helix chain 'H' and resid 554 through 565 removed outlier: 3.610A pdb=" N TYR H 559 " --> pdb=" O ARG H 555 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR H 561 " --> pdb=" O LEU H 557 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU H 562 " --> pdb=" O ALA H 558 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU H 564 " --> pdb=" O ASN H 560 " (cutoff:3.500A) Processing helix chain 'H' and resid 585 through 592 removed outlier: 4.214A pdb=" N SER H 590 " --> pdb=" O THR H 586 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU H 591 " --> pdb=" O SER H 587 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 614 removed outlier: 3.528A pdb=" N ASN H 614 " --> pdb=" O TYR H 610 " (cutoff:3.500A) Processing helix chain 'H' and resid 616 through 637 removed outlier: 3.501A pdb=" N ASN H 626 " --> pdb=" O ASN H 622 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP H 627 " --> pdb=" O GLU H 623 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA H 630 " --> pdb=" O ASN H 626 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE H 631 " --> pdb=" O ASP H 627 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA H 634 " --> pdb=" O ALA H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 655 Processing helix chain 'H' and resid 672 through 678 removed outlier: 4.065A pdb=" N ARG H 677 " --> pdb=" O ARG H 673 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 678 " --> pdb=" O ASP H 674 " (cutoff:3.500A) Processing helix chain 'H' and resid 685 through 693 removed outlier: 3.703A pdb=" N PHE H 689 " --> pdb=" O ARG H 685 " (cutoff:3.500A) Processing helix chain 'H' and resid 696 through 702 removed outlier: 3.589A pdb=" N GLU H 700 " --> pdb=" O MET H 696 " (cutoff:3.500A) Processing helix chain 'H' and resid 742 through 747 Processing helix chain 'H' and resid 752 through 759 removed outlier: 3.786A pdb=" N ASN H 756 " --> pdb=" O ALA H 752 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU H 758 " --> pdb=" O ILE H 754 " (cutoff:3.500A) Processing helix chain 'H' and resid 779 through 782 No H-bonds generated for 'chain 'H' and resid 779 through 782' Processing helix chain 'H' and resid 791 through 795 removed outlier: 3.846A pdb=" N LYS H 795 " --> pdb=" O GLN H 792 " (cutoff:3.500A) Processing helix chain 'H' and resid 816 through 821 removed outlier: 4.476A pdb=" N ASN H 821 " --> pdb=" O LEU H 818 " (cutoff:3.500A) Processing helix chain 'H' and resid 872 through 874 No H-bonds generated for 'chain 'H' and resid 872 through 874' Processing helix chain 'J' and resid 84 through 101 removed outlier: 3.505A pdb=" N HIS J 89 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN J 94 " --> pdb=" O GLN J 90 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ILE J 97 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU J 98 " --> pdb=" O GLN J 94 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR J 101 " --> pdb=" O ILE J 97 " (cutoff:3.500A) Processing helix chain 'J' and resid 108 through 116 removed outlier: 3.712A pdb=" N LEU J 112 " --> pdb=" O GLU J 109 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS J 113 " --> pdb=" O SER J 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU J 115 " --> pdb=" O LEU J 112 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU J 116 " --> pdb=" O LYS J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 182 removed outlier: 3.677A pdb=" N ARG J 170 " --> pdb=" O ASP J 166 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE J 173 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU J 174 " --> pdb=" O ARG J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 220 removed outlier: 3.761A pdb=" N CYS J 215 " --> pdb=" O THR J 211 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 234 removed outlier: 3.532A pdb=" N ALA J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 265 removed outlier: 3.735A pdb=" N ALA J 258 " --> pdb=" O PRO J 254 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE J 259 " --> pdb=" O ILE J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 274 through 278 Processing helix chain 'J' and resid 283 through 286 No H-bonds generated for 'chain 'J' and resid 283 through 286' Processing helix chain 'J' and resid 324 through 337 removed outlier: 3.818A pdb=" N ILE J 328 " --> pdb=" O LEU J 324 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N TYR J 333 " --> pdb=" O THR J 329 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA J 336 " --> pdb=" O ASN J 332 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 359 removed outlier: 3.624A pdb=" N GLN J 354 " --> pdb=" O GLU J 350 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLN J 358 " --> pdb=" O GLN J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 379 through 394 removed outlier: 3.899A pdb=" N ASN J 383 " --> pdb=" O SER J 379 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP J 384 " --> pdb=" O GLN J 380 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU J 389 " --> pdb=" O CYS J 385 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ILE J 390 " --> pdb=" O PHE J 386 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N MET J 393 " --> pdb=" O LEU J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 408 through 420 removed outlier: 4.254A pdb=" N ILE J 412 " --> pdb=" O MET J 409 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N SER J 413 " --> pdb=" O SER J 410 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU J 418 " --> pdb=" O MET J 415 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR J 419 " --> pdb=" O TRP J 416 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL J 420 " --> pdb=" O LEU J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 428 through 439 removed outlier: 3.837A pdb=" N ALA J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU J 436 " --> pdb=" O VAL J 432 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA J 437 " --> pdb=" O ALA J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 447 Processing helix chain 'J' and resid 462 through 465 No H-bonds generated for 'chain 'J' and resid 462 through 465' Processing helix chain 'J' and resid 479 through 482 No H-bonds generated for 'chain 'J' and resid 479 through 482' Processing helix chain 'J' and resid 509 through 516 Processing helix chain 'J' and resid 518 through 522 Processing helix chain 'J' and resid 530 through 541 removed outlier: 3.621A pdb=" N ARG J 534 " --> pdb=" O VAL J 530 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER J 535 " --> pdb=" O ASP J 531 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE J 536 " --> pdb=" O TYR J 532 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLY J 539 " --> pdb=" O SER J 535 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE J 540 " --> pdb=" O ILE J 536 " (cutoff:3.500A) Processing helix chain 'J' and resid 551 through 557 removed outlier: 3.919A pdb=" N LEU J 556 " --> pdb=" O ASP J 552 " (cutoff:3.500A) Processing helix chain 'J' and resid 560 through 564 Processing helix chain 'J' and resid 585 through 592 Processing helix chain 'J' and resid 604 through 636 removed outlier: 3.731A pdb=" N ASN J 616 " --> pdb=" O ASN J 612 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP J 627 " --> pdb=" O GLU J 623 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA J 630 " --> pdb=" O ASN J 626 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE J 631 " --> pdb=" O ASP J 627 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) Processing helix chain 'J' and resid 645 through 655 Processing helix chain 'J' and resid 668 through 678 removed outlier: 3.517A pdb=" N ASP J 674 " --> pdb=" O TYR J 670 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ARG J 677 " --> pdb=" O ARG J 673 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU J 678 " --> pdb=" O ASP J 674 " (cutoff:3.500A) Processing helix chain 'J' and resid 683 through 694 removed outlier: 3.512A pdb=" N ASP J 687 " --> pdb=" O ILE J 683 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE J 688 " --> pdb=" O ARG J 684 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE J 689 " --> pdb=" O ARG J 685 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N MET J 694 " --> pdb=" O ASN J 690 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 702 removed outlier: 4.092A pdb=" N GLU J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing helix chain 'J' and resid 742 through 747 Processing helix chain 'J' and resid 754 through 758 Processing helix chain 'J' and resid 779 through 782 No H-bonds generated for 'chain 'J' and resid 779 through 782' Processing helix chain 'J' and resid 785 through 788 Processing helix chain 'J' and resid 790 through 795 removed outlier: 3.523A pdb=" N ILE J 793 " --> pdb=" O PHE J 790 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL J 794 " --> pdb=" O ALA J 791 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS J 795 " --> pdb=" O GLN J 792 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 790 through 795' Processing helix chain 'J' and resid 816 through 821 removed outlier: 3.659A pdb=" N ALA J 820 " --> pdb=" O TYR J 817 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASN J 821 " --> pdb=" O LEU J 818 " (cutoff:3.500A) Processing helix chain 'J' and resid 872 through 874 No H-bonds generated for 'chain 'J' and resid 872 through 874' Processing helix chain 'K' and resid 109 through 116 removed outlier: 3.780A pdb=" N LYS K 114 " --> pdb=" O SER K 110 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU K 115 " --> pdb=" O ILE K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 166 through 170 removed outlier: 3.767A pdb=" N ARG K 170 " --> pdb=" O ASP K 166 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 166 through 170' Processing helix chain 'K' and resid 172 through 181 removed outlier: 3.565A pdb=" N TYR K 177 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 218 removed outlier: 3.715A pdb=" N ALA K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 233 removed outlier: 3.842A pdb=" N ILE K 232 " --> pdb=" O VAL K 228 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 265 removed outlier: 3.521A pdb=" N TYR K 262 " --> pdb=" O ALA K 258 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 280 removed outlier: 3.887A pdb=" N ASN K 279 " --> pdb=" O ASP K 275 " (cutoff:3.500A) Processing helix chain 'K' and resid 283 through 286 No H-bonds generated for 'chain 'K' and resid 283 through 286' Processing helix chain 'K' and resid 322 through 337 removed outlier: 3.704A pdb=" N THR K 327 " --> pdb=" O SER K 323 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N SER K 331 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN K 332 " --> pdb=" O ILE K 328 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE K 334 " --> pdb=" O THR K 330 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU K 335 " --> pdb=" O SER K 331 " (cutoff:3.500A) Processing helix chain 'K' and resid 350 through 359 removed outlier: 3.598A pdb=" N GLN K 354 " --> pdb=" O GLU K 350 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LYS K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLN K 358 " --> pdb=" O GLN K 354 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP K 359 " --> pdb=" O LYS K 355 " (cutoff:3.500A) Processing helix chain 'K' and resid 385 through 391 removed outlier: 3.651A pdb=" N ILE K 390 " --> pdb=" O PHE K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 414 through 420 removed outlier: 3.746A pdb=" N LEU K 418 " --> pdb=" O GLY K 414 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR K 419 " --> pdb=" O MET K 415 " (cutoff:3.500A) Processing helix chain 'K' and resid 428 through 439 removed outlier: 4.285A pdb=" N ALA K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N CYS K 434 " --> pdb=" O SER K 430 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA K 437 " --> pdb=" O ALA K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 466 Processing helix chain 'K' and resid 474 through 483 removed outlier: 3.820A pdb=" N TRP K 478 " --> pdb=" O GLN K 474 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN K 483 " --> pdb=" O LEU K 479 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 506 removed outlier: 3.532A pdb=" N ASN K 506 " --> pdb=" O ASP K 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 502 through 506' Processing helix chain 'K' and resid 510 through 519 removed outlier: 4.010A pdb=" N GLU K 515 " --> pdb=" O ASN K 511 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N MET K 518 " --> pdb=" O MET K 514 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 537 removed outlier: 3.588A pdb=" N ILE K 536 " --> pdb=" O TYR K 532 " (cutoff:3.500A) Processing helix chain 'K' and resid 541 through 544 No H-bonds generated for 'chain 'K' and resid 541 through 544' Processing helix chain 'K' and resid 547 through 560 removed outlier: 3.839A pdb=" N ASP K 552 " --> pdb=" O GLY K 548 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ARG K 555 " --> pdb=" O VAL K 551 " (cutoff:3.500A) Processing helix chain 'K' and resid 562 through 565 No H-bonds generated for 'chain 'K' and resid 562 through 565' Processing helix chain 'K' and resid 585 through 592 removed outlier: 3.546A pdb=" N SER K 590 " --> pdb=" O SER K 587 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N CYS K 592 " --> pdb=" O THR K 589 " (cutoff:3.500A) Processing helix chain 'K' and resid 604 through 607 No H-bonds generated for 'chain 'K' and resid 604 through 607' Processing helix chain 'K' and resid 610 through 625 removed outlier: 3.525A pdb=" N ASN K 614 " --> pdb=" O TYR K 610 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ASN K 616 " --> pdb=" O ASN K 612 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN K 620 " --> pdb=" O ASN K 616 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG K 624 " --> pdb=" O ASN K 620 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE K 625 " --> pdb=" O TYR K 621 " (cutoff:3.500A) Processing helix chain 'K' and resid 629 through 637 removed outlier: 3.532A pdb=" N ALA K 634 " --> pdb=" O ALA K 630 " (cutoff:3.500A) Processing helix chain 'K' and resid 652 through 655 No H-bonds generated for 'chain 'K' and resid 652 through 655' Processing helix chain 'K' and resid 666 through 676 removed outlier: 3.578A pdb=" N ASP K 674 " --> pdb=" O TYR K 670 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG K 675 " --> pdb=" O ARG K 671 " (cutoff:3.500A) Processing helix chain 'K' and resid 683 through 693 removed outlier: 3.658A pdb=" N ILE K 692 " --> pdb=" O ILE K 688 " (cutoff:3.500A) Processing helix chain 'K' and resid 696 through 701 removed outlier: 3.886A pdb=" N GLU K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 742 through 748 Processing helix chain 'K' and resid 779 through 782 No H-bonds generated for 'chain 'K' and resid 779 through 782' Processing helix chain 'K' and resid 785 through 787 No H-bonds generated for 'chain 'K' and resid 785 through 787' Processing helix chain 'K' and resid 791 through 796 removed outlier: 3.970A pdb=" N LYS K 795 " --> pdb=" O ALA K 791 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 820 removed outlier: 3.729A pdb=" N ALA K 820 " --> pdb=" O TYR K 817 " (cutoff:3.500A) Processing helix chain 'K' and resid 843 through 845 No H-bonds generated for 'chain 'K' and resid 843 through 845' Processing helix chain 'K' and resid 872 through 874 No H-bonds generated for 'chain 'K' and resid 872 through 874' Processing helix chain 'L' and resid 84 through 101 removed outlier: 3.505A pdb=" N HIS L 89 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU L 92 " --> pdb=" O GLU L 88 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU L 98 " --> pdb=" O GLN L 94 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N THR L 101 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 116 removed outlier: 3.553A pdb=" N LEU L 112 " --> pdb=" O GLU L 109 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS L 113 " --> pdb=" O SER L 110 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU L 116 " --> pdb=" O LYS L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 182 removed outlier: 3.579A pdb=" N ASN L 175 " --> pdb=" O GLU L 171 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR L 182 " --> pdb=" O ASP L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 220 removed outlier: 3.797A pdb=" N PHE L 219 " --> pdb=" O CYS L 215 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 231 Processing helix chain 'L' and resid 254 through 265 removed outlier: 3.580A pdb=" N ALA L 258 " --> pdb=" O PRO L 254 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE L 263 " --> pdb=" O PHE L 259 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU L 264 " --> pdb=" O ASN L 260 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 278 removed outlier: 3.960A pdb=" N PHE L 278 " --> pdb=" O ASN L 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 274 through 278' Processing helix chain 'L' and resid 283 through 286 No H-bonds generated for 'chain 'L' and resid 283 through 286' Processing helix chain 'L' and resid 325 through 328 No H-bonds generated for 'chain 'L' and resid 325 through 328' Processing helix chain 'L' and resid 331 through 337 Processing helix chain 'L' and resid 349 through 359 removed outlier: 3.748A pdb=" N ILE L 353 " --> pdb=" O THR L 349 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLN L 354 " --> pdb=" O GLU L 350 " (cutoff:3.500A) Processing helix chain 'L' and resid 381 through 394 removed outlier: 3.507A pdb=" N ILE L 390 " --> pdb=" O PHE L 386 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N MET L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 420 removed outlier: 4.256A pdb=" N ILE L 412 " --> pdb=" O MET L 409 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER L 413 " --> pdb=" O SER L 410 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 418 " --> pdb=" O MET L 415 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 419 " --> pdb=" O TRP L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 441 removed outlier: 3.676A pdb=" N ALA L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA L 437 " --> pdb=" O ALA L 433 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR L 441 " --> pdb=" O ALA L 437 " (cutoff:3.500A) Processing helix chain 'L' and resid 444 through 447 No H-bonds generated for 'chain 'L' and resid 444 through 447' Processing helix chain 'L' and resid 462 through 469 removed outlier: 4.473A pdb=" N GLN L 468 " --> pdb=" O GLN L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 473 through 482 removed outlier: 3.802A pdb=" N TRP L 478 " --> pdb=" O GLN L 474 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N PHE L 481 " --> pdb=" O ASN L 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 508 through 519 removed outlier: 3.691A pdb=" N GLN L 512 " --> pdb=" O HIS L 508 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLU L 515 " --> pdb=" O ASN L 511 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLN L 519 " --> pdb=" O GLU L 515 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 544 removed outlier: 3.592A pdb=" N SER L 535 " --> pdb=" O ASP L 531 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE L 536 " --> pdb=" O TYR L 532 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY L 539 " --> pdb=" O SER L 535 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE L 540 " --> pdb=" O ILE L 536 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU L 543 " --> pdb=" O GLY L 539 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 567 removed outlier: 3.528A pdb=" N ASP L 552 " --> pdb=" O GLY L 548 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU L 553 " --> pdb=" O GLN L 549 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU L 556 " --> pdb=" O ASP L 552 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N TYR L 561 " --> pdb=" O LEU L 557 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU L 562 " --> pdb=" O ALA L 558 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ALA L 566 " --> pdb=" O GLU L 562 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N CYS L 567 " --> pdb=" O THR L 563 " (cutoff:3.500A) Processing helix chain 'L' and resid 585 through 588 No H-bonds generated for 'chain 'L' and resid 585 through 588' Processing helix chain 'L' and resid 609 through 637 removed outlier: 3.626A pdb=" N PHE L 617 " --> pdb=" O VAL L 613 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP L 627 " --> pdb=" O GLU L 623 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 629 " --> pdb=" O ILE L 625 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE L 631 " --> pdb=" O ASP L 627 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ALA L 634 " --> pdb=" O ALA L 630 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN L 636 " --> pdb=" O ILE L 632 " (cutoff:3.500A) Processing helix chain 'L' and resid 646 through 655 Processing helix chain 'L' and resid 672 through 675 No H-bonds generated for 'chain 'L' and resid 672 through 675' Processing helix chain 'L' and resid 683 through 686 No H-bonds generated for 'chain 'L' and resid 683 through 686' Processing helix chain 'L' and resid 690 through 693 No H-bonds generated for 'chain 'L' and resid 690 through 693' Processing helix chain 'L' and resid 696 through 701 removed outlier: 3.922A pdb=" N GLU L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 742 through 748 removed outlier: 3.578A pdb=" N ARG L 747 " --> pdb=" O GLU L 743 " (cutoff:3.500A) Processing helix chain 'L' and resid 754 through 758 Processing helix chain 'L' and resid 779 through 782 No H-bonds generated for 'chain 'L' and resid 779 through 782' Processing helix chain 'L' and resid 790 through 795 removed outlier: 3.519A pdb=" N ILE L 793 " --> pdb=" O PHE L 790 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL L 794 " --> pdb=" O ALA L 791 " (cutoff:3.500A) Processing helix chain 'L' and resid 816 through 820 removed outlier: 3.508A pdb=" N ALA L 820 " --> pdb=" O TYR L 817 " (cutoff:3.500A) Processing helix chain 'L' and resid 872 through 874 No H-bonds generated for 'chain 'L' and resid 872 through 874' Processing helix chain 'M' and resid 66 through 69 No H-bonds generated for 'chain 'M' and resid 66 through 69' Processing helix chain 'M' and resid 75 through 78 No H-bonds generated for 'chain 'M' and resid 75 through 78' Processing helix chain 'M' and resid 80 through 99 removed outlier: 4.470A pdb=" N THR M 85 " --> pdb=" O GLU M 81 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLU M 92 " --> pdb=" O GLU M 88 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN M 94 " --> pdb=" O GLN M 90 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR M 95 " --> pdb=" O LYS M 91 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE M 97 " --> pdb=" O VAL M 93 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU M 98 " --> pdb=" O GLN M 94 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 116 removed outlier: 3.892A pdb=" N LYS M 114 " --> pdb=" O SER M 110 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU M 115 " --> pdb=" O ILE M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 183 removed outlier: 3.966A pdb=" N PHE M 173 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU M 174 " --> pdb=" O ARG M 170 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR M 177 " --> pdb=" O PHE M 173 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR M 182 " --> pdb=" O ASP M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 216 removed outlier: 3.996A pdb=" N ILE M 214 " --> pdb=" O GLU M 210 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 233 removed outlier: 3.972A pdb=" N ALA M 233 " --> pdb=" O ARG M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 254 through 265 removed outlier: 3.587A pdb=" N PHE M 259 " --> pdb=" O ILE M 255 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN M 265 " --> pdb=" O GLU M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 278 Processing helix chain 'M' and resid 283 through 286 No H-bonds generated for 'chain 'M' and resid 283 through 286' Processing helix chain 'M' and resid 324 through 337 removed outlier: 3.590A pdb=" N SER M 331 " --> pdb=" O THR M 327 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU M 335 " --> pdb=" O SER M 331 " (cutoff:3.500A) Processing helix chain 'M' and resid 349 through 359 removed outlier: 3.567A pdb=" N ILE M 353 " --> pdb=" O THR M 349 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLN M 354 " --> pdb=" O GLU M 350 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLN M 358 " --> pdb=" O GLN M 354 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 393 removed outlier: 3.613A pdb=" N ASN M 383 " --> pdb=" O SER M 379 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP M 384 " --> pdb=" O GLN M 380 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N LYS M 387 " --> pdb=" O ASN M 383 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU M 389 " --> pdb=" O CYS M 385 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA M 392 " --> pdb=" O THR M 388 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET M 393 " --> pdb=" O LEU M 389 " (cutoff:3.500A) Processing helix chain 'M' and resid 409 through 412 No H-bonds generated for 'chain 'M' and resid 409 through 412' Processing helix chain 'M' and resid 414 through 417 No H-bonds generated for 'chain 'M' and resid 414 through 417' Processing helix chain 'M' and resid 428 through 441 removed outlier: 4.003A pdb=" N ALA M 433 " --> pdb=" O GLU M 429 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS M 434 " --> pdb=" O SER M 430 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA M 437 " --> pdb=" O ALA M 433 " (cutoff:3.500A) Processing helix chain 'M' and resid 444 through 447 No H-bonds generated for 'chain 'M' and resid 444 through 447' Processing helix chain 'M' and resid 462 through 465 No H-bonds generated for 'chain 'M' and resid 462 through 465' Processing helix chain 'M' and resid 474 through 481 removed outlier: 3.559A pdb=" N TRP M 478 " --> pdb=" O GLN M 474 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU M 479 " --> pdb=" O VAL M 475 " (cutoff:3.500A) Processing helix chain 'M' and resid 510 through 513 No H-bonds generated for 'chain 'M' and resid 510 through 513' Processing helix chain 'M' and resid 517 through 520 No H-bonds generated for 'chain 'M' and resid 517 through 520' Processing helix chain 'M' and resid 530 through 537 Processing helix chain 'M' and resid 539 through 546 removed outlier: 3.803A pdb=" N LEU M 543 " --> pdb=" O GLY M 539 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER M 544 " --> pdb=" O ILE M 540 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG M 546 " --> pdb=" O LEU M 542 " (cutoff:3.500A) Processing helix chain 'M' and resid 548 through 551 No H-bonds generated for 'chain 'M' and resid 548 through 551' Processing helix chain 'M' and resid 553 through 567 removed outlier: 3.963A pdb=" N GLU M 562 " --> pdb=" O ALA M 558 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU M 564 " --> pdb=" O ASN M 560 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA M 566 " --> pdb=" O GLU M 562 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N CYS M 567 " --> pdb=" O THR M 563 " (cutoff:3.500A) Processing helix chain 'M' and resid 586 through 592 removed outlier: 3.505A pdb=" N LEU M 591 " --> pdb=" O SER M 587 " (cutoff:3.500A) Processing helix chain 'M' and resid 612 through 637 removed outlier: 3.815A pdb=" N PHE M 617 " --> pdb=" O VAL M 613 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN M 620 " --> pdb=" O ASN M 616 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU M 623 " --> pdb=" O SER M 619 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN M 626 " --> pdb=" O ASN M 622 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP M 627 " --> pdb=" O GLU M 623 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA M 630 " --> pdb=" O ASN M 626 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE M 631 " --> pdb=" O ASP M 627 " (cutoff:3.500A) Processing helix chain 'M' and resid 646 through 655 Processing helix chain 'M' and resid 667 through 670 No H-bonds generated for 'chain 'M' and resid 667 through 670' Processing helix chain 'M' and resid 673 through 676 No H-bonds generated for 'chain 'M' and resid 673 through 676' Processing helix chain 'M' and resid 683 through 687 Processing helix chain 'M' and resid 689 through 692 No H-bonds generated for 'chain 'M' and resid 689 through 692' Processing helix chain 'M' and resid 698 through 701 No H-bonds generated for 'chain 'M' and resid 698 through 701' Processing helix chain 'M' and resid 743 through 748 Processing helix chain 'M' and resid 755 through 758 No H-bonds generated for 'chain 'M' and resid 755 through 758' Processing helix chain 'M' and resid 779 through 782 No H-bonds generated for 'chain 'M' and resid 779 through 782' Processing helix chain 'M' and resid 792 through 795 No H-bonds generated for 'chain 'M' and resid 792 through 795' Processing helix chain 'M' and resid 816 through 821 removed outlier: 4.388A pdb=" N ASN M 821 " --> pdb=" O LEU M 818 " (cutoff:3.500A) Processing helix chain 'M' and resid 861 through 863 No H-bonds generated for 'chain 'M' and resid 861 through 863' Processing helix chain 'M' and resid 872 through 874 No H-bonds generated for 'chain 'M' and resid 872 through 874' Processing helix chain 'N' and resid 84 through 101 removed outlier: 3.718A pdb=" N GLU N 92 " --> pdb=" O GLU N 88 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN N 94 " --> pdb=" O GLN N 90 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU N 96 " --> pdb=" O GLU N 92 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ILE N 97 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU N 98 " --> pdb=" O GLN N 94 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR N 101 " --> pdb=" O ILE N 97 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 110 No H-bonds generated for 'chain 'N' and resid 108 through 110' Processing helix chain 'N' and resid 113 through 116 No H-bonds generated for 'chain 'N' and resid 113 through 116' Processing helix chain 'N' and resid 168 through 182 removed outlier: 3.965A pdb=" N PHE N 173 " --> pdb=" O VAL N 169 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU N 174 " --> pdb=" O ARG N 170 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR N 177 " --> pdb=" O PHE N 173 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU N 181 " --> pdb=" O TYR N 177 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR N 182 " --> pdb=" O ASP N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 209 through 213 Processing helix chain 'N' and resid 216 through 219 No H-bonds generated for 'chain 'N' and resid 216 through 219' Processing helix chain 'N' and resid 226 through 232 removed outlier: 3.661A pdb=" N ARG N 230 " --> pdb=" O GLY N 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 254 through 265 removed outlier: 3.823A pdb=" N TYR N 262 " --> pdb=" O ALA N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 274 through 278 Processing helix chain 'N' and resid 283 through 286 No H-bonds generated for 'chain 'N' and resid 283 through 286' Processing helix chain 'N' and resid 325 through 337 removed outlier: 4.037A pdb=" N THR N 330 " --> pdb=" O ASP N 326 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR N 333 " --> pdb=" O THR N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 349 through 359 removed outlier: 3.760A pdb=" N GLN N 354 " --> pdb=" O GLU N 350 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN N 358 " --> pdb=" O GLN N 354 " (cutoff:3.500A) Processing helix chain 'N' and resid 384 through 394 removed outlier: 4.204A pdb=" N LEU N 389 " --> pdb=" O CYS N 385 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE N 390 " --> pdb=" O PHE N 386 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N MET N 393 " --> pdb=" O LEU N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 409 through 420 removed outlier: 3.662A pdb=" N SER N 413 " --> pdb=" O MET N 409 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY N 414 " --> pdb=" O SER N 410 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET N 415 " --> pdb=" O LEU N 411 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TRP N 416 " --> pdb=" O ILE N 412 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU N 418 " --> pdb=" O GLY N 414 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR N 419 " --> pdb=" O MET N 415 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL N 420 " --> pdb=" O TRP N 416 " (cutoff:3.500A) Processing helix chain 'N' and resid 428 through 439 removed outlier: 3.885A pdb=" N ALA N 433 " --> pdb=" O GLU N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 443 through 447 removed outlier: 3.578A pdb=" N PHE N 447 " --> pdb=" O ILE N 443 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 443 through 447' Processing helix chain 'N' and resid 462 through 469 removed outlier: 4.003A pdb=" N GLN N 468 " --> pdb=" O GLN N 464 " (cutoff:3.500A) Processing helix chain 'N' and resid 476 through 484 removed outlier: 3.996A pdb=" N PHE N 481 " --> pdb=" O ASN N 477 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN N 483 " --> pdb=" O LEU N 479 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASN N 484 " --> pdb=" O HIS N 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 508 through 522 removed outlier: 3.611A pdb=" N MET N 514 " --> pdb=" O ASN N 511 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LEU N 517 " --> pdb=" O MET N 514 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET N 518 " --> pdb=" O GLU N 515 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN N 519 " --> pdb=" O ALA N 516 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG N 522 " --> pdb=" O GLN N 519 " (cutoff:3.500A) Processing helix chain 'N' and resid 530 through 544 removed outlier: 3.699A pdb=" N SER N 535 " --> pdb=" O ASP N 531 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY N 539 " --> pdb=" O SER N 535 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE N 540 " --> pdb=" O ILE N 536 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU N 543 " --> pdb=" O GLY N 539 " (cutoff:3.500A) Processing helix chain 'N' and resid 547 through 567 removed outlier: 3.705A pdb=" N VAL N 551 " --> pdb=" O LEU N 547 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU N 553 " --> pdb=" O GLN N 549 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR N 559 " --> pdb=" O ARG N 555 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR N 561 " --> pdb=" O LEU N 557 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU N 562 " --> pdb=" O ALA N 558 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA N 566 " --> pdb=" O GLU N 562 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N CYS N 567 " --> pdb=" O THR N 563 " (cutoff:3.500A) Processing helix chain 'N' and resid 585 through 591 removed outlier: 3.853A pdb=" N SER N 590 " --> pdb=" O THR N 586 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU N 591 " --> pdb=" O SER N 587 " (cutoff:3.500A) Processing helix chain 'N' and resid 604 through 636 removed outlier: 3.544A pdb=" N TYR N 611 " --> pdb=" O LEU N 607 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN N 614 " --> pdb=" O TYR N 610 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN N 616 " --> pdb=" O ASN N 612 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN N 620 " --> pdb=" O ASN N 616 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE N 625 " --> pdb=" O TYR N 621 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP N 627 " --> pdb=" O GLU N 623 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA N 630 " --> pdb=" O ASN N 626 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE N 631 " --> pdb=" O ASP N 627 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA N 634 " --> pdb=" O ALA N 630 " (cutoff:3.500A) Processing helix chain 'N' and resid 646 through 650 Processing helix chain 'N' and resid 652 through 655 No H-bonds generated for 'chain 'N' and resid 652 through 655' Processing helix chain 'N' and resid 668 through 674 Processing helix chain 'N' and resid 683 through 686 No H-bonds generated for 'chain 'N' and resid 683 through 686' Processing helix chain 'N' and resid 690 through 694 removed outlier: 3.548A pdb=" N MET N 694 " --> pdb=" O ASN N 690 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 690 through 694' Processing helix chain 'N' and resid 696 through 702 removed outlier: 3.921A pdb=" N GLU N 700 " --> pdb=" O MET N 696 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA N 702 " --> pdb=" O GLN N 698 " (cutoff:3.500A) Processing helix chain 'N' and resid 742 through 748 Processing helix chain 'N' and resid 752 through 759 removed outlier: 3.615A pdb=" N ASN N 756 " --> pdb=" O ALA N 752 " (cutoff:3.500A) Processing helix chain 'N' and resid 779 through 782 No H-bonds generated for 'chain 'N' and resid 779 through 782' Processing helix chain 'N' and resid 785 through 787 No H-bonds generated for 'chain 'N' and resid 785 through 787' Processing helix chain 'N' and resid 790 through 795 removed outlier: 3.514A pdb=" N VAL N 794 " --> pdb=" O ALA N 791 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS N 795 " --> pdb=" O GLN N 792 " (cutoff:3.500A) Processing helix chain 'N' and resid 816 through 820 removed outlier: 3.675A pdb=" N ALA N 820 " --> pdb=" O TYR N 817 " (cutoff:3.500A) Processing helix chain 'N' and resid 872 through 874 No H-bonds generated for 'chain 'N' and resid 872 through 874' Processing sheet with id= A, first strand: chain 'A' and resid 22 through 28 removed outlier: 6.298A pdb=" N TYR A 28 " --> pdb=" O LEU A 71 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU A 71 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 748 " --> pdb=" O THR A 745 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR A 745 " --> pdb=" O LEU A 748 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 750 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ALA A 743 " --> pdb=" O LEU A 750 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 260 through 263 Processing sheet with id= C, first strand: chain 'A' and resid 406 through 410 removed outlier: 3.580A pdb=" N ARG A 406 " --> pdb=" O SER A 417 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER A 417 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N PHE A 410 " --> pdb=" O LYS A 413 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 413 " --> pdb=" O PHE A 410 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 448 through 452 removed outlier: 3.647A pdb=" N ARG A 460 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 516 through 521 removed outlier: 3.777A pdb=" N ASP A 520 " --> pdb=" O LYS A 667 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N LYS A 667 " --> pdb=" O ASP A 520 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 572 through 577 Processing sheet with id= G, first strand: chain 'A' and resid 626 through 629 Processing sheet with id= H, first strand: chain 'E' and resid 133 through 139 Processing sheet with id= I, first strand: chain 'E' and resid 238 through 240 removed outlier: 3.688A pdb=" N SER E 851 " --> pdb=" O VAL E 246 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 399 through 402 removed outlier: 5.927A pdb=" N GLU E 581 " --> pdb=" O SER E 400 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ASP E 402 " --> pdb=" O GLU E 581 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU E 583 " --> pdb=" O ASP E 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'E' and resid 488 through 492 removed outlier: 3.567A pdb=" N VAL E 499 " --> pdb=" O ARG E 488 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL E 490 " --> pdb=" O ASN E 497 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 738 through 741 Processing sheet with id= M, first strand: chain 'E' and resid 773 through 775 Processing sheet with id= N, first strand: chain 'F' and resid 238 through 240 Processing sheet with id= O, first strand: chain 'F' and resid 269 through 271 Processing sheet with id= P, first strand: chain 'F' and resid 291 through 295 Processing sheet with id= Q, first strand: chain 'F' and resid 399 through 402 removed outlier: 6.466A pdb=" N GLU F 581 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ASP F 402 " --> pdb=" O GLU F 581 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU F 583 " --> pdb=" O ASP F 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'F' and resid 830 through 832 Processing sheet with id= S, first strand: chain 'F' and resid 720 through 722 removed outlier: 3.536A pdb=" N VAL F 728 " --> pdb=" O GLU F 720 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 773 through 775 Processing sheet with id= U, first strand: chain 'G' and resid 133 through 139 removed outlier: 3.532A pdb=" N LEU G 138 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG G 152 " --> pdb=" O LEU G 138 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'G' and resid 238 through 240 removed outlier: 3.649A pdb=" N VAL G 245 " --> pdb=" O GLN G 240 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'G' and resid 293 through 295 Processing sheet with id= X, first strand: chain 'G' and resid 399 through 402 removed outlier: 6.689A pdb=" N GLU G 581 " --> pdb=" O SER G 400 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ASP G 402 " --> pdb=" O GLU G 581 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU G 583 " --> pdb=" O ASP G 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 488 through 492 removed outlier: 3.546A pdb=" N VAL G 490 " --> pdb=" O ASN G 497 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 830 through 832 removed outlier: 5.671A pdb=" N GLN G 738 " --> pdb=" O ALA G 765 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL G 767 " --> pdb=" O GLN G 738 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N ILE G 740 " --> pdb=" O VAL G 767 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 773 through 775 Processing sheet with id= AB, first strand: chain 'I' and resid 133 through 138 Processing sheet with id= AC, first strand: chain 'I' and resid 238 through 240 Processing sheet with id= AD, first strand: chain 'I' and resid 400 through 402 Processing sheet with id= AE, first strand: chain 'I' and resid 488 through 492 Processing sheet with id= AF, first strand: chain 'I' and resid 830 through 832 removed outlier: 6.044A pdb=" N GLN I 738 " --> pdb=" O ALA I 765 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL I 767 " --> pdb=" O GLN I 738 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ILE I 740 " --> pdb=" O VAL I 767 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 772 through 775 removed outlier: 7.441A pdb=" N ASP I 775 " --> pdb=" O PRO I 804 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LEU I 806 " --> pdb=" O ASP I 775 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.701A pdb=" N ARG H 152 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'H' and resid 238 through 240 Processing sheet with id= AJ, first strand: chain 'H' and resid 269 through 271 removed outlier: 5.781A pdb=" N THR H 856 " --> pdb=" O ARG H 304 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N ILE H 306 " --> pdb=" O THR H 856 " (cutoff:3.500A) removed outlier: 8.206A pdb=" N TYR H 858 " --> pdb=" O ILE H 306 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 291 through 295 Processing sheet with id= AL, first strand: chain 'H' and resid 488 through 492 removed outlier: 3.537A pdb=" N VAL H 499 " --> pdb=" O ARG H 488 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL H 490 " --> pdb=" O ASN H 497 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 710 through 712 Processing sheet with id= AN, first strand: chain 'H' and resid 720 through 722 Processing sheet with id= AO, first strand: chain 'H' and resid 738 through 741 Processing sheet with id= AP, first strand: chain 'H' and resid 773 through 775 Processing sheet with id= AQ, first strand: chain 'J' and resid 136 through 139 Processing sheet with id= AR, first strand: chain 'J' and resid 238 through 240 Processing sheet with id= AS, first strand: chain 'J' and resid 291 through 295 removed outlier: 3.955A pdb=" N ASN J 294 " --> pdb=" O SER J 866 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'J' and resid 303 through 305 removed outlier: 5.692A pdb=" N THR J 856 " --> pdb=" O ARG J 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'J' and resid 399 through 402 removed outlier: 6.366A pdb=" N GLU J 581 " --> pdb=" O SER J 400 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N ASP J 402 " --> pdb=" O GLU J 581 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU J 583 " --> pdb=" O ASP J 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'J' and resid 488 through 492 removed outlier: 3.512A pdb=" N VAL J 490 " --> pdb=" O ASN J 497 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'J' and resid 830 through 832 removed outlier: 5.987A pdb=" N GLN J 738 " --> pdb=" O ALA J 765 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL J 767 " --> pdb=" O GLN J 738 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ILE J 740 " --> pdb=" O VAL J 767 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'J' and resid 772 through 775 removed outlier: 7.592A pdb=" N ASP J 775 " --> pdb=" O PRO J 804 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU J 806 " --> pdb=" O ASP J 775 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'K' and resid 133 through 139 removed outlier: 3.777A pdb=" N LEU K 138 " --> pdb=" O ARG K 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG K 152 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'K' and resid 238 through 240 Processing sheet with id= BA, first strand: chain 'K' and resid 399 through 402 removed outlier: 6.062A pdb=" N GLU K 581 " --> pdb=" O SER K 400 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ASP K 402 " --> pdb=" O GLU K 581 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU K 583 " --> pdb=" O ASP K 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'K' and resid 488 through 492 removed outlier: 3.648A pdb=" N VAL K 499 " --> pdb=" O ARG K 488 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL K 490 " --> pdb=" O ASN K 497 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'K' and resid 720 through 722 Processing sheet with id= BD, first strand: chain 'K' and resid 738 through 741 Processing sheet with id= BE, first strand: chain 'K' and resid 773 through 775 Processing sheet with id= BF, first strand: chain 'L' and resid 136 through 139 removed outlier: 3.524A pdb=" N ARG L 152 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'L' and resid 238 through 240 Processing sheet with id= BH, first strand: chain 'L' and resid 269 through 271 Processing sheet with id= BI, first strand: chain 'L' and resid 291 through 295 Processing sheet with id= BJ, first strand: chain 'L' and resid 488 through 492 removed outlier: 3.618A pdb=" N VAL L 499 " --> pdb=" O ARG L 488 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'L' and resid 764 through 766 Processing sheet with id= BL, first strand: chain 'L' and resid 720 through 722 Processing sheet with id= BM, first strand: chain 'L' and resid 773 through 775 Processing sheet with id= BN, first strand: chain 'M' and resid 133 through 139 removed outlier: 3.625A pdb=" N ARG M 152 " --> pdb=" O LEU M 138 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'M' and resid 238 through 240 removed outlier: 3.686A pdb=" N VAL M 245 " --> pdb=" O GLN M 240 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'M' and resid 291 through 295 removed outlier: 3.658A pdb=" N ILE M 292 " --> pdb=" O ASP M 868 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'M' and resid 399 through 402 removed outlier: 6.600A pdb=" N GLU M 581 " --> pdb=" O SER M 400 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N ASP M 402 " --> pdb=" O GLU M 581 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LEU M 583 " --> pdb=" O ASP M 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'M' and resid 488 through 492 Processing sheet with id= BS, first strand: chain 'M' and resid 830 through 832 removed outlier: 3.587A pdb=" N VAL M 710 " --> pdb=" O LEU M 766 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLN M 738 " --> pdb=" O ALA M 765 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL M 767 " --> pdb=" O GLN M 738 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE M 740 " --> pdb=" O VAL M 767 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'M' and resid 773 through 775 Processing sheet with id= BU, first strand: chain 'N' and resid 136 through 139 Processing sheet with id= BV, first strand: chain 'N' and resid 238 through 240 Processing sheet with id= BW, first strand: chain 'N' and resid 269 through 271 removed outlier: 5.787A pdb=" N THR N 856 " --> pdb=" O ARG N 304 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N ILE N 306 " --> pdb=" O THR N 856 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N TYR N 858 " --> pdb=" O ILE N 306 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'N' and resid 291 through 295 Processing sheet with id= BY, first strand: chain 'N' and resid 488 through 492 removed outlier: 3.620A pdb=" N VAL N 490 " --> pdb=" O ASN N 497 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'N' and resid 710 through 712 Processing sheet with id= CA, first strand: chain 'N' and resid 720 through 722 Processing sheet with id= CB, first strand: chain 'N' and resid 738 through 741 Processing sheet with id= CC, first strand: chain 'N' and resid 773 through 775 1520 hydrogen bonds defined for protein. 4185 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: 28.44 Time building geometry restraints manager: 26.75 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: 20721 1.33 - 1.45: 12472 1.45 - 1.57: 42395 1.57 - 1.69: 79 1.69 - 1.81: 742 Bond restraints: 76409 Sorted by residual: bond pdb=" C1' UTP A1101 " pdb=" O4' UTP A1101 " ideal model delta sigma weight residual 1.605 1.414 0.191 2.00e-02 2.50e+03 9.10e+01 bond pdb=" C1' UTP A1101 " pdb=" C2' UTP A1101 " ideal model delta sigma weight residual 1.353 1.530 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" C4' UTP A1101 " pdb=" O4' UTP A1101 " ideal model delta sigma weight residual 1.311 1.447 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C4 UTP A1101 " pdb=" C5 UTP A1101 " ideal model delta sigma weight residual 1.355 1.432 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C2' UTP A1101 " pdb=" O2' UTP A1101 " ideal model delta sigma weight residual 1.480 1.410 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 76404 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.66: 1129 103.66 - 111.50: 31652 111.50 - 119.33: 32004 119.33 - 127.17: 38353 127.17 - 135.00: 641 Bond angle restraints: 103779 Sorted by residual: angle pdb=" N ILE F 504 " pdb=" CA ILE F 504 " pdb=" C ILE F 504 " ideal model delta sigma weight residual 112.96 108.25 4.71 1.00e+00 1.00e+00 2.21e+01 angle pdb=" N ILE N 390 " pdb=" CA ILE N 390 " pdb=" C ILE N 390 " ideal model delta sigma weight residual 112.96 108.26 4.70 1.00e+00 1.00e+00 2.21e+01 angle pdb=" C GLY E 596 " pdb=" N ASN E 597 " pdb=" CA ASN E 597 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" C ASP J 704 " pdb=" N LYS J 705 " pdb=" CA LYS J 705 " ideal model delta sigma weight residual 121.54 129.26 -7.72 1.91e+00 2.74e-01 1.64e+01 angle pdb=" N VAL A 441 " pdb=" CA VAL A 441 " pdb=" C VAL A 441 " ideal model delta sigma weight residual 106.21 110.50 -4.29 1.07e+00 8.73e-01 1.61e+01 ... (remaining 103774 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.56: 45694 35.56 - 71.13: 1064 71.13 - 106.69: 82 106.69 - 142.26: 1 142.26 - 177.82: 1 Dihedral angle restraints: 46842 sinusoidal: 19656 harmonic: 27186 Sorted by residual: dihedral pdb=" O4' U C 590 " pdb=" C1' U C 590 " pdb=" N1 U C 590 " pdb=" C2 U C 590 " ideal model delta sinusoidal sigma weight residual -128.00 49.82 -177.82 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" C8 GTP A1102 " pdb=" C1' GTP A1102 " pdb=" N9 GTP A1102 " pdb=" O4' GTP A1102 " ideal model delta sinusoidal sigma weight residual 104.59 -138.04 -117.37 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" CA PHE H 525 " pdb=" C PHE H 525 " pdb=" N PRO H 526 " pdb=" CA PRO H 526 " ideal model delta harmonic sigma weight residual 180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 ... (remaining 46839 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 10467 0.082 - 0.164: 1310 0.164 - 0.246: 121 0.246 - 0.329: 13 0.329 - 0.411: 6 Chirality restraints: 11917 Sorted by residual: chirality pdb=" CB ILE K 711 " pdb=" CA ILE K 711 " pdb=" CG1 ILE K 711 " pdb=" CG2 ILE K 711 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" CB VAL G 475 " pdb=" CA VAL G 475 " pdb=" CG1 VAL G 475 " pdb=" CG2 VAL G 475 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB ILE A 677 " pdb=" CA ILE A 677 " pdb=" CG1 ILE A 677 " pdb=" CG2 ILE A 677 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 11914 not shown) Planarity restraints: 13296 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' UTP A1101 " -0.228 2.00e-02 2.50e+03 5.78e-01 7.52e+03 pdb=" C2' UTP A1101 " 0.157 2.00e-02 2.50e+03 pdb=" C3' UTP A1101 " 0.629 2.00e-02 2.50e+03 pdb=" C4' UTP A1101 " -0.408 2.00e-02 2.50e+03 pdb=" C5' UTP A1101 " -0.102 2.00e-02 2.50e+03 pdb=" N1 UTP A1101 " 0.821 2.00e-02 2.50e+03 pdb=" O2' UTP A1101 " -1.029 2.00e-02 2.50e+03 pdb=" O3' UTP A1101 " 0.634 2.00e-02 2.50e+03 pdb=" O4' UTP A1101 " -0.473 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 319 " 0.055 5.00e-02 4.00e+02 8.25e-02 1.09e+01 pdb=" N PRO A 320 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO A 320 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 320 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 444 " -0.052 5.00e-02 4.00e+02 7.75e-02 9.60e+00 pdb=" N PRO G 445 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO G 445 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 445 " -0.043 5.00e-02 4.00e+02 ... (remaining 13293 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 17341 2.78 - 3.31: 65065 3.31 - 3.84: 119010 3.84 - 4.37: 143618 4.37 - 4.90: 246147 Nonbonded interactions: 591181 Sorted by model distance: nonbonded pdb=" OH TYR A1004 " pdb=" OD1 ASN A1043 " model vdw 2.244 2.440 nonbonded pdb=" OG1 THR F 580 " pdb=" OD1 ASP G 296 " model vdw 2.259 2.440 nonbonded pdb=" OH TYR L 167 " pdb=" O TYR L 641 " model vdw 2.267 2.440 nonbonded pdb=" OE1 GLN M 435 " pdb=" OG1 THR M 461 " model vdw 2.280 2.440 nonbonded pdb=" ND2 ASN K 320 " pdb=" OD1 ASN L 545 " model vdw 2.280 2.520 ... (remaining 591176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'B' and resid 583 through 599) selection = chain 'C' } ncs_group { reference = (chain 'E' and resid 107 through 887) selection = (chain 'F' and resid 107 through 887) selection = (chain 'G' and resid 107 through 887) selection = (chain 'H' and resid 107 through 887) selection = chain 'I' selection = (chain 'J' and resid 107 through 887) selection = chain 'K' selection = (chain 'L' and resid 107 through 887) selection = (chain 'M' and resid 107 through 887) selection = (chain 'N' and resid 107 through 887) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.350 Construct map_model_manager: 0.090 Extract box with map and model: 10.020 Check model and map are aligned: 0.810 Set scattering table: 0.490 Process input model: 147.890 Find NCS groups from input model: 5.070 Set up NCS constraints: 0.260 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:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 168.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 0.191 76409 Z= 0.538 Angle : 0.896 11.364 103779 Z= 0.480 Chirality : 0.058 0.411 11917 Planarity : 0.008 0.578 13296 Dihedral : 15.818 177.824 29116 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.17 % 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: -5.51 (0.06), residues: 9057 helix: -4.79 (0.03), residues: 4174 sheet: -2.86 (0.14), residues: 852 loop : -2.30 (0.08), residues: 4031 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2019 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 2005 time to evaluate : 6.671 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 5 residues processed: 2016 average time/residue: 0.7343 time to fit residues: 2495.5629 Evaluate side-chains 1535 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1530 time to evaluate : 6.818 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5255 time to fit residues: 14.5567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 765 optimal weight: 4.9990 chunk 686 optimal weight: 5.9990 chunk 381 optimal weight: 1.9990 chunk 234 optimal weight: 6.9990 chunk 463 optimal weight: 0.9990 chunk 366 optimal weight: 2.9990 chunk 710 optimal weight: 3.9990 chunk 274 optimal weight: 0.5980 chunk 431 optimal weight: 6.9990 chunk 528 optimal weight: 8.9990 chunk 822 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 ASN ** A 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 HIS A 407 GLN A 423 HIS A 649 GLN A 653 ASN A 697 ASN A 912 GLN A 954 HIS A 959 GLN A1000 ASN A1034 HIS A1044 HIS ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN E 175 ASN E 247 ASN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 GLN E 480 HIS ** E 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 573 GLN E 576 GLN E 668 GLN E 738 GLN E 760 ASN E 839 GLN E 852 ASN F 89 HIS ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 ASN F 320 ASN F 352 GLN F 358 GLN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 573 GLN F 695 ASN F 821 ASN F 835 GLN F 839 GLN ** G 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 GLN G 274 ASN G 287 ASN G 358 GLN ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** G 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 545 ASN G 574 HIS G 618 HIS G 636 ASN G 668 GLN G 753 GLN G 762 GLN G 839 GLN G 852 ASN I 126 GLN I 175 ASN I 260 ASN I 274 ASN I 287 ASN I 290 ASN I 358 GLN ** I 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 380 GLN I 396 GLN I 498 GLN I 574 HIS ** I 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 668 GLN I 753 GLN I 760 ASN I 762 GLN I 839 GLN H 240 GLN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 ASN ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 ASN H 450 GLN ** H 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 480 HIS H 636 ASN H 753 GLN ** H 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 838 GLN ** J 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 267 GLN J 352 GLN J 354 GLN J 358 GLN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 512 GLN J 545 ASN J 612 ASN J 756 ASN J 761 ASN J 762 GLN J 810 ASN J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 GLN K 247 ASN K 260 ASN K 265 GLN K 274 ASN ** K 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN ** K 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 450 GLN ** K 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 545 ASN K 573 GLN K 612 ASN K 614 ASN K 642 GLN ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 880 ASN L 94 GLN L 126 GLN ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 267 GLN L 622 ASN L 626 ASN L 636 ASN L 792 GLN L 839 GLN M 260 ASN M 274 ASN M 290 ASN M 354 GLN M 396 GLN ** M 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 574 HIS M 738 GLN M 835 GLN N 287 ASN N 352 GLN N 354 GLN N 368 GLN N 695 ASN Total number of N/Q/H flips: 119 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 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 0.046 76409 Z= 0.163 Angle : 0.533 21.136 103779 Z= 0.274 Chirality : 0.041 0.167 11917 Planarity : 0.004 0.063 13296 Dihedral : 6.413 177.341 10457 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 2.21 % 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: -4.38 (0.07), residues: 9057 helix: -3.79 (0.05), residues: 4184 sheet: -2.32 (0.15), residues: 898 loop : -1.79 (0.09), residues: 3975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1879 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1695 time to evaluate : 6.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 184 outliers final: 96 residues processed: 1793 average time/residue: 0.7249 time to fit residues: 2238.5173 Evaluate side-chains 1579 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1483 time to evaluate : 6.725 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 0 residues processed: 96 average time/residue: 0.5863 time to fit residues: 115.6270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 457 optimal weight: 8.9990 chunk 255 optimal weight: 20.0000 chunk 684 optimal weight: 7.9990 chunk 560 optimal weight: 8.9990 chunk 226 optimal weight: 0.0570 chunk 824 optimal weight: 10.0000 chunk 890 optimal weight: 20.0000 chunk 734 optimal weight: 0.9980 chunk 817 optimal weight: 8.9990 chunk 280 optimal weight: 9.9990 chunk 661 optimal weight: 0.9990 overall best weight: 3.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN A 407 GLN A 956 ASN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN ** F 378 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 GLN G 287 ASN I 137 GLN I 372 GLN I 396 GLN I 423 ASN I 498 GLN I 821 ASN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 260 ASN H 266 HIS ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 450 GLN H 512 GLN H 597 ASN ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 657 GLN J 756 ASN J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 358 GLN K 372 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 GLN ** K 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 618 HIS K 668 GLN K 792 GLN ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 519 GLN L 597 ASN M 126 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 266 HIS M 287 ASN M 368 GLN ** M 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 810 ASN M 852 ASN N 137 GLN N 354 GLN N 368 GLN ** N 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 839 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 76409 Z= 0.273 Angle : 0.562 19.232 103779 Z= 0.284 Chirality : 0.043 0.219 11917 Planarity : 0.004 0.059 13296 Dihedral : 6.236 177.730 10457 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer Outliers : 2.54 % 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: -3.67 (0.07), residues: 9057 helix: -3.06 (0.06), residues: 4179 sheet: -2.02 (0.16), residues: 890 loop : -1.58 (0.09), residues: 3988 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1754 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1542 time to evaluate : 6.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 212 outliers final: 107 residues processed: 1682 average time/residue: 0.6968 time to fit residues: 2032.3239 Evaluate side-chains 1537 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1430 time to evaluate : 6.802 Switching outliers to nearest non-outliers outliers start: 107 outliers final: 0 residues processed: 107 average time/residue: 0.5555 time to fit residues: 125.1256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 814 optimal weight: 20.0000 chunk 619 optimal weight: 2.9990 chunk 427 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 393 optimal weight: 4.9990 chunk 553 optimal weight: 9.9990 chunk 827 optimal weight: 5.9990 chunk 875 optimal weight: 6.9990 chunk 432 optimal weight: 10.0000 chunk 783 optimal weight: 6.9990 chunk 236 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 574 GLN A 862 GLN A1072 ASN E 122 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN ** G 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN I 423 ASN I 573 GLN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 573 GLN H 597 ASN ** H 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 484 ASN J 657 GLN ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN K 396 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 574 HIS ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 792 GLN ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 HIS ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 573 GLN N 220 GLN N 358 GLN ** N 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 76409 Z= 0.345 Angle : 0.595 18.554 103779 Z= 0.300 Chirality : 0.044 0.215 11917 Planarity : 0.004 0.059 13296 Dihedral : 6.273 177.849 10457 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer Outliers : 3.06 % 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: -3.36 (0.08), residues: 9057 helix: -2.73 (0.06), residues: 4220 sheet: -1.91 (0.16), residues: 898 loop : -1.48 (0.09), residues: 3939 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1763 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1508 time to evaluate : 6.744 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 255 outliers final: 131 residues processed: 1662 average time/residue: 0.7120 time to fit residues: 2044.6987 Evaluate side-chains 1558 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1427 time to evaluate : 6.719 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 0 residues processed: 131 average time/residue: 0.5620 time to fit residues: 149.7001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 729 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 652 optimal weight: 5.9990 chunk 361 optimal weight: 10.0000 chunk 747 optimal weight: 10.0000 chunk 605 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 447 optimal weight: 3.9990 chunk 786 optimal weight: 6.9990 chunk 220 optimal weight: 9.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN A 574 GLN ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1072 ASN E 122 GLN ** E 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 396 GLN ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 838 GLN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 298 ASN ** G 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN G 756 ASN I 423 ASN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 352 GLN ** H 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 537 GLN H 597 ASN H 741 ASN ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 756 ASN J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 642 GLN ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 792 GLN ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 GLN ** L 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 ASN M 90 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 839 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 126 GLN N 354 GLN ** N 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.052 76409 Z= 0.367 Angle : 0.613 18.022 103779 Z= 0.307 Chirality : 0.045 0.224 11917 Planarity : 0.004 0.059 13296 Dihedral : 6.326 177.893 10457 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer Outliers : 2.79 % 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: -3.13 (0.08), residues: 9057 helix: -2.50 (0.07), residues: 4193 sheet: -1.85 (0.16), residues: 894 loop : -1.41 (0.09), residues: 3970 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1498 time to evaluate : 6.898 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 124 residues processed: 1638 average time/residue: 0.7194 time to fit residues: 2034.7955 Evaluate side-chains 1548 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1424 time to evaluate : 6.760 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 0 residues processed: 124 average time/residue: 0.5559 time to fit residues: 141.2343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 294 optimal weight: 0.9980 chunk 788 optimal weight: 0.1980 chunk 173 optimal weight: 9.9990 chunk 514 optimal weight: 0.0470 chunk 216 optimal weight: 0.9990 chunk 876 optimal weight: 4.9990 chunk 727 optimal weight: 7.9990 chunk 405 optimal weight: 2.9990 chunk 72 optimal weight: 0.0670 chunk 289 optimal weight: 6.9990 chunk 460 optimal weight: 0.6980 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN E 267 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 835 GLN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 298 ASN G 573 GLN I 137 GLN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 597 ASN H 810 ASN ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 549 GLN ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 760 ASN ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 407 ASN L 477 ASN ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 383 ASN M 498 GLN M 614 ASN N 179 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.047 76409 Z= 0.121 Angle : 0.493 17.380 103779 Z= 0.249 Chirality : 0.040 0.218 11917 Planarity : 0.003 0.056 13296 Dihedral : 5.762 177.556 10457 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.40 % 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: -2.58 (0.08), residues: 9057 helix: -1.94 (0.07), residues: 4228 sheet: -1.71 (0.16), residues: 885 loop : -1.21 (0.10), residues: 3944 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1734 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1617 time to evaluate : 6.887 Fit side-chains revert: symmetry clash outliers start: 117 outliers final: 44 residues processed: 1682 average time/residue: 0.7255 time to fit residues: 2113.9589 Evaluate side-chains 1513 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1469 time to evaluate : 6.857 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.6174 time to fit residues: 60.7866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 845 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 chunk 499 optimal weight: 6.9990 chunk 640 optimal weight: 0.9980 chunk 495 optimal weight: 4.9990 chunk 737 optimal weight: 0.6980 chunk 489 optimal weight: 1.9990 chunk 873 optimal weight: 3.9990 chunk 546 optimal weight: 6.9990 chunk 532 optimal weight: 9.9990 chunk 403 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 653 ASN A 663 ASN E 122 GLN E 267 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 ASN ** E 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN F 497 ASN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 378 ASN ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 GLN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 573 GLN I 137 GLN I 287 ASN ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 477 ASN H 597 ASN J 240 GLN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 549 GLN J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 792 GLN ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN N 290 ASN N 497 ASN N 838 GLN N 852 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 76409 Z= 0.201 Angle : 0.529 17.251 103779 Z= 0.263 Chirality : 0.041 0.194 11917 Planarity : 0.003 0.055 13296 Dihedral : 5.764 177.619 10457 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 1.63 % 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: -2.37 (0.08), residues: 9057 helix: -1.74 (0.08), residues: 4217 sheet: -1.55 (0.16), residues: 879 loop : -1.17 (0.10), residues: 3961 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1660 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1524 time to evaluate : 6.878 Fit side-chains outliers start: 136 outliers final: 67 residues processed: 1596 average time/residue: 0.7415 time to fit residues: 2047.9422 Evaluate side-chains 1521 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1454 time to evaluate : 6.837 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.5905 time to fit residues: 85.4691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 540 optimal weight: 0.7980 chunk 348 optimal weight: 4.9990 chunk 521 optimal weight: 10.0000 chunk 263 optimal weight: 0.0370 chunk 171 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 555 optimal weight: 6.9990 chunk 594 optimal weight: 20.0000 chunk 431 optimal weight: 0.0010 chunk 81 optimal weight: 6.9990 chunk 686 optimal weight: 3.9990 overall best weight: 1.9668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN E 122 GLN E 265 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 ASN ** E 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN F 497 ASN ** F 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 378 ASN ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 GLN ** G 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 472 ASN H 597 ASN ** J 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 739 GLN ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 ASN L 835 GLN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 76409 Z= 0.171 Angle : 0.517 17.179 103779 Z= 0.257 Chirality : 0.041 0.234 11917 Planarity : 0.003 0.056 13296 Dihedral : 5.677 177.570 10457 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.03 % 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: -2.17 (0.08), residues: 9057 helix: -1.53 (0.08), residues: 4231 sheet: -1.43 (0.17), residues: 867 loop : -1.14 (0.10), residues: 3959 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1585 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1499 time to evaluate : 6.890 Fit side-chains outliers start: 86 outliers final: 49 residues processed: 1540 average time/residue: 0.7448 time to fit residues: 1989.8700 Evaluate side-chains 1486 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1437 time to evaluate : 6.776 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5797 time to fit residues: 63.9322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 794 optimal weight: 0.9990 chunk 836 optimal weight: 10.0000 chunk 763 optimal weight: 8.9990 chunk 813 optimal weight: 8.9990 chunk 489 optimal weight: 7.9990 chunk 354 optimal weight: 1.9990 chunk 638 optimal weight: 7.9990 chunk 249 optimal weight: 7.9990 chunk 735 optimal weight: 3.9990 chunk 769 optimal weight: 0.3980 chunk 810 optimal weight: 6.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN A 697 ASN E 122 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 ASN ** E 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 294 ASN ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 760 ASN ** F 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 378 ASN ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 450 GLN ** G 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 597 ASN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 792 GLN ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 597 ASN ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 839 GLN N 497 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 76409 Z= 0.219 Angle : 0.543 17.177 103779 Z= 0.268 Chirality : 0.042 0.219 11917 Planarity : 0.003 0.055 13296 Dihedral : 5.722 177.623 10457 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 0.85 % 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: -2.10 (0.08), residues: 9057 helix: -1.45 (0.08), residues: 4243 sheet: -1.42 (0.17), residues: 847 loop : -1.12 (0.10), residues: 3967 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1466 time to evaluate : 6.828 Fit side-chains outliers start: 71 outliers final: 48 residues processed: 1498 average time/residue: 0.7622 time to fit residues: 1981.2747 Evaluate side-chains 1486 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1438 time to evaluate : 6.845 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.5843 time to fit residues: 62.9712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 534 optimal weight: 0.8980 chunk 860 optimal weight: 3.9990 chunk 525 optimal weight: 10.0000 chunk 408 optimal weight: 9.9990 chunk 598 optimal weight: 3.9990 chunk 902 optimal weight: 8.9990 chunk 830 optimal weight: 7.9990 chunk 718 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 555 optimal weight: 9.9990 chunk 440 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 ASN A 697 ASN A 956 ASN E 122 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 506 ASN ** E 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 126 GLN ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 792 GLN ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN G 378 ASN ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 597 ASN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 810 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 76409 Z= 0.225 Angle : 0.551 17.201 103779 Z= 0.272 Chirality : 0.042 0.263 11917 Planarity : 0.003 0.054 13296 Dihedral : 5.739 177.654 10457 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.59 % 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: -2.03 (0.08), residues: 9057 helix: -1.39 (0.08), residues: 4244 sheet: -1.41 (0.17), residues: 817 loop : -1.08 (0.10), residues: 3996 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18114 Ramachandran restraints generated. 9057 Oldfield, 0 Emsley, 9057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1496 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1447 time to evaluate : 6.827 Fit side-chains outliers start: 49 outliers final: 24 residues processed: 1466 average time/residue: 0.7508 time to fit residues: 1911.1907 Evaluate side-chains 1447 residues out of total 8341 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1423 time to evaluate : 7.062 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.6281 time to fit residues: 38.9047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 906 random chunks: chunk 570 optimal weight: 4.9990 chunk 765 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 chunk 662 optimal weight: 6.9990 chunk 106 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 719 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 739 optimal weight: 0.0570 chunk 91 optimal weight: 0.9990 chunk 132 optimal weight: 4.9990 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN A 956 ASN E 122 GLN ** E 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN E 506 ASN ** E 574 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 698 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 287 ASN ** G 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 497 ASN H 597 ASN ** J 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 835 GLN ** J 838 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 368 GLN K 396 GLN ** K 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 821 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 597 ASN ** L 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 756 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 137 GLN N 368 GLN N 497 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.120223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.102330 restraints weight = 99873.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.104500 restraints weight = 60297.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.105972 restraints weight = 41944.749| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 76409 Z= 0.134 Angle : 0.511 17.112 103779 Z= 0.253 Chirality : 0.040 0.165 11917 Planarity : 0.003 0.057 13296 Dihedral : 5.495 177.505 10457 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.09), residues: 9057 helix: -1.10 (0.08), residues: 4229 sheet: -1.37 (0.17), residues: 859 loop : -0.97 (0.10), residues: 3969 =============================================================================== Job complete usr+sys time: 26548.36 seconds wall clock time: 461 minutes 18.61 seconds (27678.61 seconds total)