Starting phenix.real_space_refine on Sun Mar 24 19:45:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnt_29323/03_2024/8fnt_29323.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnt_29323/03_2024/8fnt_29323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnt_29323/03_2024/8fnt_29323.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnt_29323/03_2024/8fnt_29323.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnt_29323/03_2024/8fnt_29323.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnt_29323/03_2024/8fnt_29323.pdb" } resolution = 2.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.122 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 217 5.16 5 C 27833 2.51 5 N 7578 2.21 5 O 8240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 38": "NH1" <-> "NH2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ASP 75": "OD1" <-> "OD2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B GLU 119": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B GLU 171": "OE1" <-> "OE2" Residue "B TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 179": "OD1" <-> "OD2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B GLU 202": "OE1" <-> "OE2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ASP 222": "OD1" <-> "OD2" Residue "B ASP 224": "OD1" <-> "OD2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ASP 232": "OD1" <-> "OD2" Residue "B GLU 235": "OE1" <-> "OE2" Residue "B ASP 253": "OD1" <-> "OD2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 277": "OE1" <-> "OE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "B ASP 365": "OD1" <-> "OD2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B ASP 449": "OD1" <-> "OD2" Residue "B PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 457": "OD1" <-> "OD2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 473": "OE1" <-> "OE2" Residue "B LEU 502": "CD1" <-> "CD2" Residue "B GLU 529": "OE1" <-> "OE2" Residue "B TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 596": "OE1" <-> "OE2" Residue "B ASP 618": "OD1" <-> "OD2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B ASP 708": "OD1" <-> "OD2" Residue "B GLU 714": "OE1" <-> "OE2" Residue "B PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 789": "OE1" <-> "OE2" Residue "B GLU 790": "OE1" <-> "OE2" Residue "B ASP 798": "OD1" <-> "OD2" Residue "B GLU 816": "OE1" <-> "OE2" Residue "B GLU 871": "OE1" <-> "OE2" Residue "B GLU 880": "OE1" <-> "OE2" Residue "B ASP 889": "OD1" <-> "OD2" Residue "B GLU 890": "OE1" <-> "OE2" Residue "B ASP 893": "OD1" <-> "OD2" Residue "B ASP 930": "OD1" <-> "OD2" Residue "C ARG 38": "NH1" <-> "NH2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C ASP 75": "OD1" <-> "OD2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C GLU 119": "OE1" <-> "OE2" Residue "C GLU 151": "OE1" <-> "OE2" Residue "C GLU 171": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C ASP 212": "OD1" <-> "OD2" Residue "C ASP 221": "OD1" <-> "OD2" Residue "C ASP 222": "OD1" <-> "OD2" Residue "C ASP 224": "OD1" <-> "OD2" Residue "C ASP 228": "OD1" <-> "OD2" Residue "C ASP 232": "OD1" <-> "OD2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "C ASP 253": "OD1" <-> "OD2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 277": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "C ASP 365": "OD1" <-> "OD2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C ASP 449": "OD1" <-> "OD2" Residue "C PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 457": "OD1" <-> "OD2" Residue "C PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 473": "OE1" <-> "OE2" Residue "C LEU 502": "CD1" <-> "CD2" Residue "C GLU 529": "OE1" <-> "OE2" Residue "C TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 596": "OE1" <-> "OE2" Residue "C ASP 618": "OD1" <-> "OD2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "C ASP 708": "OD1" <-> "OD2" Residue "C GLU 714": "OE1" <-> "OE2" Residue "C PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 789": "OE1" <-> "OE2" Residue "C GLU 790": "OE1" <-> "OE2" Residue "C ASP 798": "OD1" <-> "OD2" Residue "C GLU 816": "OE1" <-> "OE2" Residue "C GLU 871": "OE1" <-> "OE2" Residue "C GLU 880": "OE1" <-> "OE2" Residue "C ASP 889": "OD1" <-> "OD2" Residue "C GLU 890": "OE1" <-> "OE2" Residue "C ASP 893": "OD1" <-> "OD2" Residue "D ARG 38": "NH1" <-> "NH2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D GLU 119": "OE1" <-> "OE2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D GLU 171": "OE1" <-> "OE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 179": "OD1" <-> "OD2" Residue "D GLU 201": "OE1" <-> "OE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D ASP 212": "OD1" <-> "OD2" Residue "D ASP 221": "OD1" <-> "OD2" Residue "D ASP 222": "OD1" <-> "OD2" Residue "D ASP 224": "OD1" <-> "OD2" Residue "D ASP 228": "OD1" <-> "OD2" Residue "D ASP 232": "OD1" <-> "OD2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D ASP 253": "OD1" <-> "OD2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 277": "OE1" <-> "OE2" Residue "D GLU 291": "OE1" <-> "OE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "D ASP 365": "OD1" <-> "OD2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D ASP 449": "OD1" <-> "OD2" Residue "D PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 457": "OD1" <-> "OD2" Residue "D PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 473": "OE1" <-> "OE2" Residue "D LEU 502": "CD1" <-> "CD2" Residue "D GLU 529": "OE1" <-> "OE2" Residue "D TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 596": "OE1" <-> "OE2" Residue "D ASP 618": "OD1" <-> "OD2" Residue "D GLU 638": "OE1" <-> "OE2" Residue "D ASP 708": "OD1" <-> "OD2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 789": "OE1" <-> "OE2" Residue "D GLU 790": "OE1" <-> "OE2" Residue "D ASP 798": "OD1" <-> "OD2" Residue "D GLU 816": "OE1" <-> "OE2" Residue "D GLU 871": "OE1" <-> "OE2" Residue "D GLU 880": "OE1" <-> "OE2" Residue "D ASP 889": "OD1" <-> "OD2" Residue "D GLU 890": "OE1" <-> "OE2" Residue "D ASP 893": "OD1" <-> "OD2" Residue "D ASP 930": "OD1" <-> "OD2" Residue "F ARG 38": "NH1" <-> "NH2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F ASP 75": "OD1" <-> "OD2" Residue "F ASP 111": "OD1" <-> "OD2" Residue "F GLU 119": "OE1" <-> "OE2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F GLU 171": "OE1" <-> "OE2" Residue "F TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 179": "OD1" <-> "OD2" Residue "F GLU 201": "OE1" <-> "OE2" Residue "F GLU 202": "OE1" <-> "OE2" Residue "F ASP 212": "OD1" <-> "OD2" Residue "F ASP 221": "OD1" <-> "OD2" Residue "F ASP 222": "OD1" <-> "OD2" Residue "F ASP 224": "OD1" <-> "OD2" Residue "F ASP 228": "OD1" <-> "OD2" Residue "F ASP 232": "OD1" <-> "OD2" Residue "F GLU 235": "OE1" <-> "OE2" Residue "F ASP 253": "OD1" <-> "OD2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 277": "OE1" <-> "OE2" Residue "F GLU 291": "OE1" <-> "OE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "F ASP 365": "OD1" <-> "OD2" Residue "F GLU 370": "OE1" <-> "OE2" Residue "F ASP 449": "OD1" <-> "OD2" Residue "F PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 457": "OD1" <-> "OD2" Residue "F PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 473": "OE1" <-> "OE2" Residue "F LEU 502": "CD1" <-> "CD2" Residue "F GLU 529": "OE1" <-> "OE2" Residue "F TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 596": "OE1" <-> "OE2" Residue "F ASP 618": "OD1" <-> "OD2" Residue "F GLU 638": "OE1" <-> "OE2" Residue "F ASP 708": "OD1" <-> "OD2" Residue "F GLU 714": "OE1" <-> "OE2" Residue "F PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 789": "OE1" <-> "OE2" Residue "F GLU 790": "OE1" <-> "OE2" Residue "F ASP 798": "OD1" <-> "OD2" Residue "F GLU 816": "OE1" <-> "OE2" Residue "F GLU 871": "OE1" <-> "OE2" Residue "F GLU 880": "OE1" <-> "OE2" Residue "F ASP 889": "OD1" <-> "OD2" Residue "F GLU 890": "OE1" <-> "OE2" Residue "F ASP 893": "OD1" <-> "OD2" Residue "G ARG 38": "NH1" <-> "NH2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ASP 75": "OD1" <-> "OD2" Residue "G ASP 111": "OD1" <-> "OD2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G GLU 151": "OE1" <-> "OE2" Residue "G GLU 171": "OE1" <-> "OE2" Residue "G TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 179": "OD1" <-> "OD2" Residue "G GLU 201": "OE1" <-> "OE2" Residue "G GLU 202": "OE1" <-> "OE2" Residue "G ASP 212": "OD1" <-> "OD2" Residue "G ASP 221": "OD1" <-> "OD2" Residue "G ASP 222": "OD1" <-> "OD2" Residue "G ASP 224": "OD1" <-> "OD2" Residue "G ASP 228": "OD1" <-> "OD2" Residue "G ASP 232": "OD1" <-> "OD2" Residue "G GLU 235": "OE1" <-> "OE2" Residue "G ASP 253": "OD1" <-> "OD2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 277": "OE1" <-> "OE2" Residue "G GLU 291": "OE1" <-> "OE2" Residue "G ASP 363": "OD1" <-> "OD2" Residue "G ASP 365": "OD1" <-> "OD2" Residue "G GLU 370": "OE1" <-> "OE2" Residue "G ASP 449": "OD1" <-> "OD2" Residue "G PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 457": "OD1" <-> "OD2" Residue "G PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 473": "OE1" <-> "OE2" Residue "G LEU 502": "CD1" <-> "CD2" Residue "G GLU 529": "OE1" <-> "OE2" Residue "G TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 596": "OE1" <-> "OE2" Residue "G ASP 618": "OD1" <-> "OD2" Residue "G GLU 638": "OE1" <-> "OE2" Residue "G ASP 708": "OD1" <-> "OD2" Residue "G GLU 714": "OE1" <-> "OE2" Residue "G PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 789": "OE1" <-> "OE2" Residue "G GLU 790": "OE1" <-> "OE2" Residue "G ASP 798": "OD1" <-> "OD2" Residue "G GLU 816": "OE1" <-> "OE2" Residue "G GLU 871": "OE1" <-> "OE2" Residue "G GLU 880": "OE1" <-> "OE2" Residue "G ASP 889": "OD1" <-> "OD2" Residue "G GLU 890": "OE1" <-> "OE2" Residue "G ASP 893": "OD1" <-> "OD2" Residue "E ARG 38": "NH1" <-> "NH2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E ASP 75": "OD1" <-> "OD2" Residue "E ASP 111": "OD1" <-> "OD2" Residue "E GLU 119": "OE1" <-> "OE2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E GLU 171": "OE1" <-> "OE2" Residue "E TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 179": "OD1" <-> "OD2" Residue "E GLU 201": "OE1" <-> "OE2" Residue "E GLU 202": "OE1" <-> "OE2" Residue "E ASP 212": "OD1" <-> "OD2" Residue "E ASP 221": "OD1" <-> "OD2" Residue "E ASP 222": "OD1" <-> "OD2" Residue "E ASP 224": "OD1" <-> "OD2" Residue "E ASP 228": "OD1" <-> "OD2" Residue "E ASP 232": "OD1" <-> "OD2" Residue "E GLU 235": "OE1" <-> "OE2" Residue "E ASP 253": "OD1" <-> "OD2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 277": "OE1" <-> "OE2" Residue "E GLU 291": "OE1" <-> "OE2" Residue "E ASP 363": "OD1" <-> "OD2" Residue "E ASP 365": "OD1" <-> "OD2" Residue "E GLU 370": "OE1" <-> "OE2" Residue "E ASP 449": "OD1" <-> "OD2" Residue "E PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 457": "OD1" <-> "OD2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 473": "OE1" <-> "OE2" Residue "E LEU 502": "CD1" <-> "CD2" Residue "E GLU 529": "OE1" <-> "OE2" Residue "E TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 596": "OE1" <-> "OE2" Residue "E ASP 618": "OD1" <-> "OD2" Residue "E GLU 638": "OE1" <-> "OE2" Residue "E ASP 708": "OD1" <-> "OD2" Residue "E GLU 714": "OE1" <-> "OE2" Residue "E PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 789": "OE1" <-> "OE2" Residue "E GLU 790": "OE1" <-> "OE2" Residue "E ASP 798": "OD1" <-> "OD2" Residue "E GLU 816": "OE1" <-> "OE2" Residue "E GLU 871": "OE1" <-> "OE2" Residue "E GLU 880": "OE1" <-> "OE2" Residue "E ASP 889": "OD1" <-> "OD2" Residue "E GLU 890": "OE1" <-> "OE2" Residue "E ASP 893": "OD1" <-> "OD2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "A ASP 111": "OD1" <-> "OD2" Residue "A GLU 119": "OE1" <-> "OE2" Residue "A GLU 151": "OE1" <-> "OE2" Residue "A GLU 171": "OE1" <-> "OE2" Residue "A TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 179": "OD1" <-> "OD2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A ASP 221": "OD1" <-> "OD2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A GLU 235": "OE1" <-> "OE2" Residue "A ASP 253": "OD1" <-> "OD2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A GLU 291": "OE1" <-> "OE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "A ASP 365": "OD1" <-> "OD2" Residue "A GLU 370": "OE1" <-> "OE2" Residue "A ASP 449": "OD1" <-> "OD2" Residue "A PHE 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 457": "OD1" <-> "OD2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 473": "OE1" <-> "OE2" Residue "A LEU 502": "CD1" <-> "CD2" Residue "A GLU 529": "OE1" <-> "OE2" Residue "A TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A ASP 618": "OD1" <-> "OD2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A ASP 708": "OD1" <-> "OD2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 789": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A ASP 798": "OD1" <-> "OD2" Residue "A GLU 816": "OE1" <-> "OE2" Residue "A GLU 871": "OE1" <-> "OE2" Residue "A GLU 880": "OE1" <-> "OE2" Residue "A ASP 889": "OD1" <-> "OD2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "A ASP 893": "OD1" <-> "OD2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43868 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "C" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "D" Number of atoms: 6264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 784, 6264 Classifications: {'peptide': 784} Link IDs: {'PTRANS': 21, 'TRANS': 762} Chain breaks: 9 Chain: "F" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "G" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Chain: "E" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 781, 6239 Classifications: {'peptide': 781} Link IDs: {'PTRANS': 20, 'TRANS': 760} Chain breaks: 9 Chain: "A" Number of atoms: 6273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 6273 Classifications: {'peptide': 785} Link IDs: {'PTRANS': 21, 'TRANS': 763} Chain breaks: 9 Time building chain proxies: 20.41, per 1000 atoms: 0.47 Number of scatterers: 43868 At special positions: 0 Unit cell: (155.925, 160.875, 131.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 217 16.00 O 8240 8.00 N 7578 7.00 C 27833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.75 Conformation dependent library (CDL) restraints added in 7.4 seconds 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10434 Finding SS restraints... Secondary structure from input PDB file: 259 helices and 14 sheets defined 63.2% alpha, 3.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.28 Creating SS restraints... Processing helix chain 'B' and resid 35 through 47 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'B' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR B 124 " --> pdb=" O PRO B 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 163 removed outlier: 4.128A pdb=" N HIS B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.107A pdb=" N THR B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 181 removed outlier: 3.640A pdb=" N SER B 178 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 181 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 269 removed outlier: 3.578A pdb=" N TYR B 257 " --> pdb=" O ASP B 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN B 268 " --> pdb=" O LYS B 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR B 269 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 277 Processing helix chain 'B' and resid 279 through 302 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 312 through 317 Processing helix chain 'B' and resid 344 through 357 Processing helix chain 'B' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP B 365 " --> pdb=" O GLY B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR B 387 " --> pdb=" O LEU B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 425 Processing helix chain 'B' and resid 425 through 433 Processing helix chain 'B' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 466 Processing helix chain 'B' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 516 removed outlier: 3.592A pdb=" N CYS B 505 " --> pdb=" O LEU B 501 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL B 508 " --> pdb=" O GLY B 504 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE B 511 " --> pdb=" O SER B 507 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 540 Processing helix chain 'B' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA B 556 " --> pdb=" O ASN B 552 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 607 removed outlier: 3.857A pdb=" N SER B 607 " --> pdb=" O ALA B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 622 through 632 Processing helix chain 'B' and resid 639 through 651 removed outlier: 3.549A pdb=" N VAL B 649 " --> pdb=" O ALA B 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR B 711 " --> pdb=" O SER B 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE B 723 " --> pdb=" O ASN B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 727 No H-bonds generated for 'chain 'B' and resid 725 through 727' Processing helix chain 'B' and resid 730 through 752 removed outlier: 3.585A pdb=" N ASN B 746 " --> pdb=" O TYR B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 756 removed outlier: 4.027A pdb=" N LEU B 756 " --> pdb=" O LYS B 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 753 through 756' Processing helix chain 'B' and resid 770 through 794 removed outlier: 3.583A pdb=" N MET B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS B 794 " --> pdb=" O GLU B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS B 822 " --> pdb=" O GLU B 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS B 827 " --> pdb=" O ILE B 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS B 829 " --> pdb=" O GLY B 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 830 " --> pdb=" O GLU B 826 " (cutoff:3.500A) Processing helix chain 'B' and resid 839 through 847 Processing helix chain 'B' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE B 856 " --> pdb=" O HIS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.928A pdb=" N ASN B 869 " --> pdb=" O VAL B 865 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 870 " --> pdb=" O LYS B 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER B 873 " --> pdb=" O ASN B 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS B 876 " --> pdb=" O THR B 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU B 877 " --> pdb=" O SER B 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE B 878 " --> pdb=" O PHE B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 897 removed outlier: 4.705A pdb=" N TYR B 894 " --> pdb=" O GLU B 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 895 " --> pdb=" O GLU B 891 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 47 Processing helix chain 'C' and resid 82 through 93 Processing helix chain 'C' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR C 124 " --> pdb=" O PRO C 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY C 139 " --> pdb=" O ASP C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS C 156 " --> pdb=" O GLN C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR C 168 " --> pdb=" O LEU C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER C 178 " --> pdb=" O GLU C 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU C 181 " --> pdb=" O SER C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 212 removed outlier: 3.502A pdb=" N ILE C 199 " --> pdb=" O ASP C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 240 removed outlier: 4.072A pdb=" N ASP C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN C 268 " --> pdb=" O LYS C 264 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N TYR C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 277 Processing helix chain 'C' and resid 279 through 302 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 344 through 357 Processing helix chain 'C' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP C 365 " --> pdb=" O GLY C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR C 387 " --> pdb=" O LEU C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 425 Processing helix chain 'C' and resid 425 through 433 Processing helix chain 'C' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 466 Processing helix chain 'C' and resid 472 through 490 removed outlier: 3.518A pdb=" N ILE C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS C 505 " --> pdb=" O LEU C 501 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL C 508 " --> pdb=" O GLY C 504 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE C 511 " --> pdb=" O SER C 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR C 516 " --> pdb=" O ASN C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 540 Processing helix chain 'C' and resid 546 through 559 removed outlier: 3.707A pdb=" N ALA C 556 " --> pdb=" O ASN C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER C 607 " --> pdb=" O ALA C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 622 through 632 Processing helix chain 'C' and resid 639 through 651 removed outlier: 3.549A pdb=" N VAL C 649 " --> pdb=" O ALA C 645 " (cutoff:3.500A) Processing helix chain 'C' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR C 711 " --> pdb=" O SER C 707 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE C 723 " --> pdb=" O ASN C 719 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 727 No H-bonds generated for 'chain 'C' and resid 725 through 727' Processing helix chain 'C' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN C 746 " --> pdb=" O TYR C 742 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 756 removed outlier: 4.027A pdb=" N LEU C 756 " --> pdb=" O LYS C 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 753 through 756' Processing helix chain 'C' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS C 794 " --> pdb=" O GLU C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 831 removed outlier: 3.560A pdb=" N LYS C 822 " --> pdb=" O GLU C 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS C 827 " --> pdb=" O ILE C 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS C 829 " --> pdb=" O GLY C 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA C 830 " --> pdb=" O GLU C 826 " (cutoff:3.500A) Processing helix chain 'C' and resid 839 through 847 Processing helix chain 'C' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE C 856 " --> pdb=" O HIS C 852 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN C 869 " --> pdb=" O VAL C 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS C 870 " --> pdb=" O LYS C 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER C 873 " --> pdb=" O ASN C 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 877 " --> pdb=" O SER C 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE C 878 " --> pdb=" O PHE C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 888 through 897 removed outlier: 4.706A pdb=" N TYR C 894 " --> pdb=" O GLU C 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU C 895 " --> pdb=" O GLU C 891 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 47 Processing helix chain 'D' and resid 82 through 93 Processing helix chain 'D' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR D 124 " --> pdb=" O PRO D 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY D 139 " --> pdb=" O ASP D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER D 178 " --> pdb=" O GLU D 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU D 181 " --> pdb=" O SER D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE D 199 " --> pdb=" O ASP D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 277 Processing helix chain 'D' and resid 279 through 302 Processing helix chain 'D' and resid 303 through 305 No H-bonds generated for 'chain 'D' and resid 303 through 305' Processing helix chain 'D' and resid 312 through 317 Processing helix chain 'D' and resid 344 through 357 Processing helix chain 'D' and resid 361 through 373 removed outlier: 3.598A pdb=" N ASP D 365 " --> pdb=" O GLY D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR D 387 " --> pdb=" O LEU D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 413 through 425 Processing helix chain 'D' and resid 425 through 433 Processing helix chain 'D' and resid 443 through 457 removed outlier: 3.686A pdb=" N LYS D 448 " --> pdb=" O ASP D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 462 through 466 Processing helix chain 'D' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE D 480 " --> pdb=" O ARG D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL D 508 " --> pdb=" O GLY D 504 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE D 511 " --> pdb=" O SER D 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR D 516 " --> pdb=" O ASN D 512 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 540 Processing helix chain 'D' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA D 556 " --> pdb=" O ASN D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER D 607 " --> pdb=" O ALA D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 622 through 632 Processing helix chain 'D' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL D 649 " --> pdb=" O ALA D 645 " (cutoff:3.500A) Processing helix chain 'D' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR D 711 " --> pdb=" O SER D 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE D 723 " --> pdb=" O ASN D 719 " (cutoff:3.500A) Processing helix chain 'D' and resid 725 through 727 No H-bonds generated for 'chain 'D' and resid 725 through 727' Processing helix chain 'D' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN D 746 " --> pdb=" O TYR D 742 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU D 756 " --> pdb=" O LYS D 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 753 through 756' Processing helix chain 'D' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET D 775 " --> pdb=" O ALA D 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS D 794 " --> pdb=" O GLU D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS D 822 " --> pdb=" O GLU D 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS D 827 " --> pdb=" O ILE D 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS D 829 " --> pdb=" O GLY D 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA D 830 " --> pdb=" O GLU D 826 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 847 Processing helix chain 'D' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE D 856 " --> pdb=" O HIS D 852 " (cutoff:3.500A) Processing helix chain 'D' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN D 869 " --> pdb=" O VAL D 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS D 870 " --> pdb=" O LYS D 866 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER D 873 " --> pdb=" O ASN D 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS D 876 " --> pdb=" O THR D 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU D 877 " --> pdb=" O SER D 873 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 878 " --> pdb=" O PHE D 874 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 896 removed outlier: 4.705A pdb=" N TYR D 894 " --> pdb=" O GLU D 890 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU D 895 " --> pdb=" O GLU D 891 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 47 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'F' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR F 124 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY F 139 " --> pdb=" O ASP F 135 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR F 168 " --> pdb=" O LEU F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER F 178 " --> pdb=" O GLU F 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 181 " --> pdb=" O SER F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 240 removed outlier: 4.073A pdb=" N ASP F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR F 257 " --> pdb=" O ASP F 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 277 Processing helix chain 'F' and resid 279 through 302 Processing helix chain 'F' and resid 303 through 305 No H-bonds generated for 'chain 'F' and resid 303 through 305' Processing helix chain 'F' and resid 312 through 317 Processing helix chain 'F' and resid 344 through 357 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP F 365 " --> pdb=" O GLY F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR F 387 " --> pdb=" O LEU F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 413 through 425 Processing helix chain 'F' and resid 425 through 433 Processing helix chain 'F' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS F 448 " --> pdb=" O ASP F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 466 Processing helix chain 'F' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE F 480 " --> pdb=" O ARG F 476 " (cutoff:3.500A) Processing helix chain 'F' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS F 505 " --> pdb=" O LEU F 501 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL F 508 " --> pdb=" O GLY F 504 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N PHE F 511 " --> pdb=" O SER F 507 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR F 516 " --> pdb=" O ASN F 512 " (cutoff:3.500A) Processing helix chain 'F' and resid 525 through 540 Processing helix chain 'F' and resid 546 through 559 removed outlier: 3.707A pdb=" N ALA F 556 " --> pdb=" O ASN F 552 " (cutoff:3.500A) Processing helix chain 'F' and resid 597 through 607 removed outlier: 3.857A pdb=" N SER F 607 " --> pdb=" O ALA F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 632 Processing helix chain 'F' and resid 639 through 651 removed outlier: 3.549A pdb=" N VAL F 649 " --> pdb=" O ALA F 645 " (cutoff:3.500A) Processing helix chain 'F' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR F 711 " --> pdb=" O SER F 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE F 723 " --> pdb=" O ASN F 719 " (cutoff:3.500A) Processing helix chain 'F' and resid 725 through 727 No H-bonds generated for 'chain 'F' and resid 725 through 727' Processing helix chain 'F' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN F 746 " --> pdb=" O TYR F 742 " (cutoff:3.500A) Processing helix chain 'F' and resid 753 through 756 removed outlier: 4.028A pdb=" N LEU F 756 " --> pdb=" O LYS F 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 753 through 756' Processing helix chain 'F' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET F 775 " --> pdb=" O ALA F 771 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS F 794 " --> pdb=" O GLU F 790 " (cutoff:3.500A) Processing helix chain 'F' and resid 814 through 831 removed outlier: 3.560A pdb=" N LYS F 822 " --> pdb=" O GLU F 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 827 " --> pdb=" O ILE F 823 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N LYS F 829 " --> pdb=" O GLY F 825 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA F 830 " --> pdb=" O GLU F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 847 Processing helix chain 'F' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE F 856 " --> pdb=" O HIS F 852 " (cutoff:3.500A) Processing helix chain 'F' and resid 864 through 883 removed outlier: 3.926A pdb=" N ASN F 869 " --> pdb=" O VAL F 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS F 870 " --> pdb=" O LYS F 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 873 " --> pdb=" O ASN F 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS F 876 " --> pdb=" O THR F 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F 877 " --> pdb=" O SER F 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE F 878 " --> pdb=" O PHE F 874 " (cutoff:3.500A) Processing helix chain 'F' and resid 888 through 897 removed outlier: 4.706A pdb=" N TYR F 894 " --> pdb=" O GLU F 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU F 895 " --> pdb=" O GLU F 891 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS F 897 " --> pdb=" O ASP F 893 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 47 Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 120 through 139 removed outlier: 3.520A pdb=" N THR G 124 " --> pdb=" O PRO G 120 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLY G 139 " --> pdb=" O ASP G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS G 156 " --> pdb=" O GLN G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 169 removed outlier: 4.107A pdb=" N THR G 168 " --> pdb=" O LEU G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 181 removed outlier: 3.640A pdb=" N SER G 178 " --> pdb=" O GLU G 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU G 181 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE G 199 " --> pdb=" O ASP G 195 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP G 232 " --> pdb=" O ASP G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 269 removed outlier: 3.579A pdb=" N TYR G 257 " --> pdb=" O ASP G 253 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASN G 268 " --> pdb=" O LYS G 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR G 269 " --> pdb=" O GLN G 265 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 277 Processing helix chain 'G' and resid 279 through 302 Processing helix chain 'G' and resid 303 through 305 No H-bonds generated for 'chain 'G' and resid 303 through 305' Processing helix chain 'G' and resid 312 through 317 Processing helix chain 'G' and resid 344 through 357 Processing helix chain 'G' and resid 361 through 373 removed outlier: 3.597A pdb=" N ASP G 365 " --> pdb=" O GLY G 361 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR G 387 " --> pdb=" O LEU G 383 " (cutoff:3.500A) Processing helix chain 'G' and resid 413 through 425 Processing helix chain 'G' and resid 425 through 433 Processing helix chain 'G' and resid 443 through 457 removed outlier: 3.686A pdb=" N LYS G 448 " --> pdb=" O ASP G 444 " (cutoff:3.500A) Processing helix chain 'G' and resid 462 through 466 Processing helix chain 'G' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE G 480 " --> pdb=" O ARG G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS G 505 " --> pdb=" O LEU G 501 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL G 508 " --> pdb=" O GLY G 504 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE G 511 " --> pdb=" O SER G 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR G 516 " --> pdb=" O ASN G 512 " (cutoff:3.500A) Processing helix chain 'G' and resid 525 through 540 Processing helix chain 'G' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA G 556 " --> pdb=" O ASN G 552 " (cutoff:3.500A) Processing helix chain 'G' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER G 607 " --> pdb=" O ALA G 603 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 632 Processing helix chain 'G' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL G 649 " --> pdb=" O ALA G 645 " (cutoff:3.500A) Processing helix chain 'G' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR G 711 " --> pdb=" O SER G 707 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE G 723 " --> pdb=" O ASN G 719 " (cutoff:3.500A) Processing helix chain 'G' and resid 725 through 727 No H-bonds generated for 'chain 'G' and resid 725 through 727' Processing helix chain 'G' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN G 746 " --> pdb=" O TYR G 742 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU G 756 " --> pdb=" O LYS G 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 753 through 756' Processing helix chain 'G' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET G 775 " --> pdb=" O ALA G 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS G 794 " --> pdb=" O GLU G 790 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS G 822 " --> pdb=" O GLU G 818 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS G 827 " --> pdb=" O ILE G 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS G 829 " --> pdb=" O GLY G 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 830 " --> pdb=" O GLU G 826 " (cutoff:3.500A) Processing helix chain 'G' and resid 839 through 847 Processing helix chain 'G' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE G 856 " --> pdb=" O HIS G 852 " (cutoff:3.500A) Processing helix chain 'G' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN G 869 " --> pdb=" O VAL G 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS G 870 " --> pdb=" O LYS G 866 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER G 873 " --> pdb=" O ASN G 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS G 876 " --> pdb=" O THR G 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU G 877 " --> pdb=" O SER G 873 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE G 878 " --> pdb=" O PHE G 874 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 897 removed outlier: 4.707A pdb=" N TYR G 894 " --> pdb=" O GLU G 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU G 895 " --> pdb=" O GLU G 891 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 47 Processing helix chain 'E' and resid 81 through 93 Processing helix chain 'E' and resid 120 through 139 removed outlier: 3.519A pdb=" N THR E 124 " --> pdb=" O PRO E 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY E 139 " --> pdb=" O ASP E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 163 removed outlier: 4.128A pdb=" N HIS E 156 " --> pdb=" O GLN E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR E 168 " --> pdb=" O LEU E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER E 178 " --> pdb=" O GLU E 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 181 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE E 199 " --> pdb=" O ASP E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 240 removed outlier: 4.074A pdb=" N ASP E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 269 removed outlier: 3.578A pdb=" N TYR E 257 " --> pdb=" O ASP E 253 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR E 269 " --> pdb=" O GLN E 265 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 277 Processing helix chain 'E' and resid 279 through 302 Processing helix chain 'E' and resid 303 through 305 No H-bonds generated for 'chain 'E' and resid 303 through 305' Processing helix chain 'E' and resid 312 through 317 Processing helix chain 'E' and resid 344 through 357 Processing helix chain 'E' and resid 361 through 373 removed outlier: 3.598A pdb=" N ASP E 365 " --> pdb=" O GLY E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR E 387 " --> pdb=" O LEU E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 413 through 425 Processing helix chain 'E' and resid 425 through 433 Processing helix chain 'E' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS E 448 " --> pdb=" O ASP E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 466 Processing helix chain 'E' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE E 480 " --> pdb=" O ARG E 476 " (cutoff:3.500A) Processing helix chain 'E' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS E 505 " --> pdb=" O LEU E 501 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL E 508 " --> pdb=" O GLY E 504 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N PHE E 511 " --> pdb=" O SER E 507 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR E 516 " --> pdb=" O ASN E 512 " (cutoff:3.500A) Processing helix chain 'E' and resid 525 through 540 Processing helix chain 'E' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA E 556 " --> pdb=" O ASN E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER E 607 " --> pdb=" O ALA E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 622 through 632 Processing helix chain 'E' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL E 649 " --> pdb=" O ALA E 645 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 724 removed outlier: 3.550A pdb=" N THR E 711 " --> pdb=" O SER E 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE E 723 " --> pdb=" O ASN E 719 " (cutoff:3.500A) Processing helix chain 'E' and resid 725 through 727 No H-bonds generated for 'chain 'E' and resid 725 through 727' Processing helix chain 'E' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN E 746 " --> pdb=" O TYR E 742 " (cutoff:3.500A) Processing helix chain 'E' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU E 756 " --> pdb=" O LYS E 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 753 through 756' Processing helix chain 'E' and resid 770 through 794 removed outlier: 3.584A pdb=" N MET E 775 " --> pdb=" O ALA E 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS E 794 " --> pdb=" O GLU E 790 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 831 removed outlier: 3.562A pdb=" N LYS E 822 " --> pdb=" O GLU E 818 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS E 827 " --> pdb=" O ILE E 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS E 829 " --> pdb=" O GLY E 825 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 830 " --> pdb=" O GLU E 826 " (cutoff:3.500A) Processing helix chain 'E' and resid 839 through 847 Processing helix chain 'E' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE E 856 " --> pdb=" O HIS E 852 " (cutoff:3.500A) Processing helix chain 'E' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN E 869 " --> pdb=" O VAL E 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS E 870 " --> pdb=" O LYS E 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER E 873 " --> pdb=" O ASN E 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS E 876 " --> pdb=" O THR E 872 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU E 877 " --> pdb=" O SER E 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE E 878 " --> pdb=" O PHE E 874 " (cutoff:3.500A) Processing helix chain 'E' and resid 888 through 896 removed outlier: 4.706A pdb=" N TYR E 894 " --> pdb=" O GLU E 890 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU E 895 " --> pdb=" O GLU E 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 47 Processing helix chain 'A' and resid 82 through 93 Processing helix chain 'A' and resid 120 through 139 removed outlier: 3.521A pdb=" N THR A 124 " --> pdb=" O PRO A 120 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY A 139 " --> pdb=" O ASP A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 163 removed outlier: 4.127A pdb=" N HIS A 156 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 169 removed outlier: 4.108A pdb=" N THR A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.641A pdb=" N SER A 178 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 181 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 212 removed outlier: 3.501A pdb=" N ILE A 199 " --> pdb=" O ASP A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 240 removed outlier: 4.073A pdb=" N ASP A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 269 removed outlier: 3.578A pdb=" N TYR A 257 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR A 269 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 279 through 302 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 344 through 357 Processing helix chain 'A' and resid 361 through 373 removed outlier: 3.598A pdb=" N ASP A 365 " --> pdb=" O GLY A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 394 removed outlier: 3.513A pdb=" N TYR A 387 " --> pdb=" O LEU A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 Processing helix chain 'A' and resid 425 through 433 Processing helix chain 'A' and resid 443 through 457 removed outlier: 3.687A pdb=" N LYS A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 466 Processing helix chain 'A' and resid 472 through 490 removed outlier: 3.519A pdb=" N ILE A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 516 removed outlier: 3.591A pdb=" N CYS A 505 " --> pdb=" O LEU A 501 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE A 511 " --> pdb=" O SER A 507 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR A 516 " --> pdb=" O ASN A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 540 Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.706A pdb=" N ALA A 556 " --> pdb=" O ASN A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 607 removed outlier: 3.858A pdb=" N SER A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 622 through 632 Processing helix chain 'A' and resid 639 through 651 removed outlier: 3.548A pdb=" N VAL A 649 " --> pdb=" O ALA A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 724 removed outlier: 3.549A pdb=" N THR A 711 " --> pdb=" O SER A 707 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ILE A 723 " --> pdb=" O ASN A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 727 No H-bonds generated for 'chain 'A' and resid 725 through 727' Processing helix chain 'A' and resid 730 through 752 removed outlier: 3.584A pdb=" N ASN A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 756 removed outlier: 4.026A pdb=" N LEU A 756 " --> pdb=" O LYS A 753 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 770 through 794 removed outlier: 3.583A pdb=" N MET A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS A 794 " --> pdb=" O GLU A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 831 removed outlier: 3.561A pdb=" N LYS A 822 " --> pdb=" O GLU A 818 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 827 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS A 829 " --> pdb=" O GLY A 825 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 830 " --> pdb=" O GLU A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 Processing helix chain 'A' and resid 851 through 856 removed outlier: 3.829A pdb=" N PHE A 856 " --> pdb=" O HIS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.927A pdb=" N ASN A 869 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS A 870 " --> pdb=" O LYS A 866 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER A 873 " --> pdb=" O ASN A 869 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS A 876 " --> pdb=" O THR A 872 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 877 " --> pdb=" O SER A 873 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE A 878 " --> pdb=" O PHE A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 897 removed outlier: 4.706A pdb=" N TYR A 894 " --> pdb=" O GLU A 890 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 895 " --> pdb=" O GLU A 891 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 105 through 106 removed outlier: 7.250A pdb=" N LYS B 105 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR B 219 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE B 216 " --> pdb=" O VAL B 247 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL B 249 " --> pdb=" O ILE B 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE B 218 " --> pdb=" O VAL B 249 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR B 251 " --> pdb=" O ILE B 218 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE B 308 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE B 73 " --> pdb=" O ILE B 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP B 618 " --> pdb=" O LEU B 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL B 611 " --> pdb=" O MET B 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS B 655 " --> pdb=" O LEU B 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR B 610 " --> pdb=" O CYS B 655 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 105 through 106 removed outlier: 7.252A pdb=" N LYS C 105 " --> pdb=" O LEU C 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR C 219 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE C 216 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL C 249 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE C 218 " --> pdb=" O VAL C 249 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR C 251 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE C 308 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE C 73 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP C 618 " --> pdb=" O LEU C 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 611 " --> pdb=" O MET C 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS C 655 " --> pdb=" O LEU C 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR C 610 " --> pdb=" O CYS C 655 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS D 105 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR D 219 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE D 216 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 249 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 218 " --> pdb=" O VAL D 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR D 251 " --> pdb=" O ILE D 218 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N ILE D 308 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE D 73 " --> pdb=" O ILE D 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 573 through 576 removed outlier: 4.296A pdb=" N ASP D 618 " --> pdb=" O LEU D 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL D 611 " --> pdb=" O MET D 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS D 655 " --> pdb=" O LEU D 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR D 610 " --> pdb=" O CYS D 655 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 105 through 106 removed outlier: 7.250A pdb=" N LYS F 105 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR F 219 " --> pdb=" O LYS F 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE F 216 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL F 249 " --> pdb=" O ILE F 216 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE F 218 " --> pdb=" O VAL F 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR F 251 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE F 308 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE F 73 " --> pdb=" O ILE F 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP F 618 " --> pdb=" O LEU F 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL F 611 " --> pdb=" O MET F 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS F 655 " --> pdb=" O LEU F 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR F 610 " --> pdb=" O CYS F 655 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS G 105 " --> pdb=" O LEU G 217 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR G 219 " --> pdb=" O LYS G 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE G 216 " --> pdb=" O VAL G 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL G 249 " --> pdb=" O ILE G 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE G 218 " --> pdb=" O VAL G 249 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N THR G 251 " --> pdb=" O ILE G 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE G 308 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N PHE G 73 " --> pdb=" O ILE G 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP G 618 " --> pdb=" O LEU G 576 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL G 611 " --> pdb=" O MET G 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS G 655 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR G 610 " --> pdb=" O CYS G 655 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS E 105 " --> pdb=" O LEU E 217 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR E 219 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE E 216 " --> pdb=" O VAL E 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL E 249 " --> pdb=" O ILE E 216 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE E 218 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR E 251 " --> pdb=" O ILE E 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE E 308 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE E 73 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP E 618 " --> pdb=" O LEU E 576 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL E 611 " --> pdb=" O MET E 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS E 655 " --> pdb=" O LEU E 608 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N THR E 610 " --> pdb=" O CYS E 655 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 105 through 106 removed outlier: 7.251A pdb=" N LYS A 105 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N THR A 219 " --> pdb=" O LYS A 105 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE A 216 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N VAL A 249 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ILE A 218 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 8.172A pdb=" N THR A 251 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILE A 308 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N PHE A 73 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.295A pdb=" N ASP A 618 " --> pdb=" O LEU A 576 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL A 611 " --> pdb=" O MET A 617 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N CYS A 655 " --> pdb=" O LEU A 608 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N THR A 610 " --> pdb=" O CYS A 655 " (cutoff:3.500A) 2245 hydrogen bonds defined for protein. 6588 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: 15.26 Time building geometry restraints manager: 19.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 11579 1.33 - 1.47: 12942 1.47 - 1.60: 19730 1.60 - 1.73: 8 1.73 - 1.86: 322 Bond restraints: 44581 Sorted by residual: bond pdb=" CA VAL D 413 " pdb=" CB VAL D 413 " ideal model delta sigma weight residual 1.539 1.488 0.051 5.40e-03 3.43e+04 9.00e+01 bond pdb=" CA VAL E 413 " pdb=" CB VAL E 413 " ideal model delta sigma weight residual 1.539 1.488 0.051 5.40e-03 3.43e+04 8.93e+01 bond pdb=" CA VAL B 413 " pdb=" CB VAL B 413 " ideal model delta sigma weight residual 1.539 1.488 0.051 5.40e-03 3.43e+04 8.77e+01 bond pdb=" CA VAL F 413 " pdb=" CB VAL F 413 " ideal model delta sigma weight residual 1.539 1.489 0.050 5.40e-03 3.43e+04 8.66e+01 bond pdb=" CA VAL G 413 " pdb=" CB VAL G 413 " ideal model delta sigma weight residual 1.539 1.489 0.050 5.40e-03 3.43e+04 8.62e+01 ... (remaining 44576 not shown) Histogram of bond angle deviations from ideal: 91.55 - 102.16: 151 102.16 - 112.77: 23095 112.77 - 123.38: 35064 123.38 - 134.00: 1710 134.00 - 144.61: 24 Bond angle restraints: 60044 Sorted by residual: angle pdb=" CB LYS G 311 " pdb=" CG LYS G 311 " pdb=" CD LYS G 311 " ideal model delta sigma weight residual 111.30 137.27 -25.97 2.30e+00 1.89e-01 1.28e+02 angle pdb=" CB LYS F 311 " pdb=" CG LYS F 311 " pdb=" CD LYS F 311 " ideal model delta sigma weight residual 111.30 137.24 -25.94 2.30e+00 1.89e-01 1.27e+02 angle pdb=" CB LYS C 311 " pdb=" CG LYS C 311 " pdb=" CD LYS C 311 " ideal model delta sigma weight residual 111.30 137.22 -25.92 2.30e+00 1.89e-01 1.27e+02 angle pdb=" CB LYS A 311 " pdb=" CG LYS A 311 " pdb=" CD LYS A 311 " ideal model delta sigma weight residual 111.30 137.21 -25.91 2.30e+00 1.89e-01 1.27e+02 angle pdb=" CB LYS E 311 " pdb=" CG LYS E 311 " pdb=" CD LYS E 311 " ideal model delta sigma weight residual 111.30 137.20 -25.90 2.30e+00 1.89e-01 1.27e+02 ... (remaining 60039 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 22595 17.97 - 35.93: 3101 35.93 - 53.90: 1087 53.90 - 71.86: 331 71.86 - 89.83: 84 Dihedral angle restraints: 27198 sinusoidal: 11162 harmonic: 16036 Sorted by residual: dihedral pdb=" CD ARG B 38 " pdb=" NE ARG B 38 " pdb=" CZ ARG B 38 " pdb=" NH1 ARG B 38 " ideal model delta sinusoidal sigma weight residual 0.00 89.27 -89.27 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " pdb=" CZ ARG A 38 " pdb=" NH1 ARG A 38 " ideal model delta sinusoidal sigma weight residual 0.00 89.25 -89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CD ARG C 38 " pdb=" NE ARG C 38 " pdb=" CZ ARG C 38 " pdb=" NH1 ARG C 38 " ideal model delta sinusoidal sigma weight residual 0.00 89.25 -89.25 1 1.00e+01 1.00e-02 9.47e+01 ... (remaining 27195 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.522: 6770 0.522 - 1.044: 7 1.044 - 1.566: 0 1.566 - 2.087: 0 2.087 - 2.609: 7 Chirality restraints: 6784 Sorted by residual: chirality pdb=" CG LEU G 502 " pdb=" CB LEU G 502 " pdb=" CD1 LEU G 502 " pdb=" CD2 LEU G 502 " both_signs ideal model delta sigma weight residual False -2.59 0.02 -2.61 2.00e-01 2.50e+01 1.70e+02 chirality pdb=" CG LEU B 502 " pdb=" CB LEU B 502 " pdb=" CD1 LEU B 502 " pdb=" CD2 LEU B 502 " both_signs ideal model delta sigma weight residual False -2.59 0.02 -2.61 2.00e-01 2.50e+01 1.70e+02 chirality pdb=" CG LEU A 502 " pdb=" CB LEU A 502 " pdb=" CD1 LEU A 502 " pdb=" CD2 LEU A 502 " both_signs ideal model delta sigma weight residual False -2.59 0.02 -2.61 2.00e-01 2.50e+01 1.70e+02 ... (remaining 6781 not shown) Planarity restraints: 7672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 38 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG A 38 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG A 38 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 38 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG A 38 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 38 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG B 38 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 38 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG B 38 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG B 38 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 38 " -1.000 9.50e-02 1.11e+02 4.48e-01 1.22e+02 pdb=" NE ARG G 38 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG G 38 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG G 38 " -0.012 2.00e-02 2.50e+03 pdb=" NH2 ARG G 38 " -0.013 2.00e-02 2.50e+03 ... (remaining 7669 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 16 1.81 - 2.59: 694 2.59 - 3.36: 58726 3.36 - 4.13: 110456 4.13 - 4.90: 203934 Nonbonded interactions: 373826 Sorted by model distance: nonbonded pdb=" OD1 ASN F 759 " pdb=" OD1 ASP F 930 " model vdw 1.042 3.040 nonbonded pdb=" OD1 ASN F 759 " pdb=" CG ASP F 930 " model vdw 1.152 3.270 nonbonded pdb=" CG ASN F 759 " pdb=" OD1 ASP F 930 " model vdw 1.200 3.270 nonbonded pdb=" NH1 ARG F 758 " pdb=" O ASP F 928 " model vdw 1.492 2.520 nonbonded pdb=" ND2 ASN F 759 " pdb=" OD1 ASP F 930 " model vdw 1.603 2.520 ... (remaining 373821 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 'A' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'B' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'C' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'D' and resid 35 through 930) selection = (chain 'E' and (resid 35 through 76 or resid 81 through 930)) selection = (chain 'F' and (resid 35 through 896 or resid 910 through 930)) selection = (chain 'G' and (resid 35 through 896 or resid 910 through 930)) } 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: 3.930 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: 0.040 Extract box with map and model: 17.380 Check model and map are aligned: 0.630 Set scattering table: 0.390 Process input model: 106.150 Find NCS groups from input model: 3.360 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 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 : 0.010 0.159 44581 Z= 0.636 Angle : 1.798 31.906 60044 Z= 0.856 Chirality : 0.106 2.609 6784 Planarity : 0.025 0.448 7672 Dihedral : 19.926 89.828 16764 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 23.04 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.95 % Favored : 89.79 % Rotamer: Outliers : 10.57 % Allowed : 19.43 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.16 (0.11), residues: 5350 helix: -0.90 (0.09), residues: 3048 sheet: -0.07 (0.39), residues: 224 loop : -2.32 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 660 HIS 0.027 0.004 HIS G 118 PHE 0.036 0.003 PHE G 177 TYR 0.140 0.006 TYR G 436 ARG 0.058 0.005 ARG G 740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 515 poor density : 812 time to evaluate : 4.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 LYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6579 (mmtt) REVERT: B 209 GLU cc_start: 0.7159 (mt-10) cc_final: 0.6931 (mt-10) REVERT: B 311 LYS cc_start: 0.3903 (OUTLIER) cc_final: 0.3553 (mttp) REVERT: B 431 ARG cc_start: 0.7266 (tpt170) cc_final: 0.7024 (tpt170) REVERT: B 617 MET cc_start: 0.4225 (OUTLIER) cc_final: 0.3739 (mmm) REVERT: B 621 SER cc_start: 0.7135 (OUTLIER) cc_final: 0.6801 (p) REVERT: B 648 LYS cc_start: 0.7193 (mtpm) cc_final: 0.6983 (tppt) REVERT: B 868 LEU cc_start: 0.4745 (OUTLIER) cc_final: 0.4420 (tp) REVERT: C 496 LYS cc_start: 0.8377 (mttp) cc_final: 0.8066 (mttt) REVERT: C 617 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.3583 (mmm) REVERT: D 38 ARG cc_start: 0.6311 (OUTLIER) cc_final: 0.5978 (ttp-170) REVERT: D 75 ASP cc_start: 0.6203 (m-30) cc_final: 0.5990 (m-30) REVERT: D 346 GLN cc_start: 0.7182 (tt0) cc_final: 0.6920 (mt0) REVERT: D 494 LEU cc_start: 0.7633 (tm) cc_final: 0.7398 (tp) REVERT: D 540 SER cc_start: 0.7633 (OUTLIER) cc_final: 0.7389 (t) REVERT: D 617 MET cc_start: 0.5199 (OUTLIER) cc_final: 0.4770 (mtm) REVERT: D 633 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.8047 (m) REVERT: D 775 MET cc_start: 0.6186 (mmm) cc_final: 0.5957 (mmm) REVERT: D 873 SER cc_start: 0.8037 (OUTLIER) cc_final: 0.7611 (p) REVERT: D 893 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5514 (t0) REVERT: F 336 MET cc_start: 0.6220 (mtt) cc_final: 0.5781 (mtt) REVERT: F 338 ASP cc_start: 0.5062 (OUTLIER) cc_final: 0.4587 (t70) REVERT: F 340 ASP cc_start: 0.4952 (OUTLIER) cc_final: 0.4634 (p0) REVERT: F 392 HIS cc_start: 0.4576 (OUTLIER) cc_final: 0.4375 (t-90) REVERT: F 431 ARG cc_start: 0.6815 (tpt170) cc_final: 0.6496 (tpt170) REVERT: F 617 MET cc_start: 0.3426 (OUTLIER) cc_final: 0.1360 (tpp) REVERT: F 934 ARG cc_start: 0.0980 (OUTLIER) cc_final: 0.0780 (mmp80) REVERT: G 270 SER cc_start: 0.9080 (OUTLIER) cc_final: 0.8857 (p) REVERT: G 271 LYS cc_start: 0.6770 (OUTLIER) cc_final: 0.6568 (mmmt) REVERT: G 527 LYS cc_start: 0.7537 (mttm) cc_final: 0.7150 (ptmt) REVERT: E 170 LYS cc_start: 0.6397 (OUTLIER) cc_final: 0.6196 (mppt) REVERT: E 171 GLU cc_start: 0.6309 (OUTLIER) cc_final: 0.6101 (pm20) REVERT: E 380 MET cc_start: 0.5497 (OUTLIER) cc_final: 0.5077 (mtm) REVERT: E 387 TYR cc_start: 0.5623 (m-80) cc_final: 0.5146 (m-80) REVERT: E 497 PHE cc_start: 0.5196 (t80) cc_final: 0.4759 (t80) REVERT: E 620 CYS cc_start: 0.4633 (t) cc_final: 0.4078 (t) REVERT: E 639 ARG cc_start: 0.6095 (ttt-90) cc_final: 0.5048 (ttp80) REVERT: E 715 GLN cc_start: 0.7298 (OUTLIER) cc_final: 0.6743 (tm-30) REVERT: E 740 ARG cc_start: 0.6190 (ttm-80) cc_final: 0.5975 (tpp80) REVERT: E 745 LEU cc_start: 0.6461 (mt) cc_final: 0.6229 (tt) REVERT: E 765 MET cc_start: 0.3191 (OUTLIER) cc_final: 0.2613 (ttt) REVERT: A 40 GLN cc_start: 0.5791 (OUTLIER) cc_final: 0.5537 (tp40) REVERT: A 198 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7500 (mt-10) REVERT: A 338 ASP cc_start: 0.4852 (OUTLIER) cc_final: 0.3599 (t70) REVERT: A 340 ASP cc_start: 0.5188 (OUTLIER) cc_final: 0.4660 (p0) REVERT: A 617 MET cc_start: 0.4690 (OUTLIER) cc_final: 0.4335 (mtm) REVERT: A 765 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4311 (ttp) outliers start: 515 outliers final: 74 residues processed: 1160 average time/residue: 1.5649 time to fit residues: 2251.0314 Evaluate side-chains 613 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 510 time to evaluate : 5.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 170 LYS Chi-restraints excluded: chain B residue 173 LYS Chi-restraints excluded: chain B residue 224 ASP Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 271 LYS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 380 MET Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 617 MET Chi-restraints excluded: chain B residue 621 SER Chi-restraints excluded: chain B residue 715 GLN Chi-restraints excluded: chain B residue 855 ILE Chi-restraints excluded: chain B residue 868 LEU Chi-restraints excluded: chain C residue 105 LYS Chi-restraints excluded: chain C residue 173 LYS Chi-restraints excluded: chain C residue 224 ASP Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain C residue 311 LYS Chi-restraints excluded: chain C residue 380 MET Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain C residue 606 SER Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain D residue 38 ARG Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 206 ARG Chi-restraints excluded: chain D residue 224 ASP Chi-restraints excluded: chain D residue 279 GLU Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain D residue 617 MET Chi-restraints excluded: chain D residue 632 ILE Chi-restraints excluded: chain D residue 633 SER Chi-restraints excluded: chain D residue 739 SER Chi-restraints excluded: chain D residue 873 SER Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain F residue 298 LEU Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 392 HIS Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 595 THR Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 723 ILE Chi-restraints excluded: chain F residue 834 THR Chi-restraints excluded: chain F residue 934 ARG Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 173 LYS Chi-restraints excluded: chain G residue 270 SER Chi-restraints excluded: chain G residue 271 LYS Chi-restraints excluded: chain G residue 328 ILE Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 380 MET Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 621 SER Chi-restraints excluded: chain G residue 633 SER Chi-restraints excluded: chain G residue 723 ILE Chi-restraints excluded: chain G residue 798 ASP Chi-restraints excluded: chain E residue 105 LYS Chi-restraints excluded: chain E residue 170 LYS Chi-restraints excluded: chain E residue 171 GLU Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain E residue 258 SER Chi-restraints excluded: chain E residue 271 LYS Chi-restraints excluded: chain E residue 380 MET Chi-restraints excluded: chain E residue 471 GLU Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 595 THR Chi-restraints excluded: chain E residue 606 SER Chi-restraints excluded: chain E residue 621 SER Chi-restraints excluded: chain E residue 715 GLN Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain E residue 834 THR Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 328 ILE Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 340 ASP Chi-restraints excluded: chain A residue 380 MET Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 540 SER Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 584 MET Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 617 MET Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 723 ILE Chi-restraints excluded: chain A residue 765 MET Chi-restraints excluded: chain A residue 798 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 461 optimal weight: 0.9990 chunk 413 optimal weight: 5.9990 chunk 229 optimal weight: 0.9980 chunk 141 optimal weight: 2.9990 chunk 279 optimal weight: 0.9990 chunk 221 optimal weight: 1.9990 chunk 427 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 260 optimal weight: 0.8980 chunk 318 optimal weight: 4.9990 chunk 495 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** B 456 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 ASN B 751 GLN C 268 ASN C 512 ASN C 513 GLN C 875 ASN ** D 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 ASN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 715 GLN ** D 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 875 ASN ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 268 ASN ** F 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 GLN F 512 ASN F 652 GLN ** F 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 156 HIS G 159 GLN G 337 GLN G 512 ASN ** G 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 747 ASN G 875 ASN E 154 GLN E 159 GLN ** E 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 575 GLN ** E 744 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 154 GLN A 156 HIS A 374 GLN A 456 GLN A 491 GLN A 512 ASN A 747 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44581 Z= 0.250 Angle : 0.678 9.600 60044 Z= 0.355 Chirality : 0.042 0.162 6784 Planarity : 0.005 0.084 7672 Dihedral : 7.429 130.587 6112 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.13 % Favored : 93.57 % Rotamer: Outliers : 5.03 % Allowed : 23.25 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5350 helix: 0.43 (0.09), residues: 3163 sheet: 0.09 (0.36), residues: 229 loop : -2.13 (0.14), residues: 1958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 892 HIS 0.007 0.001 HIS G 839 PHE 0.020 0.002 PHE A 441 TYR 0.027 0.002 TYR B 436 ARG 0.014 0.001 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 677 time to evaluate : 4.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8214 (mt) REVERT: B 311 LYS cc_start: 0.6219 (OUTLIER) cc_final: 0.5970 (pmtt) REVERT: B 340 ASP cc_start: 0.6697 (OUTLIER) cc_final: 0.6353 (p0) REVERT: B 438 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7353 (mt0) REVERT: B 570 PHE cc_start: 0.7395 (m-10) cc_final: 0.7084 (m-10) REVERT: B 584 MET cc_start: 0.6324 (OUTLIER) cc_final: 0.5940 (mtm) REVERT: B 625 LEU cc_start: 0.6994 (tt) cc_final: 0.5995 (mt) REVERT: B 728 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6326 (ptp-170) REVERT: C 331 LYS cc_start: 0.6295 (ttpt) cc_final: 0.5728 (pmtt) REVERT: C 496 LYS cc_start: 0.8537 (mttp) cc_final: 0.8190 (mttt) REVERT: C 617 MET cc_start: 0.6820 (OUTLIER) cc_final: 0.6560 (mtm) REVERT: D 291 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.7145 (mm-30) REVERT: D 346 GLN cc_start: 0.7413 (OUTLIER) cc_final: 0.6837 (mt0) REVERT: D 350 ASP cc_start: 0.7434 (m-30) cc_final: 0.7080 (m-30) REVERT: D 718 LYS cc_start: 0.7222 (OUTLIER) cc_final: 0.6845 (mmpt) REVERT: D 802 ILE cc_start: 0.8073 (tt) cc_final: 0.7855 (tt) REVERT: D 893 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5483 (t0) REVERT: F 102 VAL cc_start: 0.2975 (OUTLIER) cc_final: 0.2744 (p) REVERT: F 132 MET cc_start: 0.7644 (mtp) cc_final: 0.7342 (mtp) REVERT: F 338 ASP cc_start: 0.5934 (OUTLIER) cc_final: 0.5174 (t0) REVERT: F 340 ASP cc_start: 0.5446 (OUTLIER) cc_final: 0.5014 (p0) REVERT: F 589 LYS cc_start: 0.6697 (pttp) cc_final: 0.6482 (ptpp) REVERT: F 617 MET cc_start: 0.6741 (OUTLIER) cc_final: 0.6539 (mpp) REVERT: F 714 GLU cc_start: 0.5902 (OUTLIER) cc_final: 0.5702 (tt0) REVERT: G 132 MET cc_start: 0.8131 (mtm) cc_final: 0.7879 (mtm) REVERT: G 526 GLU cc_start: 0.5433 (OUTLIER) cc_final: 0.5084 (pp20) REVERT: G 527 LYS cc_start: 0.7648 (mttm) cc_final: 0.7040 (ptmt) REVERT: G 646 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6460 (t80) REVERT: G 836 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6132 (mppt) REVERT: E 82 LYS cc_start: 0.5080 (OUTLIER) cc_final: 0.4661 (ptmt) REVERT: E 86 ILE cc_start: 0.7633 (OUTLIER) cc_final: 0.7354 (mp) REVERT: E 266 TYR cc_start: 0.6868 (OUTLIER) cc_final: 0.6227 (t80) REVERT: E 336 MET cc_start: 0.3814 (mtt) cc_final: 0.3560 (mtt) REVERT: E 366 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5451 (ttm) REVERT: E 497 PHE cc_start: 0.5263 (t80) cc_final: 0.4798 (t80) REVERT: E 554 CYS cc_start: 0.4929 (t) cc_final: 0.3788 (p) REVERT: E 745 LEU cc_start: 0.6522 (mt) cc_final: 0.6164 (tt) REVERT: E 765 MET cc_start: 0.3772 (OUTLIER) cc_final: 0.3248 (ttt) REVERT: E 829 LYS cc_start: 0.6072 (OUTLIER) cc_final: 0.5854 (mttp) REVERT: E 929 LYS cc_start: 0.6125 (OUTLIER) cc_final: 0.5614 (tttm) REVERT: A 164 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8076 (tp) outliers start: 245 outliers final: 43 residues processed: 852 average time/residue: 1.5991 time to fit residues: 1659.9001 Evaluate side-chains 572 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 502 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 595 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 328 ILE Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 313 MET Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 912 ASN Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 328 ILE Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 516 THR Chi-restraints excluded: chain F residue 617 MET Chi-restraints excluded: chain F residue 714 GLU Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 578 ARG Chi-restraints excluded: chain G residue 646 PHE Chi-restraints excluded: chain G residue 836 LYS Chi-restraints excluded: chain E residue 82 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 444 ASP Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 540 SER Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 739 SER Chi-restraints excluded: chain E residue 765 MET Chi-restraints excluded: chain E residue 829 LYS Chi-restraints excluded: chain E residue 929 LYS Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 224 ASP Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 545 GLU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 798 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 275 optimal weight: 0.8980 chunk 153 optimal weight: 5.9990 chunk 412 optimal weight: 3.9990 chunk 337 optimal weight: 6.9990 chunk 136 optimal weight: 0.5980 chunk 496 optimal weight: 5.9990 chunk 536 optimal weight: 0.7980 chunk 442 optimal weight: 6.9990 chunk 492 optimal weight: 0.0010 chunk 169 optimal weight: 7.9990 chunk 398 optimal weight: 4.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS B 159 GLN B 194 GLN B 226 GLN B 456 GLN B 549 HIS C 159 GLN C 259 GLN C 875 ASN D 156 HIS D 159 GLN D 268 ASN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 ASN D 875 ASN F 154 GLN F 259 GLN F 268 ASN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 GLN F 560 ASN ** F 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 159 GLN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 194 GLN E 259 GLN ** E 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 512 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 715 GLN A 768 GLN A 770 ASN A 875 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.4283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 44581 Z= 0.228 Angle : 0.603 9.391 60044 Z= 0.319 Chirality : 0.041 0.176 6784 Planarity : 0.005 0.058 7672 Dihedral : 5.141 82.634 5930 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.21 % Favored : 93.50 % Rotamer: Outliers : 4.66 % Allowed : 23.23 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.12), residues: 5350 helix: 0.86 (0.09), residues: 3180 sheet: 0.33 (0.35), residues: 229 loop : -1.90 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 738 HIS 0.008 0.002 HIS G 794 PHE 0.044 0.002 PHE F 782 TYR 0.022 0.002 TYR B 436 ARG 0.014 0.001 ARG B 636 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 838 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 611 time to evaluate : 4.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 164 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8386 (mt) REVERT: B 291 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7239 (mm-30) REVERT: B 340 ASP cc_start: 0.6849 (OUTLIER) cc_final: 0.6507 (p0) REVERT: B 438 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7754 (mt0) REVERT: B 473 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.5998 (tm-30) REVERT: B 570 PHE cc_start: 0.7424 (m-10) cc_final: 0.7189 (m-10) REVERT: B 573 MET cc_start: 0.6769 (ptp) cc_final: 0.6540 (ptp) REVERT: B 584 MET cc_start: 0.6325 (OUTLIER) cc_final: 0.5782 (mpp) REVERT: B 625 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6044 (mt) REVERT: B 728 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6378 (ptp-170) REVERT: B 742 TYR cc_start: 0.7153 (t80) cc_final: 0.6927 (t80) REVERT: C 138 LYS cc_start: 0.6565 (OUTLIER) cc_final: 0.5912 (mtmp) REVERT: C 151 GLU cc_start: 0.6962 (pp20) cc_final: 0.6646 (pp20) REVERT: C 311 LYS cc_start: 0.6624 (pmtt) cc_final: 0.6231 (pttm) REVERT: C 331 LYS cc_start: 0.6575 (ttpt) cc_final: 0.6058 (pmtt) REVERT: C 370 GLU cc_start: 0.7889 (tp30) cc_final: 0.7685 (tp30) REVERT: C 496 LYS cc_start: 0.8628 (mttp) cc_final: 0.8203 (mttm) REVERT: C 617 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6773 (mtm) REVERT: C 715 GLN cc_start: 0.6869 (tt0) cc_final: 0.6421 (tm-30) REVERT: C 750 ASP cc_start: 0.6428 (OUTLIER) cc_final: 0.5885 (t0) REVERT: D 164 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8482 (tp) REVERT: D 201 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7174 (tp30) REVERT: D 214 LYS cc_start: 0.7111 (ptpt) cc_final: 0.6283 (pttt) REVERT: D 222 ASP cc_start: 0.6279 (p0) cc_final: 0.5403 (p0) REVERT: D 291 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: D 310 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6409 (mp) REVERT: D 346 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.7097 (tt0) REVERT: D 350 ASP cc_start: 0.7527 (m-30) cc_final: 0.7225 (m-30) REVERT: D 717 LEU cc_start: 0.7729 (tp) cc_final: 0.7218 (mt) REVERT: D 718 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.6962 (mmpt) REVERT: D 836 LYS cc_start: 0.7058 (mttm) cc_final: 0.6596 (mppt) REVERT: D 893 ASP cc_start: 0.5856 (OUTLIER) cc_final: 0.5525 (t0) REVERT: F 132 MET cc_start: 0.7825 (mtp) cc_final: 0.7529 (mtp) REVERT: F 206 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7370 (mmp80) REVERT: F 222 ASP cc_start: 0.5946 (p0) cc_final: 0.5534 (p0) REVERT: F 291 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: F 331 LYS cc_start: 0.6918 (ttpt) cc_final: 0.6265 (pmtt) REVERT: F 338 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5521 (t0) REVERT: F 340 ASP cc_start: 0.5570 (OUTLIER) cc_final: 0.5058 (p0) REVERT: F 437 GLU cc_start: 0.8058 (mp0) cc_final: 0.7827 (mp0) REVERT: G 310 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7464 (mp) REVERT: G 526 GLU cc_start: 0.5508 (OUTLIER) cc_final: 0.5096 (pp20) REVERT: G 527 LYS cc_start: 0.7650 (mttm) cc_final: 0.6926 (ptmt) REVERT: G 573 MET cc_start: 0.8561 (ptp) cc_final: 0.8324 (ptt) REVERT: G 646 PHE cc_start: 0.7562 (OUTLIER) cc_final: 0.7299 (t80) REVERT: G 719 ASN cc_start: 0.8673 (t0) cc_final: 0.8370 (m-40) REVERT: G 725 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8173 (pp) REVERT: E 43 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6739 (tm-30) REVERT: E 82 LYS cc_start: 0.5193 (OUTLIER) cc_final: 0.4638 (ptmt) REVERT: E 86 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7634 (mp) REVERT: E 170 LYS cc_start: 0.7437 (mmtt) cc_final: 0.7111 (mppt) REVERT: E 206 ARG cc_start: 0.6912 (mmp-170) cc_final: 0.6504 (mmp80) REVERT: E 245 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7862 (mmtm) REVERT: E 354 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.5732 (tm-30) REVERT: E 425 MET cc_start: 0.7887 (OUTLIER) cc_final: 0.6156 (mmt) REVERT: E 454 VAL cc_start: 0.7413 (p) cc_final: 0.7050 (t) REVERT: E 473 GLU cc_start: 0.6110 (pt0) cc_final: 0.5846 (tt0) REVERT: E 497 PHE cc_start: 0.5660 (t80) cc_final: 0.4993 (t80) REVERT: E 554 CYS cc_start: 0.4937 (t) cc_final: 0.4265 (p) REVERT: E 745 LEU cc_start: 0.6457 (mt) cc_final: 0.5966 (tt) REVERT: E 765 MET cc_start: 0.3352 (mtm) cc_final: 0.2888 (ttt) REVERT: A 391 TYR cc_start: 0.7008 (t80) cc_final: 0.6684 (t80) REVERT: A 755 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7484 (mtt180) REVERT: A 775 MET cc_start: 0.7526 (OUTLIER) cc_final: 0.7261 (mmm) REVERT: A 889 ASP cc_start: 0.6733 (m-30) cc_final: 0.6503 (m-30) outliers start: 227 outliers final: 67 residues processed: 773 average time/residue: 1.5565 time to fit residues: 1475.8363 Evaluate side-chains 615 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 515 time to evaluate : 4.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 561 SER Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 650 ILE Chi-restraints excluded: chain B residue 722 GLU Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 310 LEU Chi-restraints excluded: chain C residue 312 THR Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 342 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 561 SER Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 708 ASP Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 310 LEU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 868 LEU Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 912 ASN Chi-restraints excluded: chain F residue 206 ARG Chi-restraints excluded: chain F residue 224 ASP Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 270 SER Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 338 ASP Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 443 MET Chi-restraints excluded: chain F residue 661 SER Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 561 SER Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 646 PHE Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain G residue 725 ILE Chi-restraints excluded: chain G residue 826 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 82 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 332 THR Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 445 SER Chi-restraints excluded: chain E residue 467 ARG Chi-restraints excluded: chain E residue 515 VAL Chi-restraints excluded: chain E residue 516 THR Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 733 LEU Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 533 SER Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 775 MET Chi-restraints excluded: chain A residue 885 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 546 random chunks: chunk 490 optimal weight: 0.8980 chunk 373 optimal weight: 4.9990 chunk 257 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 333 optimal weight: 9.9990 chunk 498 optimal weight: 1.9990 chunk 527 optimal weight: 4.9990 chunk 260 optimal weight: 1.9990 chunk 472 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 HIS B 226 GLN B 259 GLN B 456 GLN B 461 ASN B 549 HIS B 624 ASN ** B 719 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 770 ASN B 875 ASN C 47 ASN C 155 ASN C 159 GLN C 309 GLN C 768 GLN C 875 ASN D 94 ASN ** D 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 461 ASN D 875 ASN F 47 ASN F 159 GLN F 259 GLN ** F 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 513 GLN ** F 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 744 ASN F 768 GLN F 770 ASN G 159 GLN G 161 GLN G 747 ASN E 159 GLN E 226 GLN ** E 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN E 512 ASN E 575 GLN E 597 ASN E 715 GLN A 159 GLN A 560 ASN A 747 ASN A 768 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.099 44581 Z= 0.263 Angle : 0.617 10.786 60044 Z= 0.326 Chirality : 0.042 0.200 6784 Planarity : 0.005 0.058 7672 Dihedral : 4.948 91.792 5908 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.37 % Favored : 93.33 % Rotamer: Outliers : 4.84 % Allowed : 22.79 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.11), residues: 5350 helix: 0.92 (0.09), residues: 3203 sheet: 0.53 (0.34), residues: 231 loop : -1.86 (0.14), residues: 1916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 738 HIS 0.009 0.002 HIS G 794 PHE 0.050 0.002 PHE F 782 TYR 0.030 0.002 TYR G 176 ARG 0.011 0.001 ARG E 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10700 Ramachandran restraints generated. 5350 Oldfield, 0 Emsley, 5350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 839 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 603 time to evaluate : 5.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 161 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.7436 (tp40) REVERT: B 164 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8507 (mt) REVERT: B 291 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: B 340 ASP cc_start: 0.7035 (OUTLIER) cc_final: 0.6812 (p0) REVERT: B 342 ILE cc_start: 0.5815 (OUTLIER) cc_final: 0.5387 (tp) REVERT: B 438 GLN cc_start: 0.8078 (OUTLIER) cc_final: 0.7856 (mt0) REVERT: B 473 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.6374 (tm-30) REVERT: B 570 PHE cc_start: 0.7575 (m-10) cc_final: 0.7363 (m-10) REVERT: B 573 MET cc_start: 0.6779 (ptp) cc_final: 0.6480 (ptp) REVERT: B 584 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5917 (mpp) REVERT: B 625 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6165 (mt) REVERT: B 719 ASN cc_start: 0.5995 (OUTLIER) cc_final: 0.5541 (t0) REVERT: B 728 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6395 (ptp-170) REVERT: C 138 LYS cc_start: 0.7041 (OUTLIER) cc_final: 0.6399 (mtmp) REVERT: C 151 GLU cc_start: 0.6969 (pp20) cc_final: 0.6746 (pp20) REVERT: C 155 ASN cc_start: 0.7670 (m110) cc_final: 0.7465 (m-40) REVERT: C 224 ASP cc_start: 0.7217 (m-30) cc_final: 0.6817 (m-30) REVERT: C 331 LYS cc_start: 0.6978 (ttpt) cc_final: 0.6253 (pmtt) REVERT: C 336 MET cc_start: 0.5733 (OUTLIER) cc_final: 0.5352 (mmt) REVERT: C 496 LYS cc_start: 0.8559 (mttp) cc_final: 0.8192 (mttt) REVERT: C 617 MET cc_start: 0.7317 (OUTLIER) cc_final: 0.6863 (mtm) REVERT: C 715 GLN cc_start: 0.6854 (tt0) cc_final: 0.6512 (tm-30) REVERT: C 750 ASP cc_start: 0.6426 (OUTLIER) cc_final: 0.5848 (t0) REVERT: D 105 LYS cc_start: 0.8252 (mmtt) cc_final: 0.8029 (mptt) REVERT: D 201 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: D 206 ARG cc_start: 0.7276 (tpp80) cc_final: 0.7024 (mmt-90) REVERT: D 291 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7767 (tp30) REVERT: D 346 GLN cc_start: 0.7471 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: D 350 ASP cc_start: 0.7560 (m-30) cc_final: 0.7330 (m-30) REVERT: D 431 ARG cc_start: 0.7970 (tpt170) cc_final: 0.7452 (ttt180) REVERT: D 440 ARG cc_start: 0.7109 (ptm160) cc_final: 0.6781 (ptp-110) REVERT: D 717 LEU cc_start: 0.7856 (tp) cc_final: 0.7492 (mt) REVERT: D 718 LYS cc_start: 0.7329 (OUTLIER) cc_final: 0.6924 (mmpt) REVERT: D 775 MET cc_start: 0.6688 (mmm) cc_final: 0.6461 (mmm) REVERT: D 836 LYS cc_start: 0.7228 (mttm) cc_final: 0.6760 (mppt) REVERT: D 893 ASP cc_start: 0.5934 (OUTLIER) cc_final: 0.5538 (t0) REVERT: F 102 VAL cc_start: 0.3416 (OUTLIER) cc_final: 0.3079 (p) REVERT: F 132 MET cc_start: 0.7981 (mtp) cc_final: 0.7781 (mtp) REVERT: F 271 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7955 (tttt) REVERT: F 279 GLU cc_start: 0.6913 (pm20) cc_final: 0.6646 (pm20) REVERT: F 331 LYS cc_start: 0.7469 (ttpt) cc_final: 0.6678 (pmtt) REVERT: F 340 ASP cc_start: 0.5843 (OUTLIER) cc_final: 0.5564 (p0) REVERT: F 715 GLN cc_start: 0.7083 (tp40) cc_final: 0.6563 (tm-30) REVERT: G 346 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: G 380 MET cc_start: 0.8584 (mmm) cc_final: 0.8306 (mmp) REVERT: G 526 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5210 (pp20) REVERT: G 573 MET cc_start: 0.8696 (ptp) cc_final: 0.8472 (ptt) REVERT: G 590 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.8146 (ttmt) REVERT: G 719 ASN cc_start: 0.8730 (t0) cc_final: 0.8446 (m-40) REVERT: E 103 ASN cc_start: 0.5060 (t0) cc_final: 0.4763 (t0) REVERT: E 170 LYS cc_start: 0.7655 (mmtt) cc_final: 0.7337 (mppt) REVERT: E 201 GLU cc_start: 0.7638 (tt0) cc_final: 0.7395 (tt0) REVERT: E 214 LYS cc_start: 0.6434 (OUTLIER) cc_final: 0.6153 (mptt) REVERT: E 244 ARG cc_start: 0.7662 (mtt-85) cc_final: 0.7423 (mtt-85) REVERT: E 245 LYS cc_start: 0.8479 (mmtt) cc_final: 0.8248 (mmtm) REVERT: E 253 ASP cc_start: 0.8128 (p0) cc_final: 0.7812 (t0) REVERT: E 285 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5855 (pp20) REVERT: E 291 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6727 (mm-30) REVERT: E 340 ASP cc_start: 0.5435 (OUTLIER) cc_final: 0.4947 (p0) REVERT: E 354 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5791 (tm-30) REVERT: E 425 MET cc_start: 0.8104 (OUTLIER) cc_final: 0.6162 (mmt) REVERT: E 497 PHE cc_start: 0.5949 (t80) cc_final: 0.5255 (t80) REVERT: E 740 ARG cc_start: 0.6936 (tpp80) cc_final: 0.6731 (tpp-160) REVERT: E 765 MET cc_start: 0.3578 (mtm) cc_final: 0.3279 (ttt) REVERT: A 496 LYS cc_start: 0.8458 (mttp) cc_final: 0.8221 (mttm) REVERT: A 755 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7671 (mtt180) outliers start: 236 outliers final: 65 residues processed: 775 average time/residue: 1.6010 time to fit residues: 1517.2919 Evaluate side-chains 629 residues out of total 4874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 531 time to evaluate : 5.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 161 GLN Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 340 ASP Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 441 PHE Chi-restraints excluded: chain B residue 473 GLU Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 516 THR Chi-restraints excluded: chain B residue 584 MET Chi-restraints excluded: chain B residue 594 ASP Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 LEU Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 719 ASN Chi-restraints excluded: chain B residue 728 ARG Chi-restraints excluded: chain B residue 826 GLU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 281 VAL Chi-restraints excluded: chain C residue 291 GLU Chi-restraints excluded: chain C residue 332 THR Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 617 MET Chi-restraints excluded: chain C residue 661 SER Chi-restraints excluded: chain C residue 723 ILE Chi-restraints excluded: chain C residue 750 ASP Chi-restraints excluded: chain C residue 826 GLU Chi-restraints excluded: chain D residue 179 ASP Chi-restraints excluded: chain D residue 201 GLU Chi-restraints excluded: chain D residue 291 GLU Chi-restraints excluded: chain D residue 330 VAL Chi-restraints excluded: chain D residue 332 THR Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain D residue 561 SER Chi-restraints excluded: chain D residue 635 CYS Chi-restraints excluded: chain D residue 718 LYS Chi-restraints excluded: chain D residue 808 LEU Chi-restraints excluded: chain D residue 838 THR Chi-restraints excluded: chain D residue 893 ASP Chi-restraints excluded: chain D residue 912 ASN Chi-restraints excluded: chain F residue 102 VAL Chi-restraints excluded: chain F residue 197 SER Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 271 LYS Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 340 ASP Chi-restraints excluded: chain F residue 473 GLU Chi-restraints excluded: chain F residue 661 SER Chi-restraints excluded: chain F residue 719 ASN Chi-restraints excluded: chain F residue 838 THR Chi-restraints excluded: chain G residue 92 SER Chi-restraints excluded: chain G residue 247 VAL Chi-restraints excluded: chain G residue 310 LEU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 333 GLU Chi-restraints excluded: chain G residue 340 ASP Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain G residue 358 LEU Chi-restraints excluded: chain G residue 441 PHE Chi-restraints excluded: chain G residue 516 THR Chi-restraints excluded: chain G residue 526 GLU Chi-restraints excluded: chain G residue 590 LYS Chi-restraints excluded: chain G residue 595 THR Chi-restraints excluded: chain G residue 661 SER Chi-restraints excluded: chain G residue 718 LYS Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 214 LYS Chi-restraints excluded: chain E residue 247 VAL Chi-restraints excluded: chain E residue 285 GLU Chi-restraints excluded: chain E residue 291 GLU Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 340 ASP Chi-restraints excluded: chain E residue 354 GLU Chi-restraints excluded: chain E residue 425 MET Chi-restraints excluded: chain E residue 531 LEU Chi-restraints excluded: chain E residue 561 SER Chi-restraints excluded: chain E residue 632 ILE Chi-restraints excluded: chain E residue 838 THR Chi-restraints excluded: chain A residue 102 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 262 ARG Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 338 ASP Chi-restraints excluded: chain A residue 532 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain A residue 755 ARG Chi-restraints excluded: chain A residue 885 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.0477 > 50: distance: 29 - 33: 21.935 distance: 33 - 34: 10.707 distance: 34 - 35: 14.451 distance: 34 - 37: 21.539 distance: 35 - 36: 25.138 distance: 35 - 41: 20.946 distance: 37 - 38: 21.136 distance: 38 - 39: 9.666 distance: 39 - 40: 3.699 distance: 41 - 42: 11.654 distance: 41 - 47: 21.702 distance: 42 - 43: 16.440 distance: 42 - 45: 3.660 distance: 43 - 44: 29.237 distance: 43 - 48: 17.034 distance: 45 - 46: 9.505 distance: 46 - 47: 17.286 distance: 48 - 49: 7.895 distance: 49 - 50: 24.435 distance: 49 - 52: 21.867 distance: 50 - 51: 13.741 distance: 50 - 57: 10.873 distance: 52 - 53: 6.716 distance: 53 - 54: 28.949 distance: 54 - 55: 13.447 distance: 54 - 56: 14.416 distance: 57 - 58: 33.937 distance: 58 - 59: 14.361 distance: 59 - 60: 6.013 distance: 59 - 61: 11.133 distance: 61 - 62: 17.598 distance: 62 - 63: 28.666 distance: 62 - 65: 15.433 distance: 63 - 64: 25.405 distance: 63 - 73: 31.352 distance: 65 - 66: 11.288 distance: 66 - 67: 13.797 distance: 66 - 68: 14.962 distance: 67 - 69: 10.146 distance: 68 - 70: 6.337 distance: 69 - 71: 10.052 distance: 70 - 71: 6.426 distance: 71 - 72: 15.876 distance: 73 - 74: 31.555 distance: 74 - 75: 14.802 distance: 74 - 77: 15.843 distance: 75 - 76: 15.843 distance: 75 - 82: 23.142 distance: 77 - 78: 11.476 distance: 78 - 79: 7.903 distance: 79 - 80: 17.378 distance: 80 - 81: 3.709 distance: 82 - 83: 25.976 distance: 83 - 84: 20.023 distance: 83 - 86: 15.688 distance: 84 - 85: 21.108 distance: 84 - 91: 23.877 distance: 86 - 87: 9.152 distance: 87 - 88: 8.292 distance: 88 - 89: 6.818 distance: 89 - 90: 20.254 distance: 91 - 92: 16.297 distance: 92 - 93: 10.513 distance: 92 - 95: 16.958 distance: 93 - 94: 10.454 distance: 93 - 102: 6.796 distance: 95 - 96: 14.208 distance: 96 - 97: 20.177 distance: 96 - 98: 3.726 distance: 97 - 99: 9.078 distance: 98 - 100: 8.009 distance: 99 - 101: 7.077 distance: 100 - 101: 6.484 distance: 102 - 103: 26.785 distance: 103 - 104: 14.796 distance: 103 - 106: 12.615 distance: 104 - 105: 13.035 distance: 104 - 110: 18.981 distance: 106 - 107: 11.765 distance: 107 - 109: 4.901 distance: 110 - 111: 8.242 distance: 111 - 112: 13.539 distance: 111 - 114: 5.906 distance: 112 - 113: 20.977 distance: 112 - 118: 8.037 distance: 114 - 115: 22.135 distance: 114 - 116: 14.976 distance: 115 - 117: 8.034