Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 12:25:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ogy_20059/04_2023/6ogy_20059_updated.pdb" } resolution = 3.4 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= 0.004 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 9 5.49 5 S 397 5.16 5 C 47265 2.51 5 N 12750 2.21 5 O 13943 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 87": "NH1" <-> "NH2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 124": "OE1" <-> "OE2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A GLU 158": "OE1" <-> "OE2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A ARG 190": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 228": "OE1" <-> "OE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 317": "OE1" <-> "OE2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A ARG 361": "NH1" <-> "NH2" Residue "A GLU 362": "OE1" <-> "OE2" Residue "A GLU 377": "OE1" <-> "OE2" Residue "A ARG 406": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A GLU 676": "OE1" <-> "OE2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A GLU 699": "OE1" <-> "OE2" Residue "A GLU 726": "OE1" <-> "OE2" Residue "A GLU 730": "OE1" <-> "OE2" Residue "A ARG 749": "NH1" <-> "NH2" Residue "A GLU 754": "OE1" <-> "OE2" Residue "A GLU 781": "OE1" <-> "OE2" Residue "A GLU 817": "OE1" <-> "OE2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 922": "OE1" <-> "OE2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C ASP 117": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 150": "NH1" <-> "NH2" Residue "C ARG 159": "NH1" <-> "NH2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C GLU 183": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C ARG 238": "NH1" <-> "NH2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C ARG 307": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 345": "OE1" <-> "OE2" Residue "C GLU 363": "OE1" <-> "OE2" Residue "C ARG 455": "NH1" <-> "NH2" Residue "C ARG 488": "NH1" <-> "NH2" Residue "C GLU 515": "OE1" <-> "OE2" Residue "C ARG 522": "NH1" <-> "NH2" Residue "C PHE 525": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 555": "NH1" <-> "NH2" Residue "C GLU 562": "OE1" <-> "OE2" Residue "C GLU 581": "OE1" <-> "OE2" Residue "C ARG 624": "NH1" <-> "NH2" Residue "C ARG 663": "NH1" <-> "NH2" Residue "C ARG 671": "NH1" <-> "NH2" Residue "C ARG 684": "NH1" <-> "NH2" Residue "C ARG 701": "NH1" <-> "NH2" Residue "C ARG 721": "NH1" <-> "NH2" Residue "C GLU 723": "OE1" <-> "OE2" Residue "C ARG 732": "NH1" <-> "NH2" Residue "C GLU 744": "OE1" <-> "OE2" Residue "C GLU 886": "OE1" <-> "OE2" Residue "D GLU 74": "OE1" <-> "OE2" Residue "D GLU 75": "OE1" <-> "OE2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D GLU 87": "OE1" <-> "OE2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 210": "OE1" <-> "OE2" Residue "D GLU 222": "OE1" <-> "OE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 283": "OE1" <-> "OE2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "D ARG 451": "NH1" <-> "NH2" Residue "D ARG 522": "NH1" <-> "NH2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D GLU 581": "OE1" <-> "OE2" Residue "D GLU 623": "OE1" <-> "OE2" Residue "D ARG 637": "NH1" <-> "NH2" Residue "D GLU 650": "OE1" <-> "OE2" Residue "D ARG 671": "NH1" <-> "NH2" Residue "D GLU 682": "OE1" <-> "OE2" Residue "D ARG 701": "NH1" <-> "NH2" Residue "D GLU 744": "OE1" <-> "OE2" Residue "D ARG 797": "NH1" <-> "NH2" Residue "D GLU 871": "OE1" <-> "OE2" Residue "D GLU 886": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E ARG 142": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E ARG 159": "NH1" <-> "NH2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E ARG 238": "NH1" <-> "NH2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "E ARG 307": "NH1" <-> "NH2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E GLU 345": "OE1" <-> "OE2" 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 TYR 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 555": "NH1" <-> "NH2" Residue "E ARG 624": "NH1" <-> "NH2" Residue "E ARG 655": "NH1" <-> "NH2" Residue "E ARG 663": "NH1" <-> "NH2" Residue "E ARG 671": "NH1" <-> "NH2" Residue "E ARG 684": "NH1" <-> "NH2" Residue "E ARG 701": "NH1" <-> "NH2" Residue "E ARG 721": "NH1" <-> "NH2" Residue "E GLU 723": "OE1" <-> "OE2" Residue "E ARG 732": "NH1" <-> "NH2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ARG 142": "NH1" <-> "NH2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F GLU 183": "OE1" <-> "OE2" Residue "F GLU 196": "OE1" <-> "OE2" Residue "F GLU 222": "OE1" <-> "OE2" Residue "F GLU 223": "OE1" <-> "OE2" Residue "F ARG 236": "NH1" <-> "NH2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F ARG 307": "NH1" <-> "NH2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F GLU 363": "OE1" <-> "OE2" Residue "F ARG 397": "NH1" <-> "NH2" Residue "F GLU 429": "OE1" <-> "OE2" Residue "F ARG 451": "NH1" <-> "NH2" Residue "F GLU 467": "OE1" <-> "OE2" Residue "F ARG 522": "NH1" <-> "NH2" Residue "F GLU 562": "OE1" <-> "OE2" Residue "F GLU 581": "OE1" <-> "OE2" Residue "F GLU 623": "OE1" <-> "OE2" Residue "F ARG 624": "NH1" <-> "NH2" Residue "F ARG 637": "NH1" <-> "NH2" Residue "F GLU 682": "OE1" <-> "OE2" Residue "F ARG 701": "NH1" <-> "NH2" Residue "F ARG 721": "NH1" <-> "NH2" Residue "F ARG 732": "NH1" <-> "NH2" Residue "F GLU 744": "OE1" <-> "OE2" Residue "F ARG 797": "NH1" <-> "NH2" Residue "F GLU 871": "OE1" <-> "OE2" Residue "F GLU 886": "OE1" <-> "OE2" Residue "G GLU 121": "OE1" <-> "OE2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G ARG 142": "NH1" <-> "NH2" Residue "G ARG 150": "NH1" <-> "NH2" Residue "G ARG 159": "NH1" <-> "NH2" Residue "G GLU 196": "OE1" <-> "OE2" Residue "G GLU 210": "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 GLU 363": "OE1" <-> "OE2" Residue "G ARG 455": "NH1" <-> "NH2" Residue "G ARG 488": "NH1" <-> "NH2" Residue "G GLU 515": "OE1" <-> "OE2" Residue "G ARG 522": "NH1" <-> "NH2" Residue "G ARG 555": "NH1" <-> "NH2" Residue "G GLU 562": "OE1" <-> "OE2" Residue "G ARG 624": "NH1" <-> "NH2" Residue "G ARG 663": "NH1" <-> "NH2" Residue "G ARG 671": "NH1" <-> "NH2" Residue "G ARG 684": "NH1" <-> "NH2" Residue "G GLU 697": "OE1" <-> "OE2" Residue "G ARG 701": "NH1" <-> "NH2" Residue "G ARG 721": "NH1" <-> "NH2" Residue "G ARG 732": "NH1" <-> "NH2" Residue "G GLU 744": "OE1" <-> "OE2" Residue "G GLU 871": "OE1" <-> "OE2" Residue "H GLU 87": "OE1" <-> "OE2" Residue "H GLU 88": "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 ARG 142": "NH1" <-> "NH2" Residue "H GLU 183": "OE1" <-> "OE2" Residue "H GLU 210": "OE1" <-> "OE2" Residue "H GLU 223": "OE1" <-> "OE2" Residue "H ARG 236": "NH1" <-> "NH2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "H GLU 283": "OE1" <-> "OE2" Residue "H ARG 307": "NH1" <-> "NH2" Residue "H ARG 314": "NH1" <-> "NH2" Residue "H PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 363": "OE1" <-> "OE2" Residue "H GLU 370": "OE1" <-> "OE2" Residue "H ARG 397": "NH1" <-> "NH2" Residue "H GLU 429": "OE1" <-> "OE2" Residue "H ARG 451": "NH1" <-> "NH2" Residue "H ARG 522": "NH1" <-> "NH2" Residue "H ARG 624": "NH1" <-> "NH2" Residue "H ARG 637": "NH1" <-> "NH2" Residue "H ARG 701": "NH1" <-> "NH2" Residue "H GLU 720": "OE1" <-> "OE2" Residue "H ARG 732": "NH1" <-> "NH2" Residue "H ARG 797": "NH1" <-> "NH2" Residue "H GLU 871": "OE1" <-> "OE2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I ARG 136": "NH1" <-> "NH2" Residue "I TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 142": "NH1" <-> "NH2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ARG 150": "NH1" <-> "NH2" Residue "I ARG 159": "NH1" <-> "NH2" Residue "I GLU 171": "OE1" <-> "OE2" Residue "I GLU 183": "OE1" <-> "OE2" Residue "I GLU 196": "OE1" <-> "OE2" Residue "I GLU 222": "OE1" <-> "OE2" Residue "I GLU 225": "OE1" <-> "OE2" Residue "I ARG 238": "NH1" <-> "NH2" Residue "I ARG 284": "NH1" <-> "NH2" Residue "I ARG 307": "NH1" <-> "NH2" Residue "I ARG 314": "NH1" <-> "NH2" Residue "I GLU 350": "OE1" <-> "OE2" Residue "I ARG 455": "NH1" <-> "NH2" Residue "I ARG 488": "NH1" <-> "NH2" Residue "I ARG 522": "NH1" <-> "NH2" Residue "I ARG 555": "NH1" <-> "NH2" Residue "I ARG 624": "NH1" <-> "NH2" Residue "I GLU 650": "OE1" <-> "OE2" Residue "I ARG 663": "NH1" <-> "NH2" Residue "I ARG 671": "NH1" <-> "NH2" Residue "I GLU 682": "OE1" <-> "OE2" Residue "I ARG 684": "NH1" <-> "NH2" Residue "I GLU 697": "OE1" <-> "OE2" Residue "I ARG 701": "NH1" <-> "NH2" Residue "I ARG 721": "NH1" <-> "NH2" Residue "I GLU 723": "OE1" <-> "OE2" Residue "I ARG 732": "NH1" <-> "NH2" Residue "I TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 87": "OE1" <-> "OE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J GLU 116": "OE1" <-> "OE2" Residue "J GLU 134": "OE1" <-> "OE2" Residue "J ARG 142": "NH1" <-> "NH2" Residue "J GLU 183": "OE1" <-> "OE2" Residue "J GLU 210": "OE1" <-> "OE2" Residue "J GLU 223": "OE1" <-> "OE2" Residue "J ARG 236": "NH1" <-> "NH2" Residue "J ARG 307": "NH1" <-> "NH2" Residue "J ARG 314": "NH1" <-> "NH2" Residue "J GLU 322": "OE1" <-> "OE2" Residue "J ARG 397": "NH1" <-> "NH2" Residue "J ARG 451": "NH1" <-> "NH2" Residue "J GLU 515": "OE1" <-> "OE2" Residue "J ARG 522": "NH1" <-> "NH2" Residue "J ARG 546": "NH1" <-> "NH2" Residue "J GLU 581": "OE1" <-> "OE2" Residue "J ARG 624": "NH1" <-> "NH2" Residue "J ARG 637": "NH1" <-> "NH2" Residue "J GLU 650": "OE1" <-> "OE2" Residue "J GLU 697": "OE1" <-> "OE2" Residue "J ARG 701": "NH1" <-> "NH2" Residue "J GLU 723": "OE1" <-> "OE2" Residue "J ARG 732": "NH1" <-> "NH2" Residue "J ARG 797": "NH1" <-> "NH2" Residue "J GLU 871": "OE1" <-> "OE2" Residue "J GLU 886": "OE1" <-> "OE2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K GLU 67": "OE1" <-> "OE2" Residue "K GLU 74": "OE1" <-> "OE2" Residue "K GLU 75": "OE1" <-> "OE2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "K GLU 87": "OE1" <-> "OE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K GLU 96": "OE1" <-> "OE2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K GLU 116": "OE1" <-> "OE2" Residue "K GLU 121": "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 223": "OE1" <-> "OE2" Residue "K GLU 234": "OE1" <-> "OE2" Residue "K ARG 238": "NH1" <-> "NH2" Residue "K ARG 243": "NH1" <-> "NH2" Residue "K ARG 284": "NH1" <-> "NH2" Residue "K ARG 307": "NH1" <-> "NH2" Residue "K ARG 314": "NH1" <-> "NH2" 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 GLU 581": "OE1" <-> "OE2" 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 ARG 684": "NH1" <-> "NH2" Residue "K ARG 701": "NH1" <-> "NH2" Residue "K ARG 721": "NH1" <-> "NH2" Residue "K GLU 723": "OE1" <-> "OE2" Residue "K ARG 732": "NH1" <-> "NH2" Residue "L GLU 87": "OE1" <-> "OE2" Residue "L GLU 88": "OE1" <-> "OE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L GLU 121": "OE1" <-> "OE2" Residue "L ARG 142": "NH1" <-> "NH2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "L GLU 183": "OE1" <-> "OE2" Residue "L GLU 196": "OE1" <-> "OE2" Residue "L GLU 210": "OE1" <-> "OE2" Residue "L GLU 222": "OE1" <-> "OE2" Residue "L GLU 223": "OE1" <-> "OE2" Residue "L ARG 229": "NH1" <-> "NH2" Residue "L ARG 236": "NH1" <-> "NH2" Residue "L ARG 243": "NH1" <-> "NH2" Residue "L GLU 261": "OE1" <-> "OE2" Residue "L ARG 307": "NH1" <-> "NH2" Residue "L GLU 350": "OE1" <-> "OE2" Residue "L GLU 363": "OE1" <-> "OE2" Residue "L GLU 370": "OE1" <-> "OE2" Residue "L ARG 397": "NH1" <-> "NH2" Residue "L GLU 429": "OE1" <-> "OE2" 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 650": "OE1" <-> "OE2" 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 ASP 815": "OD1" <-> "OD2" Residue "L PHE 840": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 74364 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 8523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8523 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 34, 'TRANS': 1018} Chain breaks: 1 Chain: "C" 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: "D" Number of atoms: 6670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 815, 6670 Classifications: {'peptide': 815} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 784} Chain: "E" 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: "F" 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: "G" 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: "I" Number of atoms: 6628 Number of conformers: 1 Conformer: "" Number of residues, atoms: 810, 6628 Classifications: {'peptide': 810} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 779} 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: 6765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6765 Classifications: {'peptide': 827} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 796} 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: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 95 Unusual residues: {'GTG': 1} Classifications: {'RNA': 2, 'undetermined': 1} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 1} Link IDs: {'rna3p': 1, None: 1} Not linked: pdbres="GTG M 1 " pdbres=" G M 2 " Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'RNA': 4} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 2} Link IDs: {'rna2p': 1, 'rna3p': 2} Time building chain proxies: 28.60, per 1000 atoms: 0.38 Number of scatterers: 74364 At special positions: 0 Unit cell: (331.7, 330.63, 123.05, 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 397 16.00 P 9 15.00 O 13943 8.00 N 12750 7.00 C 47265 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.34 Conformation dependent library (CDL) restraints added in 8.1 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: 17728 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 405 helices and 85 sheets defined 36.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.68 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 3.545A pdb=" N LEU A 12 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER A 13 " --> pdb=" O SER A 9 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 14 " --> pdb=" O GLU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' 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 141 No H-bonds generated for 'chain 'A' and resid 138 through 141' Processing helix chain 'A' and resid 143 through 146 No H-bonds generated for 'chain 'A' and resid 143 through 146' Processing helix chain 'A' and resid 148 through 151 No H-bonds generated for 'chain 'A' and resid 148 through 151' Processing helix chain 'A' and resid 159 through 180 removed outlier: 3.578A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP A 168 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LEU A 169 " --> pdb=" O ARG A 165 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE A 170 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ILE A 172 " --> pdb=" O ASP A 168 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS A 179 " --> pdb=" O SER A 175 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N TYR A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 4.095A pdb=" N SER A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N SER A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 234 removed outlier: 3.538A pdb=" N ILE A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N SER A 233 " --> pdb=" O LEU A 229 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N TYR A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 244 No H-bonds generated for 'chain 'A' and resid 241 through 244' Processing helix chain 'A' and resid 285 through 297 removed outlier: 4.075A pdb=" N GLN A 290 " --> pdb=" O ASP A 286 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET A 295 " --> pdb=" O MET A 291 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS A 297 " --> pdb=" O ASP A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 316 through 331 Proline residue: A 320 - end of helix removed outlier: 3.721A pdb=" N ALA A 323 " --> pdb=" O PRO A 320 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A 325 " --> pdb=" O MET A 322 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 326 " --> pdb=" O ALA A 323 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TRP A 328 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER A 329 " --> pdb=" O TYR A 326 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE A 330 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 342 No H-bonds generated for 'chain 'A' and resid 339 through 342' Processing helix chain 'A' and resid 357 through 374 removed outlier: 3.540A pdb=" N ARG A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU A 362 " --> pdb=" O GLU A 358 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU A 370 " --> pdb=" O LEU A 366 " (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 384 through 387 No H-bonds generated for 'chain 'A' and resid 384 through 387' Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 397 through 399 No H-bonds generated for 'chain 'A' and resid 397 through 399' Processing helix chain 'A' and resid 420 through 427 removed outlier: 3.760A pdb=" N MET A 425 " --> pdb=" O ASN A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 471 No H-bonds generated for 'chain 'A' and resid 468 through 471' Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.892A pdb=" N ILE A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR A 483 " --> pdb=" O LYS A 479 " (cutoff:3.500A) 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 539 removed outlier: 3.597A pdb=" N ILE A 538 " --> pdb=" O PHE A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 567 removed outlier: 3.612A pdb=" N TYR A 561 " --> pdb=" O THR A 557 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LYS A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 565 " --> pdb=" O TYR A 561 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 567 " --> pdb=" O GLN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 597 No H-bonds generated for 'chain 'A' and resid 595 through 597' Processing helix chain 'A' and resid 600 through 617 removed outlier: 3.614A pdb=" N LEU A 605 " --> pdb=" O SER A 601 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 610 " --> pdb=" O ALA A 606 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 613 " --> pdb=" O LYS A 609 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 616 " --> pdb=" O LEU A 612 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ASN A 617 " --> pdb=" O SER A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 646 through 655 removed outlier: 3.710A pdb=" N VAL A 651 " --> pdb=" O MET A 647 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 662 No H-bonds generated for 'chain 'A' and resid 660 through 662' Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.877A pdb=" N ALA A 711 " --> pdb=" O TRP A 707 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR A 714 " --> pdb=" O ALA A 710 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN A 720 " --> pdb=" O ASN A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 740 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 781 through 785 removed outlier: 3.500A pdb=" N GLN A 785 " --> pdb=" O GLU A 781 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 781 through 785' Processing helix chain 'A' and resid 799 through 802 No H-bonds generated for 'chain 'A' and resid 799 through 802' Processing helix chain 'A' and resid 806 through 819 removed outlier: 3.522A pdb=" N TYR A 811 " --> pdb=" O THR A 807 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLN A 818 " --> pdb=" O ARG A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 832 removed outlier: 3.518A pdb=" N ARG A 829 " --> pdb=" O ASN A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 841 removed outlier: 3.544A pdb=" N LEU A 839 " --> pdb=" O GLU A 835 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASN A 840 " --> pdb=" O LYS A 836 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 835 through 841' Processing helix chain 'A' and resid 845 through 862 removed outlier: 3.547A pdb=" N LYS A 849 " --> pdb=" O ILE A 845 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 850 " --> pdb=" O SER A 846 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR A 859 " --> pdb=" O SER A 855 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N MET A 860 " --> pdb=" O ALA A 856 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN A 862 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 884 removed outlier: 3.975A pdb=" N ASP A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 881 " --> pdb=" O ILE A 877 " (cutoff:3.500A) Proline residue: A 883 - end of helix Processing helix chain 'A' and resid 905 through 914 removed outlier: 4.107A pdb=" N ILE A 910 " --> pdb=" O ASN A 906 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N CYS A 913 " --> pdb=" O TYR A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 934 through 937 No H-bonds generated for 'chain 'A' and resid 934 through 937' Processing helix chain 'A' and resid 944 through 950 removed outlier: 4.076A pdb=" N LYS A 949 " --> pdb=" O GLU A 945 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 955 through 964 removed outlier: 3.500A pdb=" N GLN A 959 " --> pdb=" O GLU A 955 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 960 " --> pdb=" O ASN A 956 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR A 961 " --> pdb=" O GLU A 957 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 969 through 977 removed outlier: 3.521A pdb=" N VAL A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 996 removed outlier: 3.540A pdb=" N GLU A 990 " --> pdb=" O TYR A 986 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 991 " --> pdb=" O ARG A 987 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN A 995 " --> pdb=" O SER A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1047 removed outlier: 3.762A pdb=" N ILE A1032 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A1034 " --> pdb=" O THR A1030 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A1039 " --> pdb=" O LEU A1035 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A1041 " --> pdb=" O ALA A1037 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE A1042 " --> pdb=" O LYS A1038 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A1047 " --> pdb=" O ASN A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1069 removed outlier: 3.756A pdb=" N ILE A1064 " --> pdb=" O LYS A1060 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS A1065 " --> pdb=" O SER A1061 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS A1068 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS A1069 " --> pdb=" O LYS A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1084 No H-bonds generated for 'chain 'A' and resid 1082 through 1084' Processing helix chain 'C' and resid 167 through 183 removed outlier: 3.618A pdb=" N THR C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 219 Processing helix chain 'C' and resid 226 through 233 removed outlier: 4.071A pdb=" N ALA C 233 " --> pdb=" O ARG C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 265 removed outlier: 3.524A pdb=" N ALA C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N PHE C 259 " --> pdb=" O ILE C 255 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR C 262 " --> pdb=" O ALA C 258 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE C 263 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 280 removed outlier: 3.920A pdb=" N PHE C 278 " --> pdb=" O ASN C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 286 No H-bonds generated for 'chain 'C' and resid 283 through 286' Processing helix chain 'C' and resid 326 through 329 No H-bonds generated for 'chain 'C' and resid 326 through 329' Processing helix chain 'C' and resid 331 through 337 removed outlier: 3.865A pdb=" N LEU C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 359 removed outlier: 3.977A pdb=" N GLN C 354 " --> pdb=" O GLU C 350 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS C 355 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C 358 " --> pdb=" O GLN C 354 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP C 359 " --> pdb=" O LYS C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 374 removed outlier: 4.138A pdb=" N LEU C 374 " --> pdb=" O THR C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 371 through 374' Processing helix chain 'C' and resid 379 through 393 removed outlier: 3.585A pdb=" N ASN C 383 " --> pdb=" O SER C 379 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 387 " --> pdb=" O ASN C 383 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE C 390 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA C 392 " --> pdb=" O THR C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 412 No H-bonds generated for 'chain 'C' and resid 409 through 412' Processing helix chain 'C' and resid 414 through 417 No H-bonds generated for 'chain 'C' and resid 414 through 417' Processing helix chain 'C' and resid 428 through 441 removed outlier: 4.421A pdb=" N ALA C 433 " --> pdb=" O GLU C 429 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N CYS C 434 " --> pdb=" O SER C 430 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 447 No H-bonds generated for 'chain 'C' and resid 444 through 447' Processing helix chain 'C' and resid 462 through 469 removed outlier: 3.502A pdb=" N GLU C 467 " --> pdb=" O PHE C 463 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 483 removed outlier: 3.721A pdb=" N TRP C 478 " --> pdb=" O GLN C 474 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N HIS C 480 " --> pdb=" O ALA C 476 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE C 481 " --> pdb=" O ASN C 477 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN C 483 " --> pdb=" O LEU C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'C' and resid 510 through 513 No H-bonds generated for 'chain 'C' and resid 510 through 513' Processing helix chain 'C' and resid 530 through 539 removed outlier: 3.677A pdb=" N SER C 535 " --> pdb=" O ASP C 531 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 544 No H-bonds generated for 'chain 'C' and resid 541 through 544' Processing helix chain 'C' and resid 548 through 560 removed outlier: 3.934A pdb=" N ASP C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 554 " --> pdb=" O LEU C 550 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU C 556 " --> pdb=" O ASP C 552 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR C 559 " --> pdb=" O ARG C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 567 removed outlier: 3.502A pdb=" N CYS C 567 " --> pdb=" O LEU C 564 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 564 through 567' Processing helix chain 'C' and resid 586 through 592 removed outlier: 3.791A pdb=" N LEU C 591 " --> pdb=" O SER C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 637 removed outlier: 3.853A pdb=" N HIS C 609 " --> pdb=" O GLN C 605 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN C 612 " --> pdb=" O PHE C 608 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN C 614 " --> pdb=" O TYR C 610 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ASN C 616 " --> pdb=" O ASN C 612 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N PHE C 617 " --> pdb=" O VAL C 613 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN C 620 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN C 622 " --> pdb=" O HIS C 618 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE C 625 " --> pdb=" O TYR C 621 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN C 626 " --> pdb=" O ASN C 622 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 627 " --> pdb=" O GLU C 623 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA C 630 " --> pdb=" O ASN C 626 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C 631 " --> pdb=" O ASP C 627 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALA C 634 " --> pdb=" O ALA C 630 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASN C 636 " --> pdb=" O ILE C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 655 removed outlier: 3.750A pdb=" N PHE C 652 " --> pdb=" O ILE C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 667 through 670 No H-bonds generated for 'chain 'C' and resid 667 through 670' Processing helix chain 'C' and resid 683 through 694 removed outlier: 3.576A pdb=" N ASP C 687 " --> pdb=" O ILE C 683 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE C 692 " --> pdb=" O ILE C 688 " (cutoff:3.500A) Processing helix chain 'C' and resid 696 through 701 removed outlier: 3.730A pdb=" N GLU C 700 " --> pdb=" O MET C 696 " (cutoff:3.500A) Processing helix chain 'C' and resid 742 through 747 Processing helix chain 'C' and resid 752 through 759 removed outlier: 3.671A pdb=" N ASN C 756 " --> pdb=" O ALA C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 779 through 782 No H-bonds generated for 'chain 'C' and resid 779 through 782' Processing helix chain 'C' and resid 792 through 795 No H-bonds generated for 'chain 'C' and resid 792 through 795' Processing helix chain 'C' and resid 816 through 821 removed outlier: 3.725A pdb=" N ALA C 820 " --> pdb=" O TYR C 817 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASN C 821 " --> pdb=" O LEU C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 842 through 845 No H-bonds generated for 'chain 'C' and resid 842 through 845' Processing helix chain 'D' and resid 74 through 82 removed outlier: 3.725A pdb=" N LEU D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU D 80 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU D 81 " --> pdb=" O LYS D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.625A pdb=" N GLU D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 175 removed outlier: 3.911A pdb=" N LEU D 174 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 180 No H-bonds generated for 'chain 'D' and resid 177 through 180' Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.594A pdb=" N PHE D 219 " --> pdb=" O CYS D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.503A pdb=" N PHE D 231 " --> pdb=" O VAL D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 256 through 265 removed outlier: 3.808A pdb=" N PHE D 263 " --> pdb=" O PHE D 259 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 280 Processing helix chain 'D' and resid 325 through 337 removed outlier: 3.778A pdb=" N LEU D 335 " --> pdb=" O SER D 331 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 336 " --> pdb=" O ASN D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 359 removed outlier: 3.657A pdb=" N GLN D 354 " --> pdb=" O GLU D 350 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN D 358 " --> pdb=" O GLN D 354 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 364 No H-bonds generated for 'chain 'D' and resid 362 through 364' Processing helix chain 'D' and resid 381 through 394 removed outlier: 3.617A pdb=" N ILE D 390 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N MET D 393 " --> pdb=" O LEU D 389 " (cutoff:3.500A) Processing helix chain 'D' and resid 409 through 412 No H-bonds generated for 'chain 'D' and resid 409 through 412' Processing helix chain 'D' and resid 415 through 418 No H-bonds generated for 'chain 'D' and resid 415 through 418' Processing helix chain 'D' and resid 428 through 441 removed outlier: 3.808A pdb=" N ALA D 433 " --> pdb=" O GLU D 429 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 438 " --> pdb=" O CYS D 434 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE D 439 " --> pdb=" O GLN D 435 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR D 441 " --> pdb=" O ALA D 437 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 447 No H-bonds generated for 'chain 'D' and resid 444 through 447' Processing helix chain 'D' and resid 466 through 469 No H-bonds generated for 'chain 'D' and resid 466 through 469' Processing helix chain 'D' and resid 473 through 482 removed outlier: 3.541A pdb=" N HIS D 480 " --> pdb=" O ALA D 476 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N PHE D 481 " --> pdb=" O ASN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 505 No H-bonds generated for 'chain 'D' and resid 502 through 505' Processing helix chain 'D' and resid 508 through 518 removed outlier: 3.595A pdb=" N MET D 514 " --> pdb=" O ASN D 511 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU D 515 " --> pdb=" O GLN D 512 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N MET D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 533 No H-bonds generated for 'chain 'D' and resid 530 through 533' Processing helix chain 'D' and resid 538 through 544 removed outlier: 4.217A pdb=" N LEU D 543 " --> pdb=" O GLY D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 551 through 564 removed outlier: 3.559A pdb=" N LEU D 556 " --> pdb=" O ASP D 552 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR D 559 " --> pdb=" O ARG D 555 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR D 561 " --> pdb=" O LEU D 557 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 562 " --> pdb=" O ALA D 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 592 Processing helix chain 'D' and resid 604 through 621 removed outlier: 3.633A pdb=" N ASN D 612 " --> pdb=" O PHE D 608 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N HIS D 618 " --> pdb=" O ASN D 614 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 637 removed outlier: 3.710A pdb=" N ALA D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN D 636 " --> pdb=" O ILE D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 645 through 655 Processing helix chain 'D' and resid 667 through 670 No H-bonds generated for 'chain 'D' and resid 667 through 670' Processing helix chain 'D' and resid 683 through 687 Processing helix chain 'D' and resid 690 through 693 No H-bonds generated for 'chain 'D' and resid 690 through 693' Processing helix chain 'D' and resid 696 through 700 removed outlier: 3.642A pdb=" N GLU D 700 " --> pdb=" O MET D 696 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 696 through 700' Processing helix chain 'D' and resid 742 through 748 removed outlier: 3.576A pdb=" N ARG D 747 " --> pdb=" O GLU D 743 " (cutoff:3.500A) Processing helix chain 'D' and resid 752 through 759 removed outlier: 3.638A pdb=" N ASN D 756 " --> pdb=" O ALA D 752 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU D 758 " --> pdb=" O ILE D 754 " (cutoff:3.500A) Processing helix chain 'D' and resid 778 through 782 Processing helix chain 'D' and resid 787 through 795 removed outlier: 3.784A pdb=" N PHE D 790 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA D 791 " --> pdb=" O THR D 788 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN D 792 " --> pdb=" O VAL D 789 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE D 793 " --> pdb=" O PHE D 790 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LYS D 795 " --> pdb=" O GLN D 792 " (cutoff:3.500A) Processing helix chain 'D' and resid 816 through 820 removed outlier: 3.713A pdb=" N ALA D 820 " --> pdb=" O TYR D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 872 through 874 No H-bonds generated for 'chain 'D' and resid 872 through 874' Processing helix chain 'E' and resid 166 through 181 removed outlier: 3.971A pdb=" N ARG E 170 " --> pdb=" O ASP E 166 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 174 " --> pdb=" O ARG E 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN E 175 " --> pdb=" O GLU E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 219 removed outlier: 4.392A pdb=" N ILE E 218 " --> pdb=" O ILE E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 233 removed outlier: 3.676A pdb=" N PHE E 231 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ALA E 233 " --> pdb=" O ARG E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 265 removed outlier: 3.569A pdb=" N ALA E 258 " --> pdb=" O PRO E 254 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE E 263 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N LEU E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) 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 322 through 329 removed outlier: 3.547A pdb=" N ASP E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR E 327 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 328 " --> pdb=" O LEU E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 331 through 337 Processing helix chain 'E' and resid 350 through 359 removed outlier: 3.553A pdb=" N GLN E 354 " --> pdb=" O GLU E 350 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS E 355 " --> pdb=" O ALA E 351 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN E 358 " --> pdb=" O GLN E 354 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASP E 359 " --> pdb=" O LYS E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 380 through 395 removed outlier: 3.811A pdb=" N ALA E 392 " --> pdb=" O THR E 388 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 409 through 412 No H-bonds generated for 'chain 'E' and resid 409 through 412' Processing helix chain 'E' and resid 428 through 439 removed outlier: 4.225A pdb=" N ALA E 433 " --> pdb=" O GLU E 429 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA E 437 " --> pdb=" O ALA E 433 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE E 438 " --> pdb=" O CYS E 434 " (cutoff:3.500A) removed outlier: 3.574A 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 462 through 465 No H-bonds generated for 'chain 'E' and resid 462 through 465' Processing helix chain 'E' and resid 473 through 481 removed outlier: 4.059A pdb=" N TRP E 478 " --> pdb=" O GLN E 474 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 No H-bonds generated for 'chain 'E' and resid 502 through 505' Processing helix chain 'E' and resid 510 through 513 No H-bonds generated for 'chain 'E' and resid 510 through 513' Processing helix chain 'E' and resid 530 through 539 removed outlier: 3.505A pdb=" N SER E 535 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE E 536 " --> pdb=" O TYR E 532 " (cutoff:3.500A) Processing helix chain 'E' and resid 541 through 546 removed outlier: 3.990A pdb=" N ARG E 546 " --> pdb=" O LEU E 542 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 560 removed outlier: 4.045A pdb=" N LEU E 553 " --> pdb=" O GLN E 549 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU E 556 " --> pdb=" O ASP E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 567 Processing helix chain 'E' and resid 586 through 592 removed outlier: 3.809A pdb=" N LEU E 591 " --> pdb=" O SER E 587 " (cutoff:3.500A) Processing helix chain 'E' and resid 604 through 632 removed outlier: 3.946A pdb=" N HIS E 609 " --> pdb=" O GLN E 605 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN E 612 " --> pdb=" O PHE E 608 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN E 614 " --> pdb=" O TYR E 610 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN E 616 " --> pdb=" O ASN E 612 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN E 622 " --> pdb=" O HIS E 618 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ARG E 624 " --> pdb=" O ASN E 620 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP E 627 " --> pdb=" O GLU E 623 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 628 " --> pdb=" O ARG E 624 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 630 " --> pdb=" O ASN E 626 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE E 631 " --> pdb=" O ASP E 627 " (cutoff:3.500A) Processing helix chain 'E' and resid 634 through 637 No H-bonds generated for 'chain 'E' and resid 634 through 637' 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 670 No H-bonds generated for 'chain 'E' and resid 667 through 670' Processing helix chain 'E' and resid 683 through 687 Processing helix chain 'E' and resid 690 through 694 Processing helix chain 'E' and resid 743 through 748 removed outlier: 3.888A pdb=" N THR E 748 " --> pdb=" O GLU E 744 " (cutoff:3.500A) Processing helix chain 'E' and resid 752 through 759 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 790 through 795 removed outlier: 3.536A pdb=" N ILE E 793 " --> pdb=" O PHE E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 817 through 821 Processing helix chain 'E' and resid 861 through 863 No H-bonds generated for 'chain 'E' and resid 861 through 863' Processing helix chain 'F' and resid 84 through 99 removed outlier: 4.068A pdb=" N HIS F 89 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL F 93 " --> pdb=" O HIS F 89 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN F 94 " --> pdb=" O GLN F 90 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE F 97 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU F 98 " --> pdb=" O GLN F 94 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 116 removed outlier: 3.626A pdb=" N LYS F 113 " --> pdb=" O SER F 110 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU F 115 " --> pdb=" O LEU F 112 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLU F 116 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 183 removed outlier: 3.530A pdb=" N ARG F 170 " --> pdb=" O ASP F 166 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 179 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 220 removed outlier: 3.670A pdb=" N ALA F 213 " --> pdb=" O SER F 209 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP F 216 " --> pdb=" O ALA F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 234 removed outlier: 4.200A pdb=" N ALA F 233 " --> pdb=" O ARG F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 256 through 265 removed outlier: 3.661A pdb=" N TYR F 262 " --> pdb=" O ALA F 258 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N PHE F 263 " --> pdb=" O PHE F 259 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.535A pdb=" N PHE F 278 " --> pdb=" O ASN F 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 274 through 278' 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 336 removed outlier: 4.028A pdb=" N ILE F 328 " --> pdb=" O LEU F 324 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU F 335 " --> pdb=" O SER F 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 349 through 360 removed outlier: 3.904A pdb=" N GLN F 354 " --> pdb=" O GLU F 350 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS F 355 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN F 358 " --> pdb=" O GLN F 354 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP F 359 " --> pdb=" O LYS F 355 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU F 360 " --> pdb=" O MET F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 394 removed outlier: 3.771A pdb=" N LYS F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE F 390 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N MET F 393 " --> pdb=" O LEU F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 409 through 420 removed outlier: 3.708A pdb=" N GLY F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET F 415 " --> pdb=" O LEU F 411 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TRP F 416 " --> pdb=" O ILE F 412 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU F 417 " --> pdb=" O SER F 413 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL F 420 " --> pdb=" O TRP F 416 " (cutoff:3.500A) Processing helix chain 'F' and resid 428 through 439 removed outlier: 4.013A pdb=" N ALA F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS F 434 " --> pdb=" O SER F 430 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F 437 " --> pdb=" O ALA F 433 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE F 439 " --> pdb=" O GLN F 435 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 446 No H-bonds generated for 'chain 'F' and resid 443 through 446' 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 475 through 483 removed outlier: 3.968A pdb=" N HIS F 480 " --> pdb=" O ALA F 476 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE F 481 " --> pdb=" O ASN F 477 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN F 483 " --> pdb=" O LEU F 479 " (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 508 through 519 removed outlier: 3.758A pdb=" N MET F 514 " --> pdb=" O ASN F 511 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N MET F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLN F 519 " --> pdb=" O ALA F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 536 removed outlier: 3.912A pdb=" N SER F 535 " --> pdb=" O ASP F 531 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 564 removed outlier: 4.037A pdb=" N ASP F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU F 553 " --> pdb=" O GLN F 549 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR F 554 " --> pdb=" O LEU F 550 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU F 556 " --> pdb=" O ASP F 552 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR F 559 " --> pdb=" O ARG F 555 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR F 561 " --> pdb=" O LEU F 557 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU F 562 " --> pdb=" O ALA F 558 " (cutoff:3.500A) Processing helix chain 'F' and resid 586 through 592 removed outlier: 3.794A pdb=" N LEU F 591 " --> pdb=" O SER F 587 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 607 No H-bonds generated for 'chain 'F' and resid 604 through 607' Processing helix chain 'F' and resid 612 through 622 removed outlier: 3.881A pdb=" N PHE F 617 " --> pdb=" O VAL F 613 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N HIS F 618 " --> pdb=" O ASN F 614 " (cutoff:3.500A) Processing helix chain 'F' and resid 626 through 637 removed outlier: 3.726A pdb=" N ALA F 630 " --> pdb=" O ASN F 626 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE F 631 " --> pdb=" O ASP F 627 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA F 634 " --> pdb=" O ALA F 630 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN F 636 " --> pdb=" O ILE F 632 " (cutoff:3.500A) Processing helix chain 'F' and resid 646 through 655 Processing helix chain 'F' and resid 668 through 674 removed outlier: 3.551A pdb=" N LEU F 672 " --> pdb=" O GLN F 668 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG F 673 " --> pdb=" O MET F 669 " (cutoff:3.500A) Processing helix chain 'F' and resid 684 through 687 No H-bonds generated for 'chain 'F' and resid 684 through 687' Processing helix chain 'F' and resid 689 through 692 No H-bonds generated for 'chain 'F' and resid 689 through 692' Processing helix chain 'F' and resid 696 through 702 removed outlier: 3.826A pdb=" N GLU F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 702 " --> pdb=" O GLN F 698 " (cutoff:3.500A) Processing helix chain 'F' and resid 742 through 748 Processing helix chain 'F' and resid 752 through 759 removed outlier: 3.942A pdb=" N ASN F 756 " --> pdb=" O ALA F 752 " (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 789 through 791 No H-bonds generated for 'chain 'F' and resid 789 through 791' Processing helix chain 'F' and resid 817 through 820 No H-bonds generated for 'chain 'F' and resid 817 through 820' Processing helix chain 'F' and resid 872 through 874 No H-bonds generated for 'chain 'F' and resid 872 through 874' Processing helix chain 'G' and resid 108 through 114 removed outlier: 3.917A pdb=" N LYS G 113 " --> pdb=" O GLU G 109 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS G 114 " --> pdb=" O SER G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 183 removed outlier: 3.965A pdb=" N ARG G 170 " --> pdb=" O ASP G 166 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU G 174 " --> pdb=" O ARG G 170 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU G 181 " --> pdb=" O TYR G 177 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 219 removed outlier: 4.378A pdb=" N ILE G 218 " --> pdb=" O ILE G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 233 removed outlier: 3.684A pdb=" N ILE G 232 " --> pdb=" O VAL G 228 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ALA G 233 " --> pdb=" O ARG G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 265 removed outlier: 3.654A pdb=" N ALA G 258 " --> pdb=" O PRO G 254 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE G 259 " --> pdb=" O ILE G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 274 through 280 removed outlier: 3.576A pdb=" N PHE G 278 " --> pdb=" O ASN G 274 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN G 279 " --> pdb=" O ASP G 275 " (cutoff:3.500A) 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 337 removed outlier: 3.730A pdb=" N SER G 331 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN G 332 " --> pdb=" O ILE G 328 " (cutoff:3.500A) Processing helix chain 'G' and resid 349 through 359 removed outlier: 4.021A pdb=" N LYS G 355 " --> pdb=" O ALA G 351 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN G 358 " --> pdb=" O GLN G 354 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 379 through 395 removed outlier: 3.687A pdb=" N ASN G 383 " --> pdb=" O SER G 379 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE G 386 " --> pdb=" O ALA G 382 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS G 387 " --> pdb=" O ASN G 383 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE G 390 " --> pdb=" O PHE G 386 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ALA G 392 " --> pdb=" O THR G 388 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET G 393 " --> pdb=" O LEU G 389 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER G 395 " --> pdb=" O ALA G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 removed outlier: 3.671A pdb=" N ILE G 412 " --> pdb=" O TYR G 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 408 through 412' Processing helix chain 'G' and resid 428 through 441 removed outlier: 4.221A pdb=" N ALA G 433 " --> pdb=" O GLU G 429 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA G 437 " --> pdb=" O ALA G 433 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 447 No H-bonds generated for 'chain 'G' and resid 444 through 447' Processing helix chain 'G' and resid 462 through 466 Processing helix chain 'G' and resid 476 through 483 Processing helix chain 'G' and resid 502 through 506 removed outlier: 3.602A pdb=" N ASN G 506 " --> pdb=" O ASP G 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 502 through 506' Processing helix chain 'G' and resid 510 through 520 removed outlier: 3.903A pdb=" N GLU G 515 " --> pdb=" O ASN G 511 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA G 516 " --> pdb=" O GLN G 512 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN G 519 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 530 through 539 removed outlier: 3.590A pdb=" N ILE G 536 " --> pdb=" O TYR G 532 " (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 548 through 567 removed outlier: 3.854A pdb=" N ASP G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU G 553 " --> pdb=" O GLN G 549 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N TYR G 559 " --> pdb=" O ARG G 555 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU G 562 " --> pdb=" O ALA G 558 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU G 564 " --> pdb=" O ASN G 560 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 566 " --> pdb=" O GLU G 562 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N CYS G 567 " --> pdb=" O THR G 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 585 through 587 No H-bonds generated for 'chain 'G' and resid 585 through 587' Processing helix chain 'G' and resid 589 through 592 No H-bonds generated for 'chain 'G' and resid 589 through 592' Processing helix chain 'G' and resid 609 through 632 removed outlier: 3.611A pdb=" N ASN G 614 " --> pdb=" O TYR G 610 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU G 623 " --> pdb=" O SER G 619 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN G 626 " --> pdb=" O ASN G 622 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASP G 627 " --> pdb=" O GLU G 623 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA G 630 " --> pdb=" O ASN G 626 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ILE G 631 " --> pdb=" O ASP G 627 " (cutoff:3.500A) Processing helix chain 'G' and resid 634 through 637 No H-bonds generated for 'chain 'G' and resid 634 through 637' Processing helix chain 'G' and resid 650 through 655 Processing helix chain 'G' and resid 667 through 670 No H-bonds generated for 'chain 'G' and resid 667 through 670' Processing helix chain 'G' and resid 673 through 676 No H-bonds generated for 'chain 'G' and resid 673 through 676' Processing helix chain 'G' and resid 683 through 692 removed outlier: 3.508A pdb=" N ASP G 687 " --> pdb=" O ILE G 683 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE G 688 " --> pdb=" O ARG G 684 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 691 " --> pdb=" O ASP G 687 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE G 692 " --> pdb=" O ILE G 688 " (cutoff:3.500A) Processing helix chain 'G' and resid 696 through 701 removed outlier: 3.836A pdb=" N GLU G 700 " --> pdb=" O MET G 696 " (cutoff:3.500A) removed outlier: 3.669A 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 748 Processing helix chain 'G' and resid 752 through 758 removed outlier: 3.506A pdb=" N ASN G 756 " --> pdb=" O ALA G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 779 through 782 No H-bonds generated for 'chain 'G' and resid 779 through 782' Processing helix chain 'G' and resid 786 through 788 No H-bonds generated for 'chain 'G' and resid 786 through 788' Processing helix chain 'G' and resid 792 through 795 No H-bonds generated for 'chain 'G' and resid 792 through 795' Processing helix chain 'G' and resid 816 through 821 removed outlier: 3.830A pdb=" N ALA G 820 " --> pdb=" O TYR G 817 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN G 821 " --> pdb=" O LEU G 818 " (cutoff:3.500A) Processing helix chain 'G' and resid 842 through 844 No H-bonds generated for 'chain 'G' and resid 842 through 844' Processing helix chain 'H' and resid 84 through 101 removed outlier: 3.572A pdb=" N HIS H 89 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL H 93 " --> pdb=" O HIS H 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN H 94 " --> pdb=" O GLN H 90 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU H 96 " --> pdb=" O GLU H 92 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ILE H 97 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU H 98 " --> pdb=" O GLN H 94 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR H 101 " --> pdb=" O ILE H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 115 removed outlier: 3.562A pdb=" N ILE H 111 " --> pdb=" O LYS H 108 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU H 112 " --> pdb=" O GLU H 109 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS H 113 " --> pdb=" O SER H 110 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU H 115 " --> pdb=" O LEU H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 183 removed outlier: 3.922A pdb=" N LEU H 174 " --> pdb=" O ARG H 170 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N THR H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 220 removed outlier: 3.731A pdb=" N ALA H 217 " --> pdb=" O ALA H 213 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN H 220 " --> pdb=" O ASP H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 229 No H-bonds generated for 'chain 'H' and resid 226 through 229' Processing helix chain 'H' and resid 231 through 234 No H-bonds generated for 'chain 'H' and resid 231 through 234' Processing helix chain 'H' and resid 254 through 265 removed outlier: 3.722A pdb=" N TYR H 262 " --> pdb=" O ALA H 258 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE H 263 " --> pdb=" O PHE H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 274 through 280 removed outlier: 3.544A pdb=" N PHE H 278 " --> pdb=" O ASN H 274 " (cutoff:3.500A) removed outlier: 3.659A 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 337 removed outlier: 3.896A pdb=" N LEU H 335 " --> pdb=" O SER H 331 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA H 336 " --> pdb=" O ASN H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 360 removed outlier: 3.831A pdb=" N ILE H 353 " --> pdb=" O THR H 349 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLN H 354 " --> pdb=" O GLU H 350 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN H 358 " --> pdb=" O GLN H 354 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU H 360 " --> pdb=" O MET H 356 " (cutoff:3.500A) Processing helix chain 'H' and resid 382 through 394 removed outlier: 3.819A pdb=" N LEU H 389 " --> pdb=" O CYS H 385 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE H 390 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET H 393 " --> pdb=" O LEU H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 409 through 420 removed outlier: 3.748A pdb=" N GLY H 414 " --> pdb=" O SER H 410 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N MET H 415 " --> pdb=" O LEU H 411 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N TRP H 416 " --> pdb=" O ILE H 412 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 417 " --> pdb=" O SER H 413 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU H 418 " --> pdb=" O GLY H 414 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL H 420 " --> pdb=" O TRP H 416 " (cutoff:3.500A) Processing helix chain 'H' and resid 428 through 439 removed outlier: 3.567A pdb=" N ALA H 433 " --> pdb=" O GLU H 429 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N CYS H 434 " --> pdb=" O SER H 430 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA H 437 " --> pdb=" O ALA H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 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 483 removed outlier: 3.793A pdb=" N HIS H 480 " --> pdb=" O ALA H 476 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE H 481 " --> pdb=" O ASN H 477 " (cutoff:3.500A) Processing helix chain 'H' and resid 502 through 505 No H-bonds generated for 'chain 'H' and resid 502 through 505' Processing helix chain 'H' and resid 510 through 518 removed outlier: 3.843A pdb=" N GLU H 515 " --> pdb=" O ASN H 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 530 through 536 removed outlier: 3.644A pdb=" N SER H 535 " --> pdb=" O ASP H 531 " (cutoff:3.500A) Processing helix chain 'H' and resid 551 through 567 removed outlier: 4.018A pdb=" N LEU H 556 " --> pdb=" O ASP H 552 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR H 559 " --> pdb=" O ARG H 555 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N TYR H 561 " --> pdb=" O LEU H 557 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU H 562 " --> pdb=" O ALA H 558 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA H 566 " --> pdb=" O GLU H 562 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N CYS H 567 " --> pdb=" O THR H 563 " (cutoff:3.500A) Processing helix chain 'H' and resid 585 through 592 removed outlier: 3.618A pdb=" N THR H 589 " --> pdb=" O LEU H 585 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER H 590 " --> pdb=" O THR H 586 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU H 591 " --> pdb=" O SER H 587 " (cutoff:3.500A) Processing helix chain 'H' and resid 604 through 607 No H-bonds generated for 'chain 'H' and resid 604 through 607' Processing helix chain 'H' and resid 609 through 637 removed outlier: 3.567A pdb=" N ASN H 614 " --> pdb=" O TYR H 610 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE H 625 " --> pdb=" O TYR H 621 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN H 626 " --> pdb=" O ASN H 622 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ASP H 627 " --> pdb=" O GLU H 623 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA H 630 " --> pdb=" O ASN H 626 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE H 631 " --> pdb=" O ASP H 627 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA H 634 " --> pdb=" O ALA H 630 " (cutoff:3.500A) Processing helix chain 'H' and resid 645 through 655 removed outlier: 3.825A pdb=" N GLU H 650 " --> pdb=" O SER H 647 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU H 653 " --> pdb=" O GLU H 650 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LYS H 654 " --> pdb=" O ASP H 651 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ARG H 655 " --> pdb=" O PHE H 652 " (cutoff:3.500A) Processing helix chain 'H' and resid 672 through 677 removed outlier: 3.621A pdb=" N ARG H 677 " --> pdb=" O ARG H 673 " (cutoff:3.500A) Processing helix chain 'H' and resid 683 through 693 removed outlier: 3.505A pdb=" N ASP H 687 " --> pdb=" O ILE H 683 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE H 688 " --> pdb=" O ARG H 684 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N PHE H 689 " --> pdb=" O ARG H 685 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU H 691 " --> pdb=" O ASP H 687 " (cutoff:3.500A) Processing helix chain 'H' and resid 696 through 701 removed outlier: 3.544A pdb=" N GLU H 700 " --> pdb=" O MET H 696 " (cutoff:3.500A) Processing helix chain 'H' and resid 744 through 748 Processing helix chain 'H' and resid 752 through 759 removed outlier: 3.566A pdb=" N ASN H 756 " --> pdb=" O ALA H 752 " (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 Processing helix chain 'H' and resid 816 through 821 removed outlier: 3.652A pdb=" N ALA H 820 " --> pdb=" O TYR H 817 " (cutoff:3.500A) removed outlier: 3.996A 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 'I' and resid 80 through 83 No H-bonds generated for 'chain 'I' and resid 80 through 83' Processing helix chain 'I' and resid 87 through 90 No H-bonds generated for 'chain 'I' and resid 87 through 90' 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 181 removed outlier: 3.834A pdb=" N ARG I 170 " --> pdb=" O ASP I 166 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU I 174 " --> pdb=" O ARG I 170 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN I 179 " --> pdb=" O ASN I 175 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 219 removed outlier: 4.307A pdb=" N ILE I 218 " --> pdb=" O ILE I 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 231 Processing helix chain 'I' and resid 254 through 265 removed outlier: 3.550A pdb=" N ALA I 258 " --> pdb=" O PRO I 254 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TYR I 262 " --> pdb=" O ALA I 258 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU I 264 " --> pdb=" O ASN I 260 " (cutoff:3.500A) 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 324 through 335 removed outlier: 4.024A pdb=" N ASN I 332 " --> pdb=" O ILE I 328 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR I 333 " --> pdb=" O THR I 329 " (cutoff:3.500A) Processing helix chain 'I' and resid 350 through 360 removed outlier: 4.017A pdb=" N LYS I 355 " --> pdb=" O ALA I 351 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN I 358 " --> pdb=" O GLN I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 372 through 374 No H-bonds generated for 'chain 'I' and resid 372 through 374' Processing helix chain 'I' and resid 382 through 395 removed outlier: 3.875A pdb=" N PHE I 386 " --> pdb=" O ALA I 382 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYS I 387 " --> pdb=" O ASN I 383 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE I 390 " --> pdb=" O PHE I 386 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA I 392 " --> pdb=" O THR I 388 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N MET I 393 " --> pdb=" O LEU I 389 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER I 395 " --> pdb=" O ALA I 391 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 412 No H-bonds generated for 'chain 'I' and resid 409 through 412' Processing helix chain 'I' and resid 414 through 420 removed outlier: 3.758A pdb=" N LEU I 418 " --> pdb=" O GLY I 414 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR I 419 " --> pdb=" O MET I 415 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 439 removed outlier: 4.163A pdb=" N ALA I 433 " --> pdb=" O GLU I 429 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS I 434 " --> pdb=" O SER I 430 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA I 437 " --> pdb=" O ALA I 433 " (cutoff:3.500A) Processing helix chain 'I' and resid 444 through 447 No H-bonds generated for 'chain 'I' and resid 444 through 447' Processing helix chain 'I' and resid 478 through 481 No H-bonds generated for 'chain 'I' and resid 478 through 481' Processing helix chain 'I' and resid 508 through 513 Processing helix chain 'I' and resid 530 through 537 removed outlier: 3.605A pdb=" N SER I 535 " --> pdb=" O ASP I 531 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE I 536 " --> pdb=" O TYR I 532 " (cutoff:3.500A) Processing helix chain 'I' and resid 539 through 544 removed outlier: 4.140A pdb=" N LEU I 543 " --> pdb=" O GLY I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 547 through 567 removed outlier: 3.523A pdb=" N VAL I 551 " --> pdb=" O LEU I 547 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP I 552 " --> pdb=" O GLY I 548 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU I 556 " --> pdb=" O ASP I 552 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N TYR I 559 " --> pdb=" O ARG I 555 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU I 562 " --> pdb=" O ALA I 558 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU I 564 " --> pdb=" O ASN I 560 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA I 566 " --> pdb=" O GLU I 562 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N CYS I 567 " --> pdb=" O THR I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 586 through 592 Processing helix chain 'I' and resid 604 through 632 removed outlier: 4.104A pdb=" N HIS I 609 " --> pdb=" O GLN I 605 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASN I 612 " --> pdb=" O PHE I 608 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASN I 614 " --> pdb=" O TYR I 610 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS I 618 " --> pdb=" O ASN I 614 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU I 623 " --> pdb=" O SER I 619 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE I 625 " --> pdb=" O TYR I 621 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN I 626 " --> pdb=" O ASN I 622 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP I 627 " --> pdb=" O GLU I 623 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA I 628 " --> pdb=" O ARG I 624 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA I 630 " --> pdb=" O ASN I 626 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ILE I 631 " --> pdb=" O ASP I 627 " (cutoff:3.500A) Processing helix chain 'I' and resid 634 through 637 No H-bonds generated for 'chain 'I' and resid 634 through 637' Processing helix chain 'I' and resid 650 through 655 removed outlier: 3.504A pdb=" N LYS I 654 " --> pdb=" O GLU I 650 " (cutoff:3.500A) Processing helix chain 'I' and resid 683 through 694 removed outlier: 3.922A pdb=" N ASP I 687 " --> pdb=" O ILE I 683 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE I 688 " --> pdb=" O ARG I 684 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE I 689 " --> pdb=" O ARG I 685 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE I 692 " --> pdb=" O ILE I 688 " (cutoff:3.500A) Processing helix chain 'I' and resid 696 through 701 removed outlier: 3.760A pdb=" N GLU I 700 " --> pdb=" O MET I 696 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ARG I 701 " --> pdb=" O GLU I 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 696 through 701' Processing helix chain 'I' and resid 742 through 748 Processing helix chain 'I' and resid 752 through 758 removed outlier: 3.875A pdb=" N ASN I 756 " --> pdb=" O ALA I 752 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET I 757 " --> pdb=" O GLN I 753 " (cutoff:3.500A) 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 792 through 795 No H-bonds generated for 'chain 'I' and resid 792 through 795' Processing helix chain 'I' and resid 816 through 820 removed outlier: 3.596A pdb=" N ALA I 820 " --> pdb=" O TYR I 817 " (cutoff:3.500A) Processing helix chain 'I' and resid 842 through 845 No H-bonds generated for 'chain 'I' and resid 842 through 845' Processing helix chain 'I' and resid 872 through 874 No H-bonds generated for 'chain 'I' and resid 872 through 874' Processing helix chain 'J' and resid 84 through 97 removed outlier: 3.751A pdb=" N GLU J 88 " --> pdb=" O LYS J 84 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS J 89 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLU J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL J 93 " --> pdb=" O HIS J 89 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN J 94 " --> pdb=" O GLN J 90 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU J 96 " --> pdb=" O GLU J 92 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE J 97 " --> pdb=" O VAL J 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 101 No H-bonds generated for 'chain 'J' and resid 99 through 101' Processing helix chain 'J' and resid 108 through 110 No H-bonds generated for 'chain 'J' and resid 108 through 110' Processing helix chain 'J' and resid 112 through 115 No H-bonds generated for 'chain 'J' and resid 112 through 115' Processing helix chain 'J' and resid 166 through 170 Processing helix chain 'J' and resid 174 through 182 removed outlier: 3.979A pdb=" N GLN J 179 " --> pdb=" O ASN J 175 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 219 removed outlier: 3.588A pdb=" N ILE J 214 " --> pdb=" O GLU J 210 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA J 217 " --> pdb=" O ALA J 213 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 234 removed outlier: 3.810A pdb=" N PHE J 231 " --> pdb=" O VAL J 227 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA J 233 " --> pdb=" O ARG J 229 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 265 removed outlier: 3.712A pdb=" N ALA J 258 " --> pdb=" O PRO J 254 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE J 259 " --> pdb=" O ILE J 255 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 280 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 325 through 338 removed outlier: 3.622A pdb=" N LEU J 335 " --> pdb=" O SER J 331 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA J 336 " --> pdb=" O ASN J 332 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N SER J 338 " --> pdb=" O ILE J 334 " (cutoff:3.500A) Processing helix chain 'J' and resid 349 through 359 removed outlier: 3.710A pdb=" N ILE J 353 " --> pdb=" O THR J 349 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLN J 354 " --> pdb=" O GLU J 350 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN J 358 " --> pdb=" O GLN J 354 " (cutoff:3.500A) Processing helix chain 'J' and resid 382 through 394 removed outlier: 3.820A pdb=" N ILE J 390 " --> pdb=" O PHE J 386 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N MET J 393 " --> pdb=" O LEU J 389 " (cutoff:3.500A) Processing helix chain 'J' and resid 409 through 418 removed outlier: 3.682A pdb=" N SER J 413 " --> pdb=" O MET J 409 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY J 414 " --> pdb=" O SER J 410 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP J 416 " --> pdb=" O ILE J 412 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU J 417 " --> pdb=" O SER J 413 " (cutoff:3.500A) Processing helix chain 'J' and resid 423 through 425 No H-bonds generated for 'chain 'J' and resid 423 through 425' Processing helix chain 'J' and resid 428 through 439 removed outlier: 3.626A pdb=" N ALA J 433 " --> pdb=" O GLU J 429 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA J 437 " --> pdb=" O ALA J 433 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 469 removed outlier: 3.537A pdb=" N GLU J 467 " --> pdb=" O PHE J 463 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N GLN J 468 " --> pdb=" O GLN J 464 " (cutoff:3.500A) Processing helix chain 'J' and resid 474 through 482 removed outlier: 3.672A pdb=" N TRP J 478 " --> pdb=" O GLN J 474 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N HIS J 480 " --> pdb=" O ALA J 476 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE J 481 " --> pdb=" O ASN J 477 " (cutoff:3.500A) Processing helix chain 'J' and resid 509 through 518 removed outlier: 3.667A pdb=" N GLU J 515 " --> pdb=" O ASN J 511 " (cutoff:3.500A) Processing helix chain 'J' and resid 530 through 536 removed outlier: 3.778A pdb=" N SER J 535 " --> pdb=" O ASP J 531 " (cutoff:3.500A) Processing helix chain 'J' and resid 547 through 564 removed outlier: 3.892A pdb=" N ASP J 552 " --> pdb=" O GLY J 548 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU J 553 " --> pdb=" O GLN J 549 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR J 554 " --> pdb=" O LEU J 550 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU J 556 " --> pdb=" O ASP J 552 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR J 559 " --> pdb=" O ARG J 555 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR J 561 " --> pdb=" O LEU J 557 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLU J 562 " --> pdb=" O ALA J 558 " (cutoff:3.500A) Processing helix chain 'J' and resid 585 through 592 removed outlier: 3.503A pdb=" N SER J 590 " --> pdb=" O THR J 586 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU J 591 " --> pdb=" O SER J 587 " (cutoff:3.500A) Processing helix chain 'J' and resid 604 through 637 removed outlier: 3.706A pdb=" N HIS J 609 " --> pdb=" O GLN J 605 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR J 611 " --> pdb=" O LEU J 607 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN J 614 " --> pdb=" O TYR J 610 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN J 616 " --> pdb=" O ASN J 612 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASN J 620 " --> pdb=" O ASN J 616 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE J 625 " --> pdb=" O TYR J 621 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN J 626 " --> pdb=" O ASN J 622 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA J 630 " --> pdb=" O ASN J 626 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE J 631 " --> pdb=" O ASP J 627 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA J 634 " --> pdb=" O ALA J 630 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASN J 636 " --> pdb=" O ILE J 632 " (cutoff:3.500A) Processing helix chain 'J' and resid 646 through 655 removed outlier: 3.564A pdb=" N ASP J 651 " --> pdb=" O SER J 647 " (cutoff:3.500A) Processing helix chain 'J' and resid 669 through 672 No H-bonds generated for 'chain 'J' and resid 669 through 672' Processing helix chain 'J' and resid 683 through 692 removed outlier: 3.939A pdb=" N ILE J 688 " --> pdb=" O ARG J 684 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE J 689 " --> pdb=" O ARG J 685 " (cutoff:3.500A) Processing helix chain 'J' and resid 696 through 702 removed outlier: 4.279A pdb=" N GLU J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA J 702 " --> pdb=" O GLN J 698 " (cutoff:3.500A) Processing helix chain 'J' and resid 742 through 747 Processing helix chain 'J' and resid 752 through 759 removed outlier: 3.638A pdb=" N ASN J 756 " --> pdb=" O ALA J 752 " (cutoff:3.500A) 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 790 through 795 removed outlier: 3.507A pdb=" N ILE J 793 " --> pdb=" O PHE J 790 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS J 795 " --> pdb=" O GLN J 792 " (cutoff:3.500A) Processing helix chain 'J' and resid 816 through 820 removed outlier: 4.025A pdb=" N ALA J 820 " --> pdb=" O TYR J 817 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 69 No H-bonds generated for 'chain 'K' and resid 66 through 69' Processing helix chain 'K' and resid 77 through 85 Processing helix chain 'K' and resid 87 through 99 removed outlier: 3.678A pdb=" N LEU K 98 " --> pdb=" O GLN K 94 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLN K 99 " --> pdb=" O TYR K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 116 removed outlier: 3.650A pdb=" N GLU K 116 " --> pdb=" O LEU K 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 112 through 116' Processing helix chain 'K' and resid 166 through 183 removed outlier: 3.907A pdb=" N ARG K 170 " --> pdb=" O ASP K 166 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU K 174 " --> pdb=" O ARG K 170 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASN K 175 " --> pdb=" O GLU K 171 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 192 No H-bonds generated for 'chain 'K' and resid 190 through 192' Processing helix chain 'K' and resid 209 through 219 removed outlier: 3.583A pdb=" N ILE K 214 " --> pdb=" O GLU K 210 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA K 217 " --> pdb=" O ALA K 213 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE K 218 " --> pdb=" O ILE K 214 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE K 219 " --> pdb=" O CYS K 215 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 233 removed outlier: 3.955A pdb=" N ALA K 233 " --> pdb=" O ARG K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 254 through 260 removed outlier: 3.513A pdb=" N ALA K 258 " --> pdb=" O PRO K 254 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE K 259 " --> pdb=" O ILE K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 274 through 278 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 326 through 329 No H-bonds generated for 'chain 'K' and resid 326 through 329' Processing helix chain 'K' and resid 333 through 337 Processing helix chain 'K' and resid 349 through 359 removed outlier: 3.815A pdb=" N ILE K 353 " --> pdb=" O THR K 349 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS K 355 " --> pdb=" O ALA K 351 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLN K 358 " --> pdb=" O GLN K 354 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 374 No H-bonds generated for 'chain 'K' and resid 372 through 374' Processing helix chain 'K' and resid 380 through 393 removed outlier: 3.598A pdb=" N CYS K 385 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR K 388 " --> pdb=" O ASP K 384 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE K 390 " --> pdb=" O PHE K 386 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA K 392 " --> pdb=" O THR K 388 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET K 393 " --> pdb=" O LEU K 389 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 417 removed outlier: 3.580A pdb=" N ILE K 412 " --> pdb=" O TYR K 408 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N TRP K 416 " --> pdb=" O ILE K 412 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU K 417 " --> pdb=" O SER K 413 " (cutoff:3.500A) Processing helix chain 'K' and resid 428 through 439 removed outlier: 4.122A pdb=" N ALA K 433 " --> pdb=" O GLU K 429 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS K 434 " --> pdb=" O SER K 430 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA K 437 " --> pdb=" O ALA K 433 " (cutoff:3.500A) Processing helix chain 'K' and resid 462 through 465 No H-bonds generated for 'chain 'K' and resid 462 through 465' Processing helix chain 'K' and resid 474 through 483 removed outlier: 3.731A pdb=" N TRP K 478 " --> pdb=" O GLN K 474 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU K 479 " --> pdb=" O VAL K 475 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS K 480 " --> pdb=" O ALA K 476 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASN K 483 " --> pdb=" O LEU K 479 " (cutoff:3.500A) Processing helix chain 'K' and resid 508 through 522 removed outlier: 3.563A pdb=" N GLN K 512 " --> pdb=" O HIS K 508 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU K 515 " --> pdb=" O ASN K 511 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET K 518 " --> pdb=" O MET K 514 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN K 519 " --> pdb=" O GLU K 515 " (cutoff:3.500A) Processing helix chain 'K' and resid 530 through 542 removed outlier: 3.873A pdb=" N SER K 535 " --> pdb=" O ASP K 531 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE K 536 " --> pdb=" O TYR K 532 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLY K 539 " --> pdb=" O SER K 535 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU K 541 " --> pdb=" O GLN K 537 " (cutoff:3.500A) Processing helix chain 'K' and resid 548 through 567 removed outlier: 3.923A pdb=" N ASP K 552 " --> pdb=" O GLY K 548 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU K 553 " --> pdb=" O GLN K 549 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR K 559 " --> pdb=" O ARG K 555 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU K 562 " --> pdb=" O ALA K 558 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU K 564 " --> pdb=" O ASN K 560 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA K 566 " --> pdb=" O GLU K 562 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N CYS K 567 " --> pdb=" O THR K 563 " (cutoff:3.500A) Processing helix chain 'K' and resid 586 through 592 Processing helix chain 'K' and resid 604 through 610 removed outlier: 4.033A pdb=" N HIS K 609 " --> pdb=" O GLN K 605 " (cutoff:3.500A) Processing helix chain 'K' and resid 612 through 632 removed outlier: 3.724A pdb=" N ASN K 616 " --> pdb=" O ASN K 612 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE K 617 " --> pdb=" O VAL K 613 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASN K 626 " --> pdb=" O ASN K 622 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP K 627 " --> pdb=" O GLU K 623 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA K 628 " --> pdb=" O ARG K 624 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE K 631 " --> pdb=" O ASP K 627 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE K 632 " --> pdb=" O ALA K 628 " (cutoff:3.500A) Processing helix chain 'K' and resid 634 through 637 No H-bonds generated for 'chain 'K' and resid 634 through 637' Processing helix chain 'K' and resid 647 through 650 No H-bonds generated for 'chain 'K' and resid 647 through 650' 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 661 through 663 No H-bonds generated for 'chain 'K' and resid 661 through 663' Processing helix chain 'K' and resid 667 through 670 No H-bonds generated for 'chain 'K' and resid 667 through 670' Processing helix chain 'K' and resid 673 through 676 No H-bonds generated for 'chain 'K' and resid 673 through 676' Processing helix chain 'K' and resid 683 through 686 No H-bonds generated for 'chain 'K' and resid 683 through 686' Processing helix chain 'K' and resid 690 through 693 No H-bonds generated for 'chain 'K' and resid 690 through 693' Processing helix chain 'K' and resid 696 through 701 removed outlier: 3.841A pdb=" N GLU K 700 " --> pdb=" O MET K 696 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG K 701 " --> pdb=" O GLU K 697 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 696 through 701' Processing helix chain 'K' and resid 742 through 747 Processing helix chain 'K' and resid 754 through 759 removed outlier: 3.612A pdb=" N LEU K 759 " --> pdb=" O THR K 755 " (cutoff:3.500A) 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 788 through 795 removed outlier: 3.640A pdb=" N ALA K 791 " --> pdb=" O THR K 788 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLN K 792 " --> pdb=" O VAL K 789 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE K 793 " --> pdb=" O PHE K 790 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS K 795 " --> pdb=" O GLN K 792 " (cutoff:3.500A) Processing helix chain 'K' and resid 816 through 820 removed outlier: 3.660A pdb=" N ALA K 820 " --> pdb=" O TYR K 817 " (cutoff:3.500A) Processing helix chain 'L' and resid 85 through 101 removed outlier: 3.646A pdb=" N HIS L 89 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL L 93 " --> pdb=" O HIS L 89 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN L 94 " --> pdb=" O GLN L 90 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU L 96 " --> pdb=" O GLU L 92 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU L 98 " --> pdb=" O GLN L 94 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN L 99 " --> pdb=" O TYR L 95 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR L 101 " --> pdb=" O ILE L 97 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 116 Processing helix chain 'L' and resid 166 through 182 removed outlier: 3.666A pdb=" N LEU L 174 " --> pdb=" O ARG L 170 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU L 181 " --> pdb=" O TYR L 177 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR L 182 " --> pdb=" O ASP L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 220 removed outlier: 3.627A pdb=" N ALA L 217 " --> pdb=" O ALA L 213 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN L 220 " --> pdb=" O ASP L 216 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 232 removed outlier: 3.695A pdb=" N ARG L 230 " --> pdb=" O GLY L 226 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N PHE L 231 " --> pdb=" O VAL L 227 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE L 232 " --> pdb=" O VAL L 228 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 226 through 232' Processing helix chain 'L' and resid 254 through 265 removed outlier: 3.802A pdb=" N ALA L 258 " --> pdb=" O PRO L 254 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR L 262 " --> pdb=" O ALA L 258 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE L 263 " --> pdb=" O PHE L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 280 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 331 Processing helix chain 'L' and resid 349 through 360 removed outlier: 3.770A pdb=" N ILE L 353 " --> pdb=" O THR L 349 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN L 354 " --> pdb=" O GLU L 350 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN L 358 " --> pdb=" O GLN L 354 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP L 359 " --> pdb=" O LYS L 355 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU L 360 " --> pdb=" O MET L 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 388 through 394 removed outlier: 4.112A pdb=" N MET L 393 " --> pdb=" O LEU L 389 " (cutoff:3.500A) Processing helix chain 'L' and resid 408 through 412 Processing helix chain 'L' and resid 414 through 420 removed outlier: 3.575A pdb=" N VAL L 420 " --> pdb=" O TRP L 416 " (cutoff:3.500A) Processing helix chain 'L' and resid 428 through 439 removed outlier: 3.881A pdb=" N ALA L 433 " --> pdb=" O GLU L 429 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA L 437 " --> pdb=" O ALA L 433 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 438 " --> pdb=" O CYS L 434 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE L 439 " --> pdb=" O GLN L 435 " (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: 4.563A pdb=" N GLN L 468 " --> pdb=" O GLN L 464 " (cutoff:3.500A) Processing helix chain 'L' and resid 473 through 483 removed outlier: 3.660A pdb=" N TRP L 478 " --> pdb=" O GLN L 474 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N HIS L 480 " --> pdb=" O ALA L 476 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE L 481 " --> pdb=" O ASN L 477 " (cutoff:3.500A) Processing helix chain 'L' and resid 510 through 521 removed outlier: 3.768A pdb=" N GLU L 515 " --> pdb=" O ASN L 511 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN L 519 " --> pdb=" O GLU L 515 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU L 520 " --> pdb=" O ALA L 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 530 through 536 removed outlier: 4.249A pdb=" N SER L 535 " --> pdb=" O ASP L 531 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 557 removed outlier: 3.910A pdb=" N ASP L 552 " --> pdb=" O GLY L 548 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU L 553 " --> pdb=" O GLN L 549 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU L 556 " --> pdb=" O ASP L 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 560 through 564 Processing helix chain 'L' and resid 585 through 592 removed outlier: 3.724A pdb=" N LEU L 591 " --> pdb=" O SER L 587 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 607 No H-bonds generated for 'chain 'L' and resid 604 through 607' Processing helix chain 'L' and resid 609 through 632 removed outlier: 3.512A pdb=" N ASN L 614 " --> pdb=" O TYR L 610 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN L 616 " --> pdb=" O ASN L 612 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE L 625 " --> pdb=" O TYR L 621 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASP L 627 " --> pdb=" O GLU L 623 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA L 630 " --> pdb=" O ASN L 626 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE L 632 " --> pdb=" O ALA L 628 " (cutoff:3.500A) Processing helix chain 'L' and resid 634 through 637 No H-bonds generated for 'chain 'L' and resid 634 through 637' Processing helix chain 'L' and resid 645 through 655 removed outlier: 3.613A pdb=" N GLU L 650 " --> pdb=" O LYS L 646 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS L 654 " --> pdb=" O GLU L 650 " (cutoff:3.500A) Processing helix chain 'L' and resid 666 through 669 No H-bonds generated for 'chain 'L' and resid 666 through 669' 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 696 through 702 removed outlier: 3.816A pdb=" N GLU L 700 " --> pdb=" O MET L 696 " (cutoff:3.500A) Processing helix chain 'L' and resid 742 through 748 Processing helix chain 'L' and resid 752 through 759 removed outlier: 3.865A pdb=" N ASN L 756 " --> pdb=" O ALA L 752 " (cutoff:3.500A) 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 791 through 795 removed outlier: 3.647A pdb=" N LYS L 795 " --> pdb=" O GLN L 792 " (cutoff:3.500A) Processing helix chain 'L' and resid 816 through 820 removed outlier: 3.710A 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 sheet with id= A, first strand: chain 'A' and resid 748 through 752 removed outlier: 3.618A pdb=" N THR A 70 " --> pdb=" O TYR A 28 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE A 26 " --> pdb=" O LEU A 72 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ILE A 74 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ILE A 24 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER A 76 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL A 22 " --> pdb=" O SER A 76 " (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: 3.506A pdb=" N SER A 417 " --> pdb=" O ARG A 406 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 448 through 452 Processing sheet with id= E, first strand: chain 'A' and resid 666 through 671 removed outlier: 3.547A pdb=" N ASP A 520 " --> pdb=" O LYS A 667 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU A 669 " --> pdb=" O TYR A 518 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N THR A 519 " --> pdb=" O ASN A 633 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 633 " --> pdb=" O THR A 519 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 625 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N GLN A 638 " --> pdb=" O THR A 623 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N THR A 623 " --> pdb=" O GLN A 638 " (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 675 through 677 removed outlier: 3.651A pdb=" N ILE A 675 " --> pdb=" O ILE A 682 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE A 682 " --> pdb=" O ILE A 675 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 886 through 890 removed outlier: 4.113A pdb=" N TRP A1051 " --> pdb=" O ALA A 890 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 133 through 139 Processing sheet with id= J, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.603A pdb=" N ARG C 238 " --> pdb=" O ASN C 247 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 303 through 305 removed outlier: 5.704A pdb=" N THR C 856 " --> pdb=" O ARG C 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 488 through 492 Processing sheet with id= M, first strand: chain 'C' and resid 739 through 741 removed outlier: 6.683A pdb=" N ALA C 765 " --> pdb=" O ILE C 740 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 133 through 139 Processing sheet with id= O, first strand: chain 'D' and resid 238 through 240 Processing sheet with id= P, first strand: chain 'D' and resid 291 through 295 Processing sheet with id= Q, first strand: chain 'D' and resid 399 through 402 removed outlier: 6.109A pdb=" N GLU D 581 " --> pdb=" O SER D 400 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ASP D 402 " --> pdb=" O GLU D 581 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU D 583 " --> pdb=" O ASP D 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 488 through 492 removed outlier: 3.714A pdb=" N VAL D 490 " --> pdb=" O ASN D 497 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASN D 497 " --> pdb=" O VAL D 490 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 710 through 712 Processing sheet with id= T, first strand: chain 'D' and resid 773 through 775 Processing sheet with id= U, first strand: chain 'E' and resid 133 through 139 Processing sheet with id= V, first strand: chain 'E' and resid 238 through 240 removed outlier: 3.508A pdb=" N VAL E 245 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N SER E 851 " --> pdb=" O VAL E 246 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 291 through 294 Processing sheet with id= X, first strand: chain 'E' and resid 303 through 305 removed outlier: 5.651A pdb=" N THR E 856 " --> pdb=" O ARG E 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'E' and resid 399 through 402 removed outlier: 6.738A pdb=" N GLU E 581 " --> pdb=" O SER E 400 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N ASP E 402 " --> pdb=" O GLU E 581 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N LEU E 583 " --> pdb=" O ASP E 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 488 through 492 removed outlier: 3.579A pdb=" N VAL E 490 " --> pdb=" O ASN E 497 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 720 through 722 removed outlier: 3.526A pdb=" N GLY E 726 " --> pdb=" O ASP E 722 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 738 through 741 Processing sheet with id= AC, first strand: chain 'E' and resid 772 through 774 No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'F' and resid 133 through 139 removed outlier: 3.509A pdb=" N GLU F 134 " --> pdb=" O LYS F 156 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 238 through 240 Processing sheet with id= AF, first strand: chain 'F' and resid 292 through 295 Processing sheet with id= AG, first strand: chain 'F' and resid 399 through 402 removed outlier: 6.442A pdb=" N GLU F 581 " --> pdb=" O SER F 400 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N ASP F 402 " --> pdb=" O GLU F 581 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU F 583 " --> pdb=" O ASP F 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 488 through 492 removed outlier: 3.703A pdb=" N VAL F 490 " --> pdb=" O ASN F 497 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL F 495 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'F' and resid 710 through 712 removed outlier: 6.039A pdb=" N GLN F 738 " --> pdb=" O ALA F 765 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL F 767 " --> pdb=" O GLN F 738 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE F 740 " --> pdb=" O VAL F 767 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 720 through 722 removed outlier: 3.504A pdb=" N GLU F 720 " --> pdb=" O VAL F 728 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL F 728 " --> pdb=" O GLU F 720 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'F' and resid 773 through 775 Processing sheet with id= AL, first strand: chain 'G' and resid 133 through 139 removed outlier: 3.631A pdb=" N LEU G 138 " --> pdb=" O ARG G 152 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 245 through 248 removed outlier: 3.811A pdb=" N SER G 851 " --> pdb=" O VAL G 246 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 291 through 295 Processing sheet with id= AO, first strand: chain 'G' and resid 303 through 305 removed outlier: 5.766A pdb=" N THR G 856 " --> pdb=" O ARG G 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'G' and resid 399 through 402 removed outlier: 6.792A pdb=" N GLU G 581 " --> pdb=" O SER G 400 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N ASP G 402 " --> pdb=" O GLU G 581 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU G 583 " --> pdb=" O ASP G 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'G' and resid 488 through 492 removed outlier: 3.617A pdb=" N VAL G 490 " --> pdb=" O ASN G 497 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'G' and resid 710 through 712 Processing sheet with id= AS, first strand: chain 'G' and resid 720 through 722 Processing sheet with id= AT, first strand: chain 'G' and resid 738 through 741 Processing sheet with id= AU, first strand: chain 'G' and resid 772 through 775 removed outlier: 7.183A pdb=" N ASP G 775 " --> pdb=" O PRO G 804 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU G 806 " --> pdb=" O ASP G 775 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'H' and resid 136 through 138 removed outlier: 3.823A pdb=" N ARG H 152 " --> pdb=" O LEU H 138 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'H' and resid 238 through 240 removed outlier: 3.535A pdb=" N ARG H 238 " --> pdb=" O ASN H 247 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS H 847 " --> pdb=" O SER H 250 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'H' and resid 292 through 295 Processing sheet with id= AY, first strand: chain 'H' and resid 488 through 492 removed outlier: 3.622A pdb=" N VAL H 490 " --> pdb=" O ASN H 497 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'H' and resid 830 through 832 Processing sheet with id= BA, first strand: chain 'H' and resid 771 through 774 Processing sheet with id= BB, first strand: chain 'I' and resid 133 through 139 removed outlier: 3.513A pdb=" N LEU I 138 " --> pdb=" O ARG I 152 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'I' and resid 238 through 240 removed outlier: 3.538A pdb=" N SER I 851 " --> pdb=" O VAL I 246 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'I' and resid 291 through 295 Processing sheet with id= BE, first strand: chain 'I' and resid 399 through 402 removed outlier: 6.691A pdb=" N GLU I 581 " --> pdb=" O SER I 400 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASP I 402 " --> pdb=" O GLU I 581 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU I 583 " --> pdb=" O ASP I 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'I' and resid 488 through 492 Processing sheet with id= BG, first strand: chain 'I' and resid 738 through 741 Processing sheet with id= BH, first strand: chain 'I' and resid 772 through 775 removed outlier: 7.408A pdb=" N ASP I 775 " --> pdb=" O PRO I 804 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU I 806 " --> pdb=" O ASP I 775 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'J' and resid 136 through 138 Processing sheet with id= BJ, first strand: chain 'J' and resid 238 through 240 removed outlier: 3.559A pdb=" N ASN J 247 " --> pdb=" O ARG J 238 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'J' and resid 269 through 271 Processing sheet with id= BL, first strand: chain 'J' and resid 291 through 295 Processing sheet with id= BM, first strand: chain 'J' and resid 399 through 402 removed outlier: 6.354A pdb=" N GLU J 581 " --> pdb=" O SER J 400 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP J 402 " --> pdb=" O GLU J 581 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LEU J 583 " --> pdb=" O ASP J 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'J' and resid 488 through 492 Processing sheet with id= BO, first strand: chain 'J' and resid 830 through 832 removed outlier: 5.947A pdb=" N GLN J 738 " --> pdb=" O ALA J 765 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VAL J 767 " --> pdb=" O GLN J 738 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ILE J 740 " --> pdb=" O VAL J 767 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'J' and resid 773 through 775 Processing sheet with id= BQ, first strand: chain 'K' and resid 133 through 139 Processing sheet with id= BR, first strand: chain 'K' and resid 245 through 249 removed outlier: 3.639A pdb=" N SER K 851 " --> pdb=" O VAL K 246 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'K' and resid 303 through 305 removed outlier: 5.652A pdb=" N THR K 856 " --> pdb=" O ARG K 304 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'K' and resid 399 through 402 removed outlier: 6.831A pdb=" N GLU K 581 " --> pdb=" O SER K 400 " (cutoff:3.500A) removed outlier: 8.295A pdb=" N ASP K 402 " --> pdb=" O GLU K 581 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU K 583 " --> pdb=" O ASP K 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'K' and resid 488 through 492 Processing sheet with id= BV, first strand: chain 'K' and resid 710 through 712 Processing sheet with id= BW, first strand: chain 'K' and resid 738 through 741 removed outlier: 3.544A pdb=" N ILE K 740 " --> pdb=" O ALA K 765 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'K' and resid 772 through 775 removed outlier: 7.144A pdb=" N ASP K 775 " --> pdb=" O PRO K 804 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU K 806 " --> pdb=" O ASP K 775 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'L' and resid 136 through 139 removed outlier: 3.679A pdb=" N ARG L 152 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'L' and resid 238 through 240 Processing sheet with id= CA, first strand: chain 'L' and resid 269 through 271 Processing sheet with id= CB, first strand: chain 'L' and resid 291 through 295 removed outlier: 3.685A pdb=" N ILE L 292 " --> pdb=" O ASP L 868 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP L 868 " --> pdb=" O ILE L 292 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'L' and resid 399 through 402 removed outlier: 6.226A pdb=" N GLU L 581 " --> pdb=" O SER L 400 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ASP L 402 " --> pdb=" O GLU L 581 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU L 583 " --> pdb=" O ASP L 402 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'L' and resid 488 through 492 removed outlier: 3.796A pdb=" N VAL L 490 " --> pdb=" O ASN L 497 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'L' and resid 720 through 722 removed outlier: 3.551A pdb=" N VAL L 728 " --> pdb=" O GLU L 720 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'L' and resid 738 through 741 Processing sheet with id= CG, first strand: chain 'L' and resid 773 through 775 1422 hydrogen bonds defined for protein. 3957 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: 27.28 Time building geometry restraints manager: 24.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 23857 1.33 - 1.45: 10655 1.45 - 1.57: 40473 1.57 - 1.69: 17 1.69 - 1.81: 740 Bond restraints: 75742 Sorted by residual: bond pdb=" C2E GTG M 1 " pdb=" C3E GTG M 1 " ideal model delta sigma weight residual 1.238 1.536 -0.298 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C3D GTG M 1 " pdb=" C4D GTG M 1 " ideal model delta sigma weight residual 1.275 1.537 -0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D GTG M 1 " pdb=" C2D GTG M 1 " ideal model delta sigma weight residual 1.275 1.519 -0.244 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C1D GTG M 1 " pdb=" O4D GTG M 1 " ideal model delta sigma weight residual 1.557 1.398 0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C2D GTG M 1 " pdb=" C3D GTG M 1 " ideal model delta sigma weight residual 1.658 1.513 0.145 2.00e-02 2.50e+03 5.25e+01 ... (remaining 75737 not shown) Histogram of bond angle deviations from ideal: 96.07 - 104.07: 1112 104.07 - 112.07: 35035 112.07 - 120.06: 34214 120.06 - 128.06: 31994 128.06 - 136.05: 388 Bond angle restraints: 102743 Sorted by residual: angle pdb=" C1E GTG M 1 " pdb=" N9B GTG M 1 " pdb=" C8B GTG M 1 " ideal model delta sigma weight residual 106.21 126.09 -19.88 3.00e+00 1.11e-01 4.39e+01 angle pdb=" C1D GTG M 1 " pdb=" N9A GTG M 1 " pdb=" C8A GTG M 1 " ideal model delta sigma weight residual 139.93 120.62 19.31 3.00e+00 1.11e-01 4.14e+01 angle pdb=" N VAL J 228 " pdb=" CA VAL J 228 " pdb=" C VAL J 228 " ideal model delta sigma weight residual 112.96 108.13 4.83 1.00e+00 1.00e+00 2.33e+01 angle pdb=" N ILE G 285 " pdb=" CA ILE G 285 " pdb=" C ILE G 285 " ideal model delta sigma weight residual 112.96 108.66 4.30 1.00e+00 1.00e+00 1.85e+01 angle pdb=" N VAL K 649 " pdb=" CA VAL K 649 " pdb=" C VAL K 649 " ideal model delta sigma weight residual 113.39 107.24 6.15 1.47e+00 4.63e-01 1.75e+01 ... (remaining 102738 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.70: 45345 35.70 - 71.39: 1088 71.39 - 107.09: 68 107.09 - 142.79: 0 142.79 - 178.49: 1 Dihedral angle restraints: 46502 sinusoidal: 19314 harmonic: 27188 Sorted by residual: dihedral pdb=" O4' C N 2 " pdb=" C1' C N 2 " pdb=" N1 C N 2 " pdb=" C2 C N 2 " ideal model delta sinusoidal sigma weight residual -128.00 50.49 -178.49 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA PHE L 525 " pdb=" C PHE L 525 " pdb=" N PRO L 526 " pdb=" CA PRO L 526 " ideal model delta harmonic sigma weight residual -180.00 -156.00 -24.00 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA MET E 514 " pdb=" C MET E 514 " pdb=" N GLU E 515 " pdb=" CA GLU E 515 " ideal model delta harmonic sigma weight residual 180.00 156.06 23.94 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 46499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 9621 0.063 - 0.126: 1838 0.126 - 0.189: 267 0.189 - 0.252: 37 0.252 - 0.315: 8 Chirality restraints: 11771 Sorted by residual: chirality pdb=" CB ILE D 367 " pdb=" CA ILE D 367 " pdb=" CG1 ILE D 367 " pdb=" CG2 ILE D 367 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CB ILE H 711 " pdb=" CA ILE H 711 " pdb=" CG1 ILE H 711 " pdb=" CG2 ILE H 711 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE J 711 " pdb=" CA ILE J 711 " pdb=" CG1 ILE J 711 " pdb=" CG2 ILE J 711 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 11768 not shown) Planarity restraints: 13274 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D GTG M 1 " 0.388 2.00e-02 2.50e+03 5.50e-01 6.80e+03 pdb=" C2D GTG M 1 " -0.638 2.00e-02 2.50e+03 pdb=" C3D GTG M 1 " -0.181 2.00e-02 2.50e+03 pdb=" C4D GTG M 1 " 0.236 2.00e-02 2.50e+03 pdb=" C5D GTG M 1 " -0.755 2.00e-02 2.50e+03 pdb=" N9A GTG M 1 " 0.098 2.00e-02 2.50e+03 pdb=" O2D GTG M 1 " -0.593 2.00e-02 2.50e+03 pdb=" O3D GTG M 1 " 0.948 2.00e-02 2.50e+03 pdb=" O4D GTG M 1 " 0.495 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1E GTG M 1 " 0.386 2.00e-02 2.50e+03 3.79e-01 3.23e+03 pdb=" C2E GTG M 1 " -0.521 2.00e-02 2.50e+03 pdb=" C3E GTG M 1 " -0.300 2.00e-02 2.50e+03 pdb=" C4E GTG M 1 " 0.251 2.00e-02 2.50e+03 pdb=" C5E GTG M 1 " -0.436 2.00e-02 2.50e+03 pdb=" N9B GTG M 1 " 0.048 2.00e-02 2.50e+03 pdb=" O2E GTG M 1 " -0.264 2.00e-02 2.50e+03 pdb=" O3E GTG M 1 " 0.648 2.00e-02 2.50e+03 pdb=" O4E GTG M 1 " 0.188 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D GTG M 1 " -0.471 2.00e-02 2.50e+03 1.71e-01 9.47e+02 pdb=" C2A GTG M 1 " 0.029 2.00e-02 2.50e+03 pdb=" C4A GTG M 1 " 0.109 2.00e-02 2.50e+03 pdb=" C5A GTG M 1 " 0.031 2.00e-02 2.50e+03 pdb=" C6A GTG M 1 " -0.067 2.00e-02 2.50e+03 pdb=" C7X GTG M 1 " -0.051 2.00e-02 2.50e+03 pdb=" C8A GTG M 1 " 0.226 2.00e-02 2.50e+03 pdb=" N1A GTG M 1 " -0.058 2.00e-02 2.50e+03 pdb=" N2A GTG M 1 " 0.023 2.00e-02 2.50e+03 pdb=" N3A GTG M 1 " 0.125 2.00e-02 2.50e+03 pdb=" N7A GTG M 1 " 0.061 2.00e-02 2.50e+03 pdb=" N9A GTG M 1 " 0.197 2.00e-02 2.50e+03 pdb=" O6A GTG M 1 " -0.152 2.00e-02 2.50e+03 ... (remaining 13271 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 21609 2.81 - 3.33: 60695 3.33 - 3.85: 112060 3.85 - 4.38: 134745 4.38 - 4.90: 234533 Nonbonded interactions: 563642 Sorted by model distance: nonbonded pdb=" OH TYR F 167 " pdb=" O TYR F 641 " model vdw 2.283 2.440 nonbonded pdb=" OH TYR J 167 " pdb=" O TYR J 641 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR D 167 " pdb=" O TYR D 641 " model vdw 2.294 2.440 nonbonded pdb=" O SER D 776 " pdb=" OG SER D 776 " model vdw 2.294 2.440 nonbonded pdb=" OH TYR L 167 " pdb=" O TYR L 641 " model vdw 2.299 2.440 ... (remaining 563637 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 'C' and resid 107 through 887) selection = (chain 'D' and resid 107 through 887) selection = chain 'E' selection = (chain 'F' and resid 107 through 887) selection = chain 'G' selection = (chain 'H' and resid 107 through 887) selection = (chain 'I' and resid 107 through 887) selection = (chain 'J' and resid 107 through 887) selection = (chain 'K' and resid 107 through 887) selection = (chain 'L' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 12.490 Check model and map are aligned: 0.850 Set scattering table: 0.510 Process input model: 143.050 Find NCS groups from input model: 4.670 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.006 0.298 75742 Z= 0.419 Angle : 0.794 19.885 102743 Z= 0.422 Chirality : 0.053 0.315 11771 Planarity : 0.009 0.550 13274 Dihedral : 15.758 178.485 28774 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.84 % Favored : 96.15 % Rotamer Outliers : 0.18 % 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: -5.60 (0.06), residues: 9057 helix: -4.92 (0.02), residues: 4117 sheet: -2.38 (0.14), residues: 939 loop : -2.48 (0.08), residues: 4001 *********************** 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 1851 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1836 time to evaluate : 6.876 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 1843 average time/residue: 0.7884 time to fit residues: 2446.4973 Evaluate side-chains 1469 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1464 time to evaluate : 6.842 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.5381 time to fit residues: 14.7310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 763 optimal weight: 10.0000 chunk 685 optimal weight: 8.9990 chunk 380 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 462 optimal weight: 8.9990 chunk 366 optimal weight: 9.9990 chunk 708 optimal weight: 10.0000 chunk 274 optimal weight: 0.0870 chunk 430 optimal weight: 3.9990 chunk 527 optimal weight: 3.9990 chunk 820 optimal weight: 10.0000 overall best weight: 4.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 ASN ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 ASN ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 649 GLN A 653 ASN A 663 ASN A 697 ASN A 698 ASN A 706 GLN A 825 ASN A 908 GLN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 983 GLN A1034 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 352 GLN C 368 GLN C 545 ASN C 560 ASN C 573 GLN C 574 HIS D 94 GLN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 352 GLN D 358 GLN D 396 GLN D 464 GLN ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 573 GLN D 642 GLN D 821 ASN D 880 ASN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 ASN E 358 GLN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN E 471 GLN E 497 ASN E 574 HIS E 614 ASN E 618 HIS E 642 GLN E 839 GLN E 880 ASN F 90 GLN F 126 GLN F 144 ASN F 279 ASN F 290 ASN F 352 GLN F 469 GLN F 472 ASN F 484 ASN ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 523 GLN F 821 ASN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 266 HIS G 274 ASN G 290 ASN G 368 GLN ** G 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 511 ASN G 573 GLN G 614 ASN ** G 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN H 267 GLN H 287 ASN H 290 ASN H 294 ASN H 318 HIS H 354 GLN H 484 ASN H 519 GLN H 523 GLN H 573 GLN H 695 ASN H 810 ASN ** I 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 175 ASN I 197 ASN I 290 ASN I 312 GLN I 368 GLN I 423 ASN I 498 GLN I 537 GLN I 545 ASN I 618 HIS I 636 ASN I 708 GLN I 753 GLN I 839 GLN ** I 880 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 94 GLN J 126 GLN J 175 ASN ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 257 HIS J 290 ASN J 318 HIS J 352 GLN J 372 GLN J 378 ASN J 423 ASN J 469 GLN J 484 ASN J 523 GLN J 549 GLN J 880 ASN K 137 GLN K 253 HIS K 266 HIS K 274 ASN K 290 ASN ** K 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 396 GLN K 469 GLN K 489 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 498 GLN K 560 ASN K 573 GLN K 574 HIS K 636 ASN ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 810 ASN K 839 GLN L 90 GLN L 126 GLN L 247 ASN ** L 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 290 ASN L 361 GLN L 523 GLN L 609 HIS L 642 GLN L 761 ASN L 838 GLN Total number of N/Q/H flips: 124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 75742 Z= 0.290 Angle : 0.579 18.036 102743 Z= 0.292 Chirality : 0.043 0.164 11771 Planarity : 0.004 0.054 13274 Dihedral : 6.233 178.073 10104 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 2.35 % 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: -4.62 (0.07), residues: 9057 helix: -3.99 (0.05), residues: 4124 sheet: -1.92 (0.15), residues: 959 loop : -2.08 (0.08), residues: 3974 *********************** 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 1709 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1513 time to evaluate : 6.826 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 112 residues processed: 1620 average time/residue: 0.7458 time to fit residues: 2078.1489 Evaluate side-chains 1504 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1392 time to evaluate : 6.796 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 0 residues processed: 112 average time/residue: 0.5662 time to fit residues: 130.8822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 456 optimal weight: 3.9990 chunk 254 optimal weight: 9.9990 chunk 683 optimal weight: 5.9990 chunk 559 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 822 optimal weight: 9.9990 chunk 888 optimal weight: 9.9990 chunk 732 optimal weight: 9.9990 chunk 815 optimal weight: 6.9990 chunk 280 optimal weight: 2.9990 chunk 659 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN A 920 GLN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 GLN ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN E 274 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 GLN E 497 ASN F 94 GLN ** F 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 GLN G 497 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 354 GLN H 519 GLN H 839 GLN I 94 GLN I 290 ASN I 560 ASN I 852 ASN J 175 ASN ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 480 HIS J 549 GLN J 597 ASN J 760 ASN K 354 GLN K 489 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 HIS L 257 HIS L 484 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 75742 Z= 0.277 Angle : 0.558 16.827 102743 Z= 0.278 Chirality : 0.043 0.270 11771 Planarity : 0.004 0.050 13274 Dihedral : 5.980 177.180 10104 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.92 % 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: -3.95 (0.07), residues: 9057 helix: -3.31 (0.06), residues: 4126 sheet: -1.65 (0.15), residues: 968 loop : -1.87 (0.09), residues: 3963 *********************** 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 1600 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1440 time to evaluate : 7.242 Fit side-chains revert: symmetry clash outliers start: 160 outliers final: 62 residues processed: 1539 average time/residue: 0.7188 time to fit residues: 1891.3129 Evaluate side-chains 1432 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1370 time to evaluate : 6.819 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 0.5565 time to fit residues: 74.8088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 812 optimal weight: 7.9990 chunk 618 optimal weight: 1.9990 chunk 426 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 392 optimal weight: 10.0000 chunk 552 optimal weight: 9.9990 chunk 825 optimal weight: 5.9990 chunk 873 optimal weight: 10.0000 chunk 431 optimal weight: 10.0000 chunk 782 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN A 738 GLN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 HIS ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN ** G 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 477 ASN G 497 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 708 GLN H 260 ASN H 354 GLN I 380 GLN I 738 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN J 597 ASN J 642 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 75742 Z= 0.341 Angle : 0.584 16.922 102743 Z= 0.291 Chirality : 0.044 0.203 11771 Planarity : 0.004 0.049 13274 Dihedral : 5.985 176.210 10104 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 2.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.08), residues: 9057 helix: -2.97 (0.06), residues: 4127 sheet: -1.56 (0.16), residues: 960 loop : -1.78 (0.09), residues: 3970 *********************** 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 1637 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1405 time to evaluate : 6.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 232 outliers final: 128 residues processed: 1548 average time/residue: 0.7274 time to fit residues: 1938.3159 Evaluate side-chains 1478 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1350 time to evaluate : 6.989 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 0 residues processed: 128 average time/residue: 0.5506 time to fit residues: 144.5449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 727 optimal weight: 9.9990 chunk 496 optimal weight: 10.0000 chunk 12 optimal weight: 0.0670 chunk 650 optimal weight: 6.9990 chunk 360 optimal weight: 9.9990 chunk 745 optimal weight: 7.9990 chunk 604 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 446 optimal weight: 1.9990 chunk 784 optimal weight: 5.9990 chunk 220 optimal weight: 0.9980 overall best weight: 2.0124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN A 663 ASN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 274 ASN ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 549 GLN G 151 ASN G 361 GLN G 497 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 618 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN H 354 GLN I 290 ASN ** I 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 175 ASN ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 290 ASN J 597 ASN J 642 GLN J 810 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 75742 Z= 0.151 Angle : 0.496 16.874 102743 Z= 0.246 Chirality : 0.041 0.183 11771 Planarity : 0.003 0.048 13274 Dihedral : 5.575 175.845 10104 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.52 % 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: -3.14 (0.08), residues: 9057 helix: -2.56 (0.07), residues: 4121 sheet: -1.27 (0.16), residues: 923 loop : -1.55 (0.09), residues: 4013 *********************** 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 1572 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1445 time to evaluate : 7.002 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 49 residues processed: 1526 average time/residue: 0.7303 time to fit residues: 1914.4353 Evaluate side-chains 1421 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1372 time to evaluate : 7.188 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.5881 time to fit residues: 65.5165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 293 optimal weight: 3.9990 chunk 786 optimal weight: 3.9990 chunk 172 optimal weight: 9.9990 chunk 513 optimal weight: 7.9990 chunk 215 optimal weight: 2.9990 chunk 874 optimal weight: 5.9990 chunk 726 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 459 optimal weight: 0.3980 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 267 GLN ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 GLN E 497 ASN F 126 GLN F 354 GLN F 396 GLN G 361 GLN ** G 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 354 GLN I 290 ASN ** I 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 852 ASN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 372 GLN J 573 GLN J 597 ASN K 90 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 90 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 75742 Z= 0.216 Angle : 0.521 16.891 102743 Z= 0.257 Chirality : 0.042 0.215 11771 Planarity : 0.003 0.047 13274 Dihedral : 5.528 175.592 10104 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 1.52 % 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: -2.90 (0.08), residues: 9057 helix: -2.32 (0.07), residues: 4112 sheet: -1.24 (0.16), residues: 928 loop : -1.46 (0.09), residues: 4017 *********************** 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 1515 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1388 time to evaluate : 6.792 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 65 residues processed: 1467 average time/residue: 0.7464 time to fit residues: 1882.8773 Evaluate side-chains 1413 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1348 time to evaluate : 7.096 Switching outliers to nearest non-outliers outliers start: 65 outliers final: 0 residues processed: 65 average time/residue: 0.5734 time to fit residues: 81.1387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 843 optimal weight: 9.9990 chunk 98 optimal weight: 0.0060 chunk 498 optimal weight: 10.0000 chunk 638 optimal weight: 5.9990 chunk 494 optimal weight: 8.9990 chunk 736 optimal weight: 5.9990 chunk 488 optimal weight: 0.3980 chunk 871 optimal weight: 4.9990 chunk 545 optimal weight: 8.9990 chunk 531 optimal weight: 3.9990 chunk 402 optimal weight: 4.9990 overall best weight: 2.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 756 ASN C 760 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 GLN E 497 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN F 354 GLN G 274 ASN G 497 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 354 GLN H 549 GLN ** I 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 597 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 396 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 75742 Z= 0.194 Angle : 0.508 16.896 102743 Z= 0.250 Chirality : 0.041 0.188 11771 Planarity : 0.003 0.047 13274 Dihedral : 5.422 175.199 10104 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.10 % 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: -2.67 (0.08), residues: 9057 helix: -2.08 (0.07), residues: 4101 sheet: -1.17 (0.16), residues: 939 loop : -1.40 (0.09), residues: 4017 *********************** 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 1486 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 1394 time to evaluate : 6.856 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 92 outliers final: 44 residues processed: 1438 average time/residue: 0.7437 time to fit residues: 1839.5858 Evaluate side-chains 1398 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1354 time to evaluate : 6.814 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5518 time to fit residues: 56.0870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 539 optimal weight: 4.9990 chunk 347 optimal weight: 9.9990 chunk 520 optimal weight: 5.9990 chunk 262 optimal weight: 10.0000 chunk 171 optimal weight: 6.9990 chunk 168 optimal weight: 1.9990 chunk 553 optimal weight: 9.9990 chunk 593 optimal weight: 20.0000 chunk 430 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 684 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** A 959 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 175 ASN D 435 GLN ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 253 HIS F 354 GLN ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 GLN G 497 ASN ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 618 HIS H 354 GLN I 380 GLN I 622 ASN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN J 597 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 75742 Z= 0.264 Angle : 0.547 16.922 102743 Z= 0.269 Chirality : 0.043 0.199 11771 Planarity : 0.003 0.047 13274 Dihedral : 5.529 174.852 10104 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer Outliers : 1.11 % 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: -2.64 (0.08), residues: 9057 helix: -2.02 (0.07), residues: 4111 sheet: -1.18 (0.16), residues: 942 loop : -1.40 (0.09), residues: 4004 *********************** 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 1471 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1378 time to evaluate : 6.965 Fit side-chains outliers start: 93 outliers final: 51 residues processed: 1429 average time/residue: 0.7234 time to fit residues: 1774.7671 Evaluate side-chains 1393 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1342 time to evaluate : 6.801 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.5814 time to fit residues: 65.7077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 792 optimal weight: 7.9990 chunk 834 optimal weight: 5.9990 chunk 761 optimal weight: 8.9990 chunk 811 optimal weight: 5.9990 chunk 488 optimal weight: 5.9990 chunk 353 optimal weight: 9.9990 chunk 637 optimal weight: 9.9990 chunk 249 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 chunk 767 optimal weight: 4.9990 chunk 809 optimal weight: 3.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN A 785 GLN C 274 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN F 266 HIS ** G 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 361 GLN ** G 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 354 GLN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN J 290 ASN J 597 ASN J 839 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 75742 Z= 0.330 Angle : 0.584 16.953 102743 Z= 0.288 Chirality : 0.044 0.197 11771 Planarity : 0.004 0.052 13274 Dihedral : 5.681 174.215 10104 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.01 % 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: -2.68 (0.08), residues: 9057 helix: -2.04 (0.07), residues: 4123 sheet: -1.23 (0.16), residues: 943 loop : -1.45 (0.09), residues: 3991 *********************** 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 1438 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 1354 time to evaluate : 6.950 Fit side-chains outliers start: 84 outliers final: 45 residues processed: 1404 average time/residue: 0.7535 time to fit residues: 1818.3465 Evaluate side-chains 1370 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1325 time to evaluate : 7.010 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.6090 time to fit residues: 61.2032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 533 optimal weight: 9.9990 chunk 858 optimal weight: 0.9980 chunk 524 optimal weight: 8.9990 chunk 407 optimal weight: 8.9990 chunk 596 optimal weight: 0.9980 chunk 900 optimal weight: 20.0000 chunk 828 optimal weight: 5.9990 chunk 717 optimal weight: 5.9990 chunk 74 optimal weight: 0.7980 chunk 553 optimal weight: 0.9980 chunk 439 optimal weight: 6.9990 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN C 274 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 287 ASN ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 273 ASN ** E 560 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 354 GLN G 361 GLN ** G 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 622 ASN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN J 290 ASN J 597 ASN J 839 GLN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 240 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 75742 Z= 0.154 Angle : 0.504 16.886 102743 Z= 0.248 Chirality : 0.041 0.198 11771 Planarity : 0.003 0.048 13274 Dihedral : 5.334 174.298 10104 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.08), residues: 9057 helix: -1.73 (0.08), residues: 4117 sheet: -1.10 (0.17), residues: 929 loop : -1.30 (0.09), residues: 4011 ********************** 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 1434 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 1414 time to evaluate : 6.945 Fit side-chains outliers start: 20 outliers final: 11 residues processed: 1424 average time/residue: 0.7502 time to fit residues: 1841.5527 Evaluate side-chains 1364 residues out of total 8342 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1353 time to evaluate : 7.081 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5996 time to fit residues: 22.5265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 904 random chunks: chunk 569 optimal weight: 10.0000 chunk 763 optimal weight: 9.9990 chunk 219 optimal weight: 0.6980 chunk 661 optimal weight: 9.9990 chunk 105 optimal weight: 7.9990 chunk 199 optimal weight: 7.9990 chunk 718 optimal weight: 8.9990 chunk 300 optimal weight: 0.0050 chunk 737 optimal weight: 7.9990 chunk 90 optimal weight: 0.2980 chunk 132 optimal weight: 5.9990 overall best weight: 2.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 852 ASN ** D 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 497 ASN ** G 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 549 GLN ** I 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 622 ASN ** J 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 220 GLN J 597 ASN ** K 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.112618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.091739 restraints weight = 100304.378| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.94 r_work: 0.2812 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 75742 Z= 0.204 Angle : 0.525 16.905 102743 Z= 0.259 Chirality : 0.042 0.198 11771 Planarity : 0.003 0.047 13274 Dihedral : 5.356 174.152 10104 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer Outliers : 0.52 % 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: -2.24 (0.08), residues: 9057 helix: -1.62 (0.08), residues: 4106 sheet: -1.07 (0.17), residues: 939 loop : -1.26 (0.09), residues: 4012 =============================================================================== Job complete usr+sys time: 26355.40 seconds wall clock time: 457 minutes 14.87 seconds (27434.87 seconds total)