Starting phenix.real_space_refine on Mon Mar 25 06:31:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0b_9760/03_2024/6j0b_9760.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0b_9760/03_2024/6j0b_9760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0b_9760/03_2024/6j0b_9760.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0b_9760/03_2024/6j0b_9760.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0b_9760/03_2024/6j0b_9760.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j0b_9760/03_2024/6j0b_9760.pdb" } resolution = 2.9 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= 0.003 sd= 0.054 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 156 5.16 5 C 29808 2.51 5 N 7656 2.21 5 O 9168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A ARG 48": "NH1" <-> "NH2" Residue "A ASP 54": "OD1" <-> "OD2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 92": "OE1" <-> "OE2" Residue "A ASP 99": "OD1" <-> "OD2" Residue "A ASP 110": "OD1" <-> "OD2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 133": "OE1" <-> "OE2" Residue "A GLU 143": "OE1" <-> "OE2" Residue "A TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 243": "OD1" <-> "OD2" Residue "A ARG 248": "NH1" <-> "NH2" Residue "A ARG 254": "NH1" <-> "NH2" Residue "A PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 261": "NH1" <-> "NH2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "A ARG 339": "NH1" <-> "NH2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "B TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ASP 54": "OD1" <-> "OD2" Residue "B TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 69": "OD1" <-> "OD2" Residue "B TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B ASP 99": "OD1" <-> "OD2" Residue "B ASP 110": "OD1" <-> "OD2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 133": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 243": "OD1" <-> "OD2" Residue "B ARG 248": "NH1" <-> "NH2" Residue "B ARG 254": "NH1" <-> "NH2" Residue "B PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B GLU 273": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ARG 284": "NH1" <-> "NH2" Residue "B TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B ARG 339": "NH1" <-> "NH2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "C TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C ARG 48": "NH1" <-> "NH2" Residue "C ASP 54": "OD1" <-> "OD2" Residue "C TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C ASP 99": "OD1" <-> "OD2" Residue "C ASP 110": "OD1" <-> "OD2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 133": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 243": "OD1" <-> "OD2" Residue "C ARG 248": "NH1" <-> "NH2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "C PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 261": "NH1" <-> "NH2" Residue "C GLU 273": "OE1" <-> "OE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 284": "NH1" <-> "NH2" Residue "C TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 306": "OE1" <-> "OE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "D TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D ARG 48": "NH1" <-> "NH2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 69": "OD1" <-> "OD2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 92": "OE1" <-> "OE2" Residue "D ASP 99": "OD1" <-> "OD2" Residue "D ASP 110": "OD1" <-> "OD2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 133": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 243": "OD1" <-> "OD2" Residue "D ARG 248": "NH1" <-> "NH2" Residue "D ARG 254": "NH1" <-> "NH2" Residue "D PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 261": "NH1" <-> "NH2" Residue "D GLU 273": "OE1" <-> "OE2" Residue "D GLU 281": "OE1" <-> "OE2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "D TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 306": "OE1" <-> "OE2" Residue "D ARG 339": "NH1" <-> "NH2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "E TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ASP 54": "OD1" <-> "OD2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 69": "OD1" <-> "OD2" Residue "E TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 92": "OE1" <-> "OE2" Residue "E ASP 99": "OD1" <-> "OD2" Residue "E ASP 110": "OD1" <-> "OD2" Residue "E PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "E GLU 143": "OE1" <-> "OE2" Residue "E TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 243": "OD1" <-> "OD2" Residue "E ARG 248": "NH1" <-> "NH2" Residue "E ARG 254": "NH1" <-> "NH2" Residue "E PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 261": "NH1" <-> "NH2" Residue "E GLU 273": "OE1" <-> "OE2" Residue "E GLU 281": "OE1" <-> "OE2" Residue "E ARG 284": "NH1" <-> "NH2" Residue "E TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 306": "OE1" <-> "OE2" Residue "E ARG 339": "NH1" <-> "NH2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ASP 54": "OD1" <-> "OD2" Residue "F TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 69": "OD1" <-> "OD2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 92": "OE1" <-> "OE2" Residue "F ASP 99": "OD1" <-> "OD2" Residue "F ASP 110": "OD1" <-> "OD2" Residue "F PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F GLU 143": "OE1" <-> "OE2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 243": "OD1" <-> "OD2" Residue "F ARG 248": "NH1" <-> "NH2" Residue "F ARG 254": "NH1" <-> "NH2" Residue "F PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 261": "NH1" <-> "NH2" Residue "F GLU 273": "OE1" <-> "OE2" Residue "F GLU 281": "OE1" <-> "OE2" Residue "F ARG 284": "NH1" <-> "NH2" Residue "F TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 306": "OE1" <-> "OE2" Residue "F ARG 339": "NH1" <-> "NH2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "G TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G ARG 48": "NH1" <-> "NH2" Residue "G ASP 54": "OD1" <-> "OD2" Residue "G TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 69": "OD1" <-> "OD2" Residue "G TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G ASP 110": "OD1" <-> "OD2" Residue "G PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 133": "OE1" <-> "OE2" Residue "G GLU 143": "OE1" <-> "OE2" Residue "G TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 243": "OD1" <-> "OD2" Residue "G ARG 248": "NH1" <-> "NH2" Residue "G ARG 254": "NH1" <-> "NH2" Residue "G PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 261": "NH1" <-> "NH2" Residue "G GLU 273": "OE1" <-> "OE2" Residue "G GLU 281": "OE1" <-> "OE2" Residue "G ARG 284": "NH1" <-> "NH2" Residue "G TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 306": "OE1" <-> "OE2" Residue "G ARG 339": "NH1" <-> "NH2" Residue "G GLU 342": "OE1" <-> "OE2" Residue "H TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H ARG 48": "NH1" <-> "NH2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 69": "OD1" <-> "OD2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "H ASP 99": "OD1" <-> "OD2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 133": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 243": "OD1" <-> "OD2" Residue "H ARG 248": "NH1" <-> "NH2" Residue "H ARG 254": "NH1" <-> "NH2" Residue "H PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 261": "NH1" <-> "NH2" Residue "H GLU 273": "OE1" <-> "OE2" Residue "H GLU 281": "OE1" <-> "OE2" Residue "H ARG 284": "NH1" <-> "NH2" Residue "H TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 306": "OE1" <-> "OE2" Residue "H ARG 339": "NH1" <-> "NH2" Residue "H GLU 342": "OE1" <-> "OE2" Residue "I TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I ARG 48": "NH1" <-> "NH2" Residue "I ASP 54": "OD1" <-> "OD2" Residue "I TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 69": "OD1" <-> "OD2" Residue "I TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 92": "OE1" <-> "OE2" Residue "I ASP 99": "OD1" <-> "OD2" Residue "I ASP 110": "OD1" <-> "OD2" Residue "I PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 133": "OE1" <-> "OE2" Residue "I GLU 143": "OE1" <-> "OE2" Residue "I TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 243": "OD1" <-> "OD2" Residue "I ARG 248": "NH1" <-> "NH2" Residue "I ARG 254": "NH1" <-> "NH2" Residue "I PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 261": "NH1" <-> "NH2" Residue "I GLU 273": "OE1" <-> "OE2" Residue "I GLU 281": "OE1" <-> "OE2" Residue "I ARG 284": "NH1" <-> "NH2" Residue "I TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 306": "OE1" <-> "OE2" Residue "I ARG 339": "NH1" <-> "NH2" Residue "I GLU 342": "OE1" <-> "OE2" Residue "J TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J ASP 54": "OD1" <-> "OD2" Residue "J TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 69": "OD1" <-> "OD2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 92": "OE1" <-> "OE2" Residue "J ASP 99": "OD1" <-> "OD2" Residue "J ASP 110": "OD1" <-> "OD2" Residue "J PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 133": "OE1" <-> "OE2" Residue "J GLU 143": "OE1" <-> "OE2" Residue "J TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 243": "OD1" <-> "OD2" Residue "J ARG 248": "NH1" <-> "NH2" Residue "J ARG 254": "NH1" <-> "NH2" Residue "J PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 261": "NH1" <-> "NH2" Residue "J GLU 273": "OE1" <-> "OE2" Residue "J GLU 281": "OE1" <-> "OE2" Residue "J ARG 284": "NH1" <-> "NH2" Residue "J TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 306": "OE1" <-> "OE2" Residue "J ARG 339": "NH1" <-> "NH2" Residue "J GLU 342": "OE1" <-> "OE2" Residue "K TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K ARG 48": "NH1" <-> "NH2" Residue "K ASP 54": "OD1" <-> "OD2" Residue "K TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "K ASP 99": "OD1" <-> "OD2" Residue "K ASP 110": "OD1" <-> "OD2" Residue "K PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 133": "OE1" <-> "OE2" Residue "K GLU 143": "OE1" <-> "OE2" Residue "K TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 243": "OD1" <-> "OD2" Residue "K ARG 248": "NH1" <-> "NH2" Residue "K ARG 254": "NH1" <-> "NH2" Residue "K PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 261": "NH1" <-> "NH2" Residue "K GLU 273": "OE1" <-> "OE2" Residue "K GLU 281": "OE1" <-> "OE2" Residue "K ARG 284": "NH1" <-> "NH2" Residue "K TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 306": "OE1" <-> "OE2" Residue "K ARG 339": "NH1" <-> "NH2" Residue "K GLU 342": "OE1" <-> "OE2" Residue "L TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 43": "OE1" <-> "OE2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ASP 54": "OD1" <-> "OD2" Residue "L TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 69": "OD1" <-> "OD2" Residue "L TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 92": "OE1" <-> "OE2" Residue "L ASP 99": "OD1" <-> "OD2" Residue "L ASP 110": "OD1" <-> "OD2" Residue "L PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 133": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 243": "OD1" <-> "OD2" Residue "L ARG 248": "NH1" <-> "NH2" Residue "L ARG 254": "NH1" <-> "NH2" Residue "L PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 261": "NH1" <-> "NH2" Residue "L GLU 273": "OE1" <-> "OE2" Residue "L GLU 281": "OE1" <-> "OE2" Residue "L ARG 284": "NH1" <-> "NH2" Residue "L TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 306": "OE1" <-> "OE2" Residue "L ARG 339": "NH1" <-> "NH2" Residue "L GLU 342": "OE1" <-> "OE2" Residue "a PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 37": "OD1" <-> "OD2" Residue "a ASP 47": "OD1" <-> "OD2" Residue "a PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 90": "OE1" <-> "OE2" Residue "a GLU 136": "OE1" <-> "OE2" Residue "a ARG 143": "NH1" <-> "NH2" Residue "b PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 37": "OD1" <-> "OD2" Residue "b ASP 47": "OD1" <-> "OD2" Residue "b PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 90": "OE1" <-> "OE2" Residue "b GLU 136": "OE1" <-> "OE2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "c PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 37": "OD1" <-> "OD2" Residue "c ASP 47": "OD1" <-> "OD2" Residue "c PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c GLU 136": "OE1" <-> "OE2" Residue "c ARG 143": "NH1" <-> "NH2" Residue "d PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ASP 37": "OD1" <-> "OD2" Residue "d ASP 47": "OD1" <-> "OD2" Residue "d PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d GLU 136": "OE1" <-> "OE2" Residue "d ARG 143": "NH1" <-> "NH2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 37": "OD1" <-> "OD2" Residue "e ASP 47": "OD1" <-> "OD2" Residue "e PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 90": "OE1" <-> "OE2" Residue "e GLU 136": "OE1" <-> "OE2" Residue "e ARG 143": "NH1" <-> "NH2" Residue "f PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 37": "OD1" <-> "OD2" Residue "f ASP 47": "OD1" <-> "OD2" Residue "f PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 90": "OE1" <-> "OE2" Residue "f GLU 136": "OE1" <-> "OE2" Residue "f ARG 143": "NH1" <-> "NH2" Residue "g PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 37": "OD1" <-> "OD2" Residue "g ASP 47": "OD1" <-> "OD2" Residue "g PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 90": "OE1" <-> "OE2" Residue "g GLU 136": "OE1" <-> "OE2" Residue "g ARG 143": "NH1" <-> "NH2" Residue "h PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 37": "OD1" <-> "OD2" Residue "h ASP 47": "OD1" <-> "OD2" Residue "h PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h GLU 90": "OE1" <-> "OE2" Residue "h GLU 136": "OE1" <-> "OE2" Residue "h ARG 143": "NH1" <-> "NH2" Residue "i PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ASP 37": "OD1" <-> "OD2" Residue "i ASP 47": "OD1" <-> "OD2" Residue "i PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "i GLU 136": "OE1" <-> "OE2" Residue "i ARG 143": "NH1" <-> "NH2" Residue "j PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 37": "OD1" <-> "OD2" Residue "j ASP 47": "OD1" <-> "OD2" Residue "j PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 90": "OE1" <-> "OE2" Residue "j GLU 136": "OE1" <-> "OE2" Residue "j ARG 143": "NH1" <-> "NH2" Residue "k PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ASP 37": "OD1" <-> "OD2" Residue "k ASP 47": "OD1" <-> "OD2" Residue "k PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 90": "OE1" <-> "OE2" Residue "k GLU 136": "OE1" <-> "OE2" Residue "k ARG 143": "NH1" <-> "NH2" Residue "l PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 37": "OD1" <-> "OD2" Residue "l ASP 47": "OD1" <-> "OD2" Residue "l PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 90": "OE1" <-> "OE2" Residue "l GLU 136": "OE1" <-> "OE2" Residue "l ARG 143": "NH1" <-> "NH2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46788 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "B" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "C" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "D" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "E" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "F" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "G" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "H" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "I" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "J" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "K" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "L" Number of atoms: 2746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2746 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 15, 'TRANS': 336} Chain: "a" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "b" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "c" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "d" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "e" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "f" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "g" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "h" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "i" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "j" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "k" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "l" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1153 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Time building chain proxies: 23.44, per 1000 atoms: 0.50 Number of scatterers: 46788 At special positions: 0 Unit cell: (178.239, 180.481, 135.641, 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 156 16.00 O 9168 8.00 N 7656 7.00 C 29808 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: 16.83 Conformation dependent library (CDL) restraints added in 8.6 seconds 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11208 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 78 sheets defined 28.4% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.15 Creating SS restraints... Processing helix chain 'A' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL A 70 " --> pdb=" O ASP A 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN A 78 " --> pdb=" O ALA A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE A 94 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 117 " --> pdb=" O THR A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA A 144 " --> pdb=" O GLY A 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 140 through 145' Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL A 175 " --> pdb=" O PRO A 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 267 Processing helix chain 'A' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG A 282 " --> pdb=" O PRO A 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 308 removed outlier: 3.689A pdb=" N ALA A 308 " --> pdb=" O LYS A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 304 through 308' Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'B' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU B 58 " --> pdb=" O ASP B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL B 70 " --> pdb=" O ASP B 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN B 78 " --> pdb=" O ALA B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 90 through 95' Processing helix chain 'B' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP B 116 " --> pdb=" O LYS B 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 117 " --> pdb=" O THR B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA B 144 " --> pdb=" O GLY B 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 145 " --> pdb=" O ALA B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 140 through 145' Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL B 175 " --> pdb=" O PRO B 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR B 216 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 267 Processing helix chain 'B' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 285 " --> pdb=" O GLU B 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA B 308 " --> pdb=" O LYS B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 320 through 327 Processing helix chain 'C' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU C 58 " --> pdb=" O ASP C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL C 70 " --> pdb=" O ASP C 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN C 78 " --> pdb=" O ALA C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE C 94 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL C 117 " --> pdb=" O THR C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA C 144 " --> pdb=" O GLY C 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 145 " --> pdb=" O ALA C 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 140 through 145' Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL C 175 " --> pdb=" O PRO C 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY C 178 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU C 215 " --> pdb=" O GLU C 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR C 216 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 267 Processing helix chain 'C' and resid 276 through 297 removed outlier: 3.713A pdb=" N ARG C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 304 through 308' Processing helix chain 'C' and resid 320 through 327 Processing helix chain 'D' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU D 58 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL D 70 " --> pdb=" O ASP D 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN D 78 " --> pdb=" O ALA D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE D 94 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 90 through 95' Processing helix chain 'D' and resid 111 through 119 removed outlier: 3.792A pdb=" N ASP D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 117 " --> pdb=" O THR D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA D 144 " --> pdb=" O GLY D 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 140 through 145' Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 171 through 187 removed outlier: 4.118A pdb=" N VAL D 175 " --> pdb=" O PRO D 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY D 178 " --> pdb=" O ALA D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR D 216 " --> pdb=" O LEU D 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 267 Processing helix chain 'D' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA D 285 " --> pdb=" O GLU D 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA D 308 " --> pdb=" O LYS D 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 304 through 308' Processing helix chain 'D' and resid 320 through 327 Processing helix chain 'E' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU E 58 " --> pdb=" O ASP E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL E 70 " --> pdb=" O ASP E 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE E 94 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE E 95 " --> pdb=" O LEU E 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 90 through 95' Processing helix chain 'E' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL E 117 " --> pdb=" O THR E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA E 144 " --> pdb=" O GLY E 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 145 " --> pdb=" O ALA E 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 140 through 145' Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL E 175 " --> pdb=" O PRO E 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 217 removed outlier: 3.749A pdb=" N GLU E 215 " --> pdb=" O GLU E 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR E 216 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 267 Processing helix chain 'E' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N TYR E 290 " --> pdb=" O ALA E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA E 308 " --> pdb=" O LYS E 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 304 through 308' Processing helix chain 'E' and resid 320 through 327 Processing helix chain 'F' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU F 58 " --> pdb=" O ASP F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL F 70 " --> pdb=" O ASP F 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE F 94 " --> pdb=" O SER F 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE F 95 " --> pdb=" O LEU F 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 90 through 95' Processing helix chain 'F' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL F 117 " --> pdb=" O THR F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA F 144 " --> pdb=" O GLY F 140 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS F 145 " --> pdb=" O ALA F 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 140 through 145' Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL F 175 " --> pdb=" O PRO F 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY F 178 " --> pdb=" O ALA F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU F 215 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR F 216 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 267 Processing helix chain 'F' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG F 282 " --> pdb=" O PRO F 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA F 285 " --> pdb=" O GLU F 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR F 290 " --> pdb=" O ALA F 286 " (cutoff:3.500A) Processing helix chain 'F' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA F 308 " --> pdb=" O LYS F 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 304 through 308' Processing helix chain 'F' and resid 320 through 327 Processing helix chain 'G' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU G 58 " --> pdb=" O ASP G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL G 70 " --> pdb=" O ASP G 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE G 94 " --> pdb=" O SER G 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 95 " --> pdb=" O LEU G 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 90 through 95' Processing helix chain 'G' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL G 117 " --> pdb=" O THR G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA G 144 " --> pdb=" O GLY G 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS G 145 " --> pdb=" O ALA G 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 140 through 145' Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL G 175 " --> pdb=" O PRO G 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLY G 178 " --> pdb=" O ALA G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU G 215 " --> pdb=" O GLU G 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 267 Processing helix chain 'G' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG G 282 " --> pdb=" O PRO G 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR G 290 " --> pdb=" O ALA G 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA G 308 " --> pdb=" O LYS G 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 304 through 308' Processing helix chain 'G' and resid 320 through 327 Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL H 70 " --> pdb=" O ASP H 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE H 94 " --> pdb=" O SER H 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE H 95 " --> pdb=" O LEU H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 90 through 95' Processing helix chain 'H' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL H 117 " --> pdb=" O THR H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 removed outlier: 3.857A pdb=" N ALA H 144 " --> pdb=" O GLY H 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS H 145 " --> pdb=" O ALA H 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 140 through 145' Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL H 175 " --> pdb=" O PRO H 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY H 178 " --> pdb=" O ALA H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 217 removed outlier: 3.751A pdb=" N GLU H 215 " --> pdb=" O GLU H 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR H 216 " --> pdb=" O LEU H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 249 through 267 Processing helix chain 'H' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG H 282 " --> pdb=" O PRO H 278 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA H 285 " --> pdb=" O GLU H 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR H 290 " --> pdb=" O ALA H 286 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA H 308 " --> pdb=" O LYS H 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 304 through 308' Processing helix chain 'H' and resid 320 through 327 Processing helix chain 'I' and resid 51 through 59 removed outlier: 3.524A pdb=" N LEU I 58 " --> pdb=" O ASP I 54 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 78 removed outlier: 3.542A pdb=" N VAL I 70 " --> pdb=" O ASP I 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN I 78 " --> pdb=" O ALA I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE I 94 " --> pdb=" O SER I 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 90 through 95' Processing helix chain 'I' and resid 111 through 119 removed outlier: 3.794A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL I 117 " --> pdb=" O THR I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA I 144 " --> pdb=" O GLY I 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS I 145 " --> pdb=" O ALA I 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 140 through 145' Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL I 175 " --> pdb=" O PRO I 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY I 178 " --> pdb=" O ALA I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU I 215 " --> pdb=" O GLU I 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR I 216 " --> pdb=" O LEU I 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 267 Processing helix chain 'I' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG I 282 " --> pdb=" O PRO I 278 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA I 285 " --> pdb=" O GLU I 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR I 290 " --> pdb=" O ALA I 286 " (cutoff:3.500A) Processing helix chain 'I' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA I 308 " --> pdb=" O LYS I 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 304 through 308' Processing helix chain 'I' and resid 320 through 327 Processing helix chain 'J' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU J 58 " --> pdb=" O ASP J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL J 70 " --> pdb=" O ASP J 66 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN J 78 " --> pdb=" O ALA J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE J 95 " --> pdb=" O LEU J 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 90 through 95' Processing helix chain 'J' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP J 116 " --> pdb=" O LYS J 112 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL J 117 " --> pdb=" O THR J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA J 144 " --> pdb=" O GLY J 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS J 145 " --> pdb=" O ALA J 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 140 through 145' Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL J 175 " --> pdb=" O PRO J 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY J 178 " --> pdb=" O ALA J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU J 215 " --> pdb=" O GLU J 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR J 216 " --> pdb=" O LEU J 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 267 Processing helix chain 'J' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG J 282 " --> pdb=" O PRO J 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA J 285 " --> pdb=" O GLU J 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR J 290 " --> pdb=" O ALA J 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA J 308 " --> pdb=" O LYS J 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 304 through 308' Processing helix chain 'J' and resid 320 through 327 Processing helix chain 'K' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU K 58 " --> pdb=" O ASP K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL K 70 " --> pdb=" O ASP K 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN K 78 " --> pdb=" O ALA K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 95 removed outlier: 3.770A pdb=" N ILE K 94 " --> pdb=" O SER K 90 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE K 95 " --> pdb=" O LEU K 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 95' Processing helix chain 'K' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL K 117 " --> pdb=" O THR K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA K 144 " --> pdb=" O GLY K 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS K 145 " --> pdb=" O ALA K 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 140 through 145' Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 171 through 187 removed outlier: 4.119A pdb=" N VAL K 175 " --> pdb=" O PRO K 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY K 178 " --> pdb=" O ALA K 174 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 217 removed outlier: 3.750A pdb=" N GLU K 215 " --> pdb=" O GLU K 211 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR K 216 " --> pdb=" O LEU K 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 249 through 267 Processing helix chain 'K' and resid 276 through 297 removed outlier: 3.713A pdb=" N ARG K 282 " --> pdb=" O PRO K 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA K 285 " --> pdb=" O GLU K 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR K 290 " --> pdb=" O ALA K 286 " (cutoff:3.500A) Processing helix chain 'K' and resid 304 through 308 removed outlier: 3.690A pdb=" N ALA K 308 " --> pdb=" O LYS K 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 304 through 308' Processing helix chain 'K' and resid 320 through 327 Processing helix chain 'L' and resid 51 through 59 removed outlier: 3.525A pdb=" N LEU L 58 " --> pdb=" O ASP L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 78 removed outlier: 3.543A pdb=" N VAL L 70 " --> pdb=" O ASP L 66 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN L 78 " --> pdb=" O ALA L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 95 removed outlier: 3.769A pdb=" N ILE L 94 " --> pdb=" O SER L 90 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE L 95 " --> pdb=" O LEU L 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 90 through 95' Processing helix chain 'L' and resid 111 through 119 removed outlier: 3.793A pdb=" N ASP L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL L 117 " --> pdb=" O THR L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 145 removed outlier: 3.858A pdb=" N ALA L 144 " --> pdb=" O GLY L 140 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 140 through 145' Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 171 through 187 removed outlier: 4.120A pdb=" N VAL L 175 " --> pdb=" O PRO L 171 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY L 178 " --> pdb=" O ALA L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 217 removed outlier: 3.749A pdb=" N GLU L 215 " --> pdb=" O GLU L 211 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR L 216 " --> pdb=" O LEU L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 249 through 267 Processing helix chain 'L' and resid 276 through 297 removed outlier: 3.712A pdb=" N ARG L 282 " --> pdb=" O PRO L 278 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA L 285 " --> pdb=" O GLU L 281 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR L 290 " --> pdb=" O ALA L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 308 removed outlier: 3.691A pdb=" N ALA L 308 " --> pdb=" O LYS L 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 304 through 308' Processing helix chain 'L' and resid 320 through 327 Processing helix chain 'a' and resid 4 through 12 removed outlier: 3.825A pdb=" N ALA a 9 " --> pdb=" O THR a 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL a 10 " --> pdb=" O SER a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE a 81 " --> pdb=" O LEU a 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA b 9 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL b 10 " --> pdb=" O SER b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE b 81 " --> pdb=" O LEU b 77 " (cutoff:3.500A) Processing helix chain 'c' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA c 9 " --> pdb=" O THR c 5 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL c 10 " --> pdb=" O SER c 6 " (cutoff:3.500A) Processing helix chain 'c' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE c 81 " --> pdb=" O LEU c 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA d 9 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL d 10 " --> pdb=" O SER d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE d 81 " --> pdb=" O LEU d 77 " (cutoff:3.500A) Processing helix chain 'e' and resid 4 through 12 removed outlier: 3.825A pdb=" N ALA e 9 " --> pdb=" O THR e 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL e 10 " --> pdb=" O SER e 6 " (cutoff:3.500A) Processing helix chain 'e' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE e 81 " --> pdb=" O LEU e 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA f 9 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL f 10 " --> pdb=" O SER f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE f 81 " --> pdb=" O LEU f 77 " (cutoff:3.500A) Processing helix chain 'g' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA g 9 " --> pdb=" O THR g 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL g 10 " --> pdb=" O SER g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE g 81 " --> pdb=" O LEU g 77 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL h 10 " --> pdb=" O SER h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE h 81 " --> pdb=" O LEU h 77 " (cutoff:3.500A) Processing helix chain 'i' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA i 9 " --> pdb=" O THR i 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL i 10 " --> pdb=" O SER i 6 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 83 removed outlier: 3.559A pdb=" N ILE i 81 " --> pdb=" O LEU i 77 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE j 81 " --> pdb=" O LEU j 77 " (cutoff:3.500A) Processing helix chain 'k' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA k 9 " --> pdb=" O THR k 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL k 10 " --> pdb=" O SER k 6 " (cutoff:3.500A) Processing helix chain 'k' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE k 81 " --> pdb=" O LEU k 77 " (cutoff:3.500A) Processing helix chain 'l' and resid 4 through 12 removed outlier: 3.826A pdb=" N ALA l 9 " --> pdb=" O THR l 5 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL l 10 " --> pdb=" O SER l 6 " (cutoff:3.500A) Processing helix chain 'l' and resid 77 through 83 removed outlier: 3.560A pdb=" N ILE l 81 " --> pdb=" O LEU l 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 5.993A pdb=" N TYR A 11 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N PHE F 348 " --> pdb=" O TYR A 11 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N PHE L 310 " --> pdb=" O GLY L 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA A 106 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP A 130 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 155 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN A 223 " --> pdb=" O ALA A 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL A 156 " --> pdb=" O ASN A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 228 Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 312 removed outlier: 3.506A pdb=" N PHE A 310 " --> pdb=" O GLY A 334 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.507A pdb=" N PHE G 310 " --> pdb=" O GLY G 334 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA B 106 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP B 130 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B 155 " --> pdb=" O ALA B 127 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ASN B 223 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 156 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 161 through 163 Processing sheet with id=AA9, first strand: chain 'B' and resid 225 through 228 Processing sheet with id=AB1, first strand: chain 'B' and resid 309 through 312 removed outlier: 3.507A pdb=" N PHE B 310 " --> pdb=" O GLY B 334 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 11 removed outlier: 3.506A pdb=" N PHE H 310 " --> pdb=" O GLY H 334 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA C 106 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP C 130 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA C 155 " --> pdb=" O ALA C 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN C 223 " --> pdb=" O ALA C 154 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL C 156 " --> pdb=" O ASN C 223 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AB5, first strand: chain 'C' and resid 225 through 228 Processing sheet with id=AB6, first strand: chain 'C' and resid 309 through 312 removed outlier: 3.507A pdb=" N PHE C 310 " --> pdb=" O GLY C 334 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.507A pdb=" N PHE I 310 " --> pdb=" O GLY I 334 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA D 106 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP D 130 " --> pdb=" O ALA D 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA D 155 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN D 223 " --> pdb=" O ALA D 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL D 156 " --> pdb=" O ASN D 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 161 through 163 Processing sheet with id=AC1, first strand: chain 'D' and resid 225 through 228 Processing sheet with id=AC2, first strand: chain 'D' and resid 309 through 312 removed outlier: 3.506A pdb=" N PHE D 310 " --> pdb=" O GLY D 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 343 through 349 removed outlier: 3.506A pdb=" N PHE J 310 " --> pdb=" O GLY J 334 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA E 106 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP E 130 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA E 155 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN E 223 " --> pdb=" O ALA E 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL E 156 " --> pdb=" O ASN E 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 161 through 163 Processing sheet with id=AC6, first strand: chain 'E' and resid 225 through 228 Processing sheet with id=AC7, first strand: chain 'E' and resid 309 through 312 removed outlier: 3.507A pdb=" N PHE E 310 " --> pdb=" O GLY E 334 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 11 removed outlier: 3.507A pdb=" N PHE K 310 " --> pdb=" O GLY K 334 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 47 through 49 removed outlier: 3.587A pdb=" N ALA F 106 " --> pdb=" O VAL F 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP F 130 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA F 155 " --> pdb=" O ALA F 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN F 223 " --> pdb=" O ALA F 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL F 156 " --> pdb=" O ASN F 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 161 through 163 Processing sheet with id=AD2, first strand: chain 'F' and resid 225 through 228 Processing sheet with id=AD3, first strand: chain 'F' and resid 309 through 312 removed outlier: 3.506A pdb=" N PHE F 310 " --> pdb=" O GLY F 334 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 10 through 11 Processing sheet with id=AD5, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA G 106 " --> pdb=" O VAL G 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP G 130 " --> pdb=" O ALA G 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA G 155 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN G 223 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL G 156 " --> pdb=" O ASN G 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 161 through 163 Processing sheet with id=AD7, first strand: chain 'G' and resid 225 through 228 Processing sheet with id=AD8, first strand: chain 'G' and resid 344 through 345 removed outlier: 6.716A pdb=" N ILE G 344 " --> pdb=" O TYR H 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'H' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA H 106 " --> pdb=" O VAL H 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP H 130 " --> pdb=" O ALA H 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA H 155 " --> pdb=" O ALA H 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN H 223 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL H 156 " --> pdb=" O ASN H 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 161 through 163 Processing sheet with id=AE2, first strand: chain 'H' and resid 225 through 228 Processing sheet with id=AE3, first strand: chain 'H' and resid 344 through 345 removed outlier: 6.722A pdb=" N ILE H 344 " --> pdb=" O TYR I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'I' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA I 106 " --> pdb=" O VAL I 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP I 130 " --> pdb=" O ALA I 106 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA I 155 " --> pdb=" O ALA I 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN I 223 " --> pdb=" O ALA I 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL I 156 " --> pdb=" O ASN I 223 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 161 through 163 Processing sheet with id=AE6, first strand: chain 'I' and resid 225 through 228 Processing sheet with id=AE7, first strand: chain 'I' and resid 344 through 345 removed outlier: 6.735A pdb=" N ILE I 344 " --> pdb=" O TYR J 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'J' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA J 106 " --> pdb=" O VAL J 128 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ASP J 130 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA J 155 " --> pdb=" O ALA J 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN J 223 " --> pdb=" O ALA J 154 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N VAL J 156 " --> pdb=" O ASN J 223 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'J' and resid 161 through 163 Processing sheet with id=AF1, first strand: chain 'J' and resid 225 through 228 Processing sheet with id=AF2, first strand: chain 'J' and resid 344 through 345 removed outlier: 6.713A pdb=" N ILE J 344 " --> pdb=" O TYR K 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA K 106 " --> pdb=" O VAL K 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP K 130 " --> pdb=" O ALA K 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA K 155 " --> pdb=" O ALA K 127 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN K 223 " --> pdb=" O ALA K 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL K 156 " --> pdb=" O ASN K 223 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'K' and resid 161 through 163 Processing sheet with id=AF5, first strand: chain 'K' and resid 225 through 228 Processing sheet with id=AF6, first strand: chain 'K' and resid 344 through 345 removed outlier: 6.630A pdb=" N ILE K 344 " --> pdb=" O TYR L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'L' and resid 47 through 49 removed outlier: 3.586A pdb=" N ALA L 106 " --> pdb=" O VAL L 128 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ASP L 130 " --> pdb=" O ALA L 106 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA L 155 " --> pdb=" O ALA L 127 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASN L 223 " --> pdb=" O ALA L 154 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL L 156 " --> pdb=" O ASN L 223 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 161 through 163 Processing sheet with id=AF9, first strand: chain 'L' and resid 225 through 228 Processing sheet with id=AG1, first strand: chain 'a' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS a 92 " --> pdb=" O SER a 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER a 113 " --> pdb=" O LYS a 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE a 94 " --> pdb=" O ASN a 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN a 111 " --> pdb=" O ILE a 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE a 96 " --> pdb=" O THR a 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR a 109 " --> pdb=" O ILE a 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU a 98 " --> pdb=" O LEU a 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER a 113 " --> pdb=" O ARG a 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG a 143 " --> pdb=" O SER a 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA a 115 " --> pdb=" O ALA a 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA a 141 " --> pdb=" O ALA a 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU a 139 " --> pdb=" O PRO a 117 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER a 119 " --> pdb=" O ILE a 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE a 137 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR a 121 " --> pdb=" O GLN a 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN a 135 " --> pdb=" O THR a 121 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP a 41 " --> pdb=" O GLY a 57 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 125 through 126 removed outlier: 4.579A pdb=" N GLN f 135 " --> pdb=" O THR f 121 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR f 121 " --> pdb=" O GLN f 135 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE f 137 " --> pdb=" O SER f 119 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER f 119 " --> pdb=" O ILE f 137 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU f 139 " --> pdb=" O PRO f 117 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA f 141 " --> pdb=" O ALA f 115 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA f 115 " --> pdb=" O ALA f 141 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG f 143 " --> pdb=" O SER f 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER f 113 " --> pdb=" O ARG f 143 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU f 98 " --> pdb=" O LEU f 107 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR f 109 " --> pdb=" O ILE f 96 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE f 96 " --> pdb=" O THR f 109 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN f 111 " --> pdb=" O ILE f 94 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE f 94 " --> pdb=" O ASN f 111 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER f 113 " --> pdb=" O LYS f 92 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS f 92 " --> pdb=" O SER f 113 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'b' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS b 92 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER b 113 " --> pdb=" O LYS b 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE b 94 " --> pdb=" O ASN b 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN b 111 " --> pdb=" O ILE b 94 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE b 96 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR b 109 " --> pdb=" O ILE b 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU b 98 " --> pdb=" O LEU b 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER b 113 " --> pdb=" O ARG b 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG b 143 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA b 115 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA b 141 " --> pdb=" O ALA b 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU b 139 " --> pdb=" O PRO b 117 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER b 119 " --> pdb=" O ILE b 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE b 137 " --> pdb=" O SER b 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR b 121 " --> pdb=" O GLN b 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN b 135 " --> pdb=" O THR b 121 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP b 41 " --> pdb=" O GLY b 57 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'c' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS c 92 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER c 113 " --> pdb=" O LYS c 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE c 94 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN c 111 " --> pdb=" O ILE c 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE c 96 " --> pdb=" O THR c 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR c 109 " --> pdb=" O ILE c 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU c 98 " --> pdb=" O LEU c 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER c 113 " --> pdb=" O ARG c 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG c 143 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA c 115 " --> pdb=" O ALA c 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA c 141 " --> pdb=" O ALA c 115 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU c 139 " --> pdb=" O PRO c 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER c 119 " --> pdb=" O ILE c 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE c 137 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR c 121 " --> pdb=" O GLN c 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN c 135 " --> pdb=" O THR c 121 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP c 41 " --> pdb=" O GLY c 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd' and resid 19 through 23 removed outlier: 6.877A pdb=" N LYS d 92 " --> pdb=" O SER d 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER d 113 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE d 94 " --> pdb=" O ASN d 111 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN d 111 " --> pdb=" O ILE d 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE d 96 " --> pdb=" O THR d 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR d 109 " --> pdb=" O ILE d 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU d 98 " --> pdb=" O LEU d 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER d 113 " --> pdb=" O ARG d 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG d 143 " --> pdb=" O SER d 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA d 115 " --> pdb=" O ALA d 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA d 141 " --> pdb=" O ALA d 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU d 139 " --> pdb=" O PRO d 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER d 119 " --> pdb=" O ILE d 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE d 137 " --> pdb=" O SER d 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR d 121 " --> pdb=" O GLN d 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN d 135 " --> pdb=" O THR d 121 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'd' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP d 41 " --> pdb=" O GLY d 57 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'e' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS e 92 " --> pdb=" O SER e 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER e 113 " --> pdb=" O LYS e 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE e 94 " --> pdb=" O ASN e 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN e 111 " --> pdb=" O ILE e 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE e 96 " --> pdb=" O THR e 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR e 109 " --> pdb=" O ILE e 96 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU e 98 " --> pdb=" O LEU e 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER e 113 " --> pdb=" O ARG e 143 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG e 143 " --> pdb=" O SER e 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA e 115 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA e 141 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU e 139 " --> pdb=" O PRO e 117 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER e 119 " --> pdb=" O ILE e 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE e 137 " --> pdb=" O SER e 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR e 121 " --> pdb=" O GLN e 135 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN e 135 " --> pdb=" O THR e 121 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'e' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP e 41 " --> pdb=" O GLY e 57 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'f' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP f 41 " --> pdb=" O GLY f 57 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'g' and resid 19 through 23 removed outlier: 6.877A pdb=" N LYS g 92 " --> pdb=" O SER g 113 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER g 113 " --> pdb=" O LYS g 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE g 94 " --> pdb=" O ASN g 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN g 111 " --> pdb=" O ILE g 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE g 96 " --> pdb=" O THR g 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR g 109 " --> pdb=" O ILE g 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU g 98 " --> pdb=" O LEU g 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER g 113 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG g 143 " --> pdb=" O SER g 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA g 115 " --> pdb=" O ALA g 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA g 141 " --> pdb=" O ALA g 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU g 139 " --> pdb=" O PRO g 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER g 119 " --> pdb=" O ILE g 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE g 137 " --> pdb=" O SER g 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR g 121 " --> pdb=" O GLN g 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN g 135 " --> pdb=" O THR g 121 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'g' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP g 41 " --> pdb=" O GLY g 57 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'g' and resid 125 through 126 removed outlier: 4.579A pdb=" N GLN l 135 " --> pdb=" O THR l 121 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR l 121 " --> pdb=" O GLN l 135 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE l 137 " --> pdb=" O SER l 119 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N SER l 119 " --> pdb=" O ILE l 137 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU l 139 " --> pdb=" O PRO l 117 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA l 141 " --> pdb=" O ALA l 115 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA l 115 " --> pdb=" O ALA l 141 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG l 143 " --> pdb=" O SER l 113 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER l 113 " --> pdb=" O ARG l 143 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LEU l 98 " --> pdb=" O LEU l 107 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR l 109 " --> pdb=" O ILE l 96 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE l 96 " --> pdb=" O THR l 109 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN l 111 " --> pdb=" O ILE l 94 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE l 94 " --> pdb=" O ASN l 111 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER l 113 " --> pdb=" O LYS l 92 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS l 92 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'h' and resid 19 through 23 removed outlier: 6.877A pdb=" N LYS h 92 " --> pdb=" O SER h 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER h 113 " --> pdb=" O LYS h 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE h 94 " --> pdb=" O ASN h 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN h 111 " --> pdb=" O ILE h 94 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE h 96 " --> pdb=" O THR h 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR h 109 " --> pdb=" O ILE h 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU h 98 " --> pdb=" O LEU h 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER h 113 " --> pdb=" O ARG h 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG h 143 " --> pdb=" O SER h 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA h 115 " --> pdb=" O ALA h 141 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ALA h 141 " --> pdb=" O ALA h 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU h 139 " --> pdb=" O PRO h 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER h 119 " --> pdb=" O ILE h 137 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE h 137 " --> pdb=" O SER h 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR h 121 " --> pdb=" O GLN h 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN h 135 " --> pdb=" O THR h 121 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'h' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP h 41 " --> pdb=" O GLY h 57 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'i' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS i 92 " --> pdb=" O SER i 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER i 113 " --> pdb=" O LYS i 92 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE i 94 " --> pdb=" O ASN i 111 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN i 111 " --> pdb=" O ILE i 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE i 96 " --> pdb=" O THR i 109 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR i 109 " --> pdb=" O ILE i 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU i 98 " --> pdb=" O LEU i 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER i 113 " --> pdb=" O ARG i 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG i 143 " --> pdb=" O SER i 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA i 115 " --> pdb=" O ALA i 141 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA i 141 " --> pdb=" O ALA i 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU i 139 " --> pdb=" O PRO i 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER i 119 " --> pdb=" O ILE i 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE i 137 " --> pdb=" O SER i 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR i 121 " --> pdb=" O GLN i 135 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N GLN i 135 " --> pdb=" O THR i 121 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'i' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP i 41 " --> pdb=" O GLY i 57 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'j' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS j 92 " --> pdb=" O SER j 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER j 113 " --> pdb=" O LYS j 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE j 94 " --> pdb=" O ASN j 111 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASN j 111 " --> pdb=" O ILE j 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE j 96 " --> pdb=" O THR j 109 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR j 109 " --> pdb=" O ILE j 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU j 98 " --> pdb=" O LEU j 107 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N SER j 113 " --> pdb=" O ARG j 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG j 143 " --> pdb=" O SER j 113 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ALA j 115 " --> pdb=" O ALA j 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA j 141 " --> pdb=" O ALA j 115 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU j 139 " --> pdb=" O PRO j 117 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N SER j 119 " --> pdb=" O ILE j 137 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE j 137 " --> pdb=" O SER j 119 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N THR j 121 " --> pdb=" O GLN j 135 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN j 135 " --> pdb=" O THR j 121 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'j' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP j 41 " --> pdb=" O GLY j 57 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'k' and resid 19 through 23 removed outlier: 6.878A pdb=" N LYS k 92 " --> pdb=" O SER k 113 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N SER k 113 " --> pdb=" O LYS k 92 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE k 94 " --> pdb=" O ASN k 111 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN k 111 " --> pdb=" O ILE k 94 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ILE k 96 " --> pdb=" O THR k 109 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR k 109 " --> pdb=" O ILE k 96 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU k 98 " --> pdb=" O LEU k 107 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER k 113 " --> pdb=" O ARG k 143 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ARG k 143 " --> pdb=" O SER k 113 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA k 115 " --> pdb=" O ALA k 141 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA k 141 " --> pdb=" O ALA k 115 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU k 139 " --> pdb=" O PRO k 117 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER k 119 " --> pdb=" O ILE k 137 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ILE k 137 " --> pdb=" O SER k 119 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N THR k 121 " --> pdb=" O GLN k 135 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N GLN k 135 " --> pdb=" O THR k 121 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'k' and resid 40 through 46 removed outlier: 5.090A pdb=" N ASP k 41 " --> pdb=" O GLY k 57 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'l' and resid 40 through 46 removed outlier: 5.091A pdb=" N ASP l 41 " --> pdb=" O GLY l 57 " (cutoff:3.500A) 1467 hydrogen bonds defined for protein. 4131 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: 17.37 Time building geometry restraints manager: 18.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 14676 1.33 - 1.45: 7223 1.45 - 1.57: 25597 1.57 - 1.69: 0 1.69 - 1.81: 288 Bond restraints: 47784 Sorted by residual: bond pdb=" CB VAL k 144 " pdb=" CG2 VAL k 144 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.33e+00 bond pdb=" CB VAL f 144 " pdb=" CG2 VAL f 144 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.31e+00 bond pdb=" CG MET E 267 " pdb=" SD MET E 267 " ideal model delta sigma weight residual 1.803 1.745 0.058 2.50e-02 1.60e+03 5.31e+00 bond pdb=" CB VAL i 144 " pdb=" CG2 VAL i 144 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.30e+00 bond pdb=" CG MET B 267 " pdb=" SD MET B 267 " ideal model delta sigma weight residual 1.803 1.745 0.058 2.50e-02 1.60e+03 5.29e+00 ... (remaining 47779 not shown) Histogram of bond angle deviations from ideal: 95.45 - 103.18: 458 103.18 - 110.90: 16615 110.90 - 118.62: 20877 118.62 - 126.34: 26382 126.34 - 134.07: 804 Bond angle restraints: 65136 Sorted by residual: angle pdb=" N LEU k 86 " pdb=" CA LEU k 86 " pdb=" CB LEU k 86 " ideal model delta sigma weight residual 110.49 103.02 7.47 1.69e+00 3.50e-01 1.95e+01 angle pdb=" N LEU g 86 " pdb=" CA LEU g 86 " pdb=" CB LEU g 86 " ideal model delta sigma weight residual 110.49 103.03 7.46 1.69e+00 3.50e-01 1.95e+01 angle pdb=" N LEU j 86 " pdb=" CA LEU j 86 " pdb=" CB LEU j 86 " ideal model delta sigma weight residual 110.49 103.03 7.46 1.69e+00 3.50e-01 1.95e+01 angle pdb=" N LEU i 86 " pdb=" CA LEU i 86 " pdb=" CB LEU i 86 " ideal model delta sigma weight residual 110.49 103.06 7.43 1.69e+00 3.50e-01 1.93e+01 angle pdb=" N LEU l 86 " pdb=" CA LEU l 86 " pdb=" CB LEU l 86 " ideal model delta sigma weight residual 110.49 103.07 7.42 1.69e+00 3.50e-01 1.93e+01 ... (remaining 65131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 25298 17.83 - 35.66: 2350 35.66 - 53.48: 540 53.48 - 71.31: 120 71.31 - 89.14: 48 Dihedral angle restraints: 28356 sinusoidal: 10932 harmonic: 17424 Sorted by residual: dihedral pdb=" CA GLN g 85 " pdb=" C GLN g 85 " pdb=" N LEU g 86 " pdb=" CA LEU g 86 " ideal model delta harmonic sigma weight residual -180.00 -142.22 -37.78 0 5.00e+00 4.00e-02 5.71e+01 dihedral pdb=" CA GLN h 85 " pdb=" C GLN h 85 " pdb=" N LEU h 86 " pdb=" CA LEU h 86 " ideal model delta harmonic sigma weight residual 180.00 -142.25 -37.75 0 5.00e+00 4.00e-02 5.70e+01 dihedral pdb=" CA GLN l 85 " pdb=" C GLN l 85 " pdb=" N LEU l 86 " pdb=" CA LEU l 86 " ideal model delta harmonic sigma weight residual -180.00 -142.25 -37.75 0 5.00e+00 4.00e-02 5.70e+01 ... (remaining 28353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 5589 0.057 - 0.114: 1379 0.114 - 0.172: 401 0.172 - 0.229: 45 0.229 - 0.286: 14 Chirality restraints: 7428 Sorted by residual: chirality pdb=" CA ASN E 195 " pdb=" N ASN E 195 " pdb=" C ASN E 195 " pdb=" CB ASN E 195 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASN K 195 " pdb=" N ASN K 195 " pdb=" C ASN K 195 " pdb=" CB ASN K 195 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASN G 195 " pdb=" N ASN G 195 " pdb=" C ASN G 195 " pdb=" CB ASN G 195 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 7425 not shown) Planarity restraints: 8424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN j 85 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C GLN j 85 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN j 85 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU j 86 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN i 85 " 0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C GLN i 85 " -0.055 2.00e-02 2.50e+03 pdb=" O GLN i 85 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU i 86 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN h 85 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C GLN h 85 " 0.055 2.00e-02 2.50e+03 pdb=" O GLN h 85 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU h 86 " -0.019 2.00e-02 2.50e+03 ... (remaining 8421 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 15006 2.83 - 3.35: 39029 3.35 - 3.86: 77998 3.86 - 4.38: 88805 4.38 - 4.90: 155308 Nonbonded interactions: 376146 Sorted by model distance: nonbonded pdb=" O THR k 75 " pdb=" OG1 THR k 75 " model vdw 2.311 2.440 nonbonded pdb=" O THR b 75 " pdb=" OG1 THR b 75 " model vdw 2.311 2.440 nonbonded pdb=" O THR f 75 " pdb=" OG1 THR f 75 " model vdw 2.311 2.440 nonbonded pdb=" O THR c 75 " pdb=" OG1 THR c 75 " model vdw 2.311 2.440 nonbonded pdb=" O THR d 75 " pdb=" OG1 THR d 75 " model vdw 2.311 2.440 ... (remaining 376141 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 6.600 Check model and map are aligned: 0.670 Set scattering table: 0.390 Process input model: 114.420 Find NCS groups from input model: 3.230 Set up NCS constraints: 0.440 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 47784 Z= 0.489 Angle : 0.957 10.718 65136 Z= 0.513 Chirality : 0.057 0.286 7428 Planarity : 0.007 0.057 8424 Dihedral : 15.441 89.140 17148 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.83 % Favored : 95.97 % Rotamer: Outliers : 4.01 % Allowed : 11.65 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.08), residues: 5952 helix: -4.13 (0.06), residues: 1536 sheet: -0.97 (0.13), residues: 1452 loop : -2.29 (0.08), residues: 2964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 165 PHE 0.042 0.003 PHE C 269 TYR 0.015 0.002 TYR K 158 ARG 0.005 0.001 ARG A 261 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1688 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1484 time to evaluate : 5.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ILE cc_start: 0.8939 (mt) cc_final: 0.8726 (mm) REVERT: A 35 ASP cc_start: 0.7490 (p0) cc_final: 0.7201 (p0) REVERT: A 54 ASP cc_start: 0.8232 (t0) cc_final: 0.8032 (t0) REVERT: A 212 LEU cc_start: 0.8852 (tt) cc_final: 0.8605 (tm) REVERT: A 264 LYS cc_start: 0.8041 (mttt) cc_final: 0.7810 (tptt) REVERT: A 325 ASP cc_start: 0.7551 (m-30) cc_final: 0.7314 (m-30) REVERT: A 332 LYS cc_start: 0.8541 (mttp) cc_final: 0.8283 (mtpm) REVERT: B 15 LEU cc_start: 0.8564 (pp) cc_final: 0.8104 (pp) REVERT: B 24 ASN cc_start: 0.8045 (m-40) cc_final: 0.7819 (m-40) REVERT: B 41 ILE cc_start: 0.8500 (pt) cc_final: 0.8271 (pt) REVERT: B 54 ASP cc_start: 0.7986 (t0) cc_final: 0.7715 (t0) REVERT: B 87 LYS cc_start: 0.8226 (mttt) cc_final: 0.7924 (tppt) REVERT: B 103 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8772 (mt) REVERT: B 112 LYS cc_start: 0.8466 (mttp) cc_final: 0.7685 (ttmt) REVERT: B 195 ASN cc_start: 0.8254 (p0) cc_final: 0.7573 (t0) REVERT: B 243 ASP cc_start: 0.7357 (t0) cc_final: 0.7102 (t70) REVERT: B 325 ASP cc_start: 0.7680 (m-30) cc_final: 0.7432 (m-30) REVERT: B 332 LYS cc_start: 0.8300 (mttp) cc_final: 0.8003 (mtpp) REVERT: C 54 ASP cc_start: 0.8031 (t0) cc_final: 0.7809 (m-30) REVERT: C 67 LYS cc_start: 0.8215 (ttmt) cc_final: 0.7996 (ttmt) REVERT: C 112 LYS cc_start: 0.8435 (mttp) cc_final: 0.8132 (ttmt) REVERT: C 116 ASP cc_start: 0.8236 (m-30) cc_final: 0.7985 (m-30) REVERT: C 195 ASN cc_start: 0.7993 (p0) cc_final: 0.7405 (t0) REVERT: C 203 GLU cc_start: 0.7735 (pt0) cc_final: 0.7528 (pt0) REVERT: C 212 LEU cc_start: 0.8755 (tt) cc_final: 0.8519 (tp) REVERT: C 325 ASP cc_start: 0.7563 (m-30) cc_final: 0.7124 (m-30) REVERT: C 332 LYS cc_start: 0.8403 (mttp) cc_final: 0.8087 (mtpp) REVERT: D 40 TYR cc_start: 0.7862 (m-80) cc_final: 0.7621 (m-80) REVERT: D 54 ASP cc_start: 0.7989 (t0) cc_final: 0.7740 (t0) REVERT: D 117 VAL cc_start: 0.8238 (m) cc_final: 0.8007 (p) REVERT: D 212 LEU cc_start: 0.8756 (tt) cc_final: 0.8376 (tm) REVERT: D 281 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7418 (mm-30) REVERT: D 332 LYS cc_start: 0.8540 (mttp) cc_final: 0.8254 (mtpp) REVERT: E 15 LEU cc_start: 0.8602 (pp) cc_final: 0.8284 (pp) REVERT: E 24 ASN cc_start: 0.8109 (m-40) cc_final: 0.7863 (m-40) REVERT: E 35 ASP cc_start: 0.7497 (p0) cc_final: 0.7147 (p0) REVERT: E 41 ILE cc_start: 0.8528 (pt) cc_final: 0.8285 (pt) REVERT: E 54 ASP cc_start: 0.7979 (t0) cc_final: 0.7366 (m-30) REVERT: E 103 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8668 (mt) REVERT: E 130 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: E 195 ASN cc_start: 0.8092 (p0) cc_final: 0.7602 (t0) REVERT: E 212 LEU cc_start: 0.8811 (tt) cc_final: 0.8560 (tm) REVERT: E 325 ASP cc_start: 0.7730 (m-30) cc_final: 0.7363 (m-30) REVERT: E 332 LYS cc_start: 0.8481 (mttp) cc_final: 0.8218 (mtpp) REVERT: F 67 LYS cc_start: 0.8334 (ttmt) cc_final: 0.8124 (tttt) REVERT: F 112 LYS cc_start: 0.8369 (mttp) cc_final: 0.8095 (ttmt) REVERT: F 182 SER cc_start: 0.8871 (t) cc_final: 0.8285 (p) REVERT: F 195 ASN cc_start: 0.7969 (p0) cc_final: 0.7627 (t0) REVERT: F 203 GLU cc_start: 0.7837 (pt0) cc_final: 0.7622 (pt0) REVERT: F 325 ASP cc_start: 0.7618 (m-30) cc_final: 0.7150 (m-30) REVERT: F 332 LYS cc_start: 0.8412 (mttp) cc_final: 0.8176 (mtpp) REVERT: G 15 LEU cc_start: 0.8392 (pp) cc_final: 0.7612 (pp) REVERT: G 100 ASP cc_start: 0.7620 (p0) cc_final: 0.6888 (p0) REVERT: G 117 VAL cc_start: 0.8482 (m) cc_final: 0.8261 (p) REVERT: G 167 ASN cc_start: 0.8119 (t0) cc_final: 0.7716 (m-40) REVERT: G 175 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8951 (t) REVERT: H 40 TYR cc_start: 0.7705 (m-80) cc_final: 0.7424 (m-80) REVERT: H 87 LYS cc_start: 0.8024 (mttt) cc_final: 0.7808 (mttp) REVERT: H 100 ASP cc_start: 0.7497 (p0) cc_final: 0.7104 (p0) REVERT: H 113 THR cc_start: 0.8323 (p) cc_final: 0.8083 (m) REVERT: H 130 ASP cc_start: 0.7829 (OUTLIER) cc_final: 0.7547 (m-30) REVERT: H 162 LYS cc_start: 0.8542 (pttt) cc_final: 0.8326 (pttm) REVERT: H 195 ASN cc_start: 0.8329 (p0) cc_final: 0.8032 (t0) REVERT: I 54 ASP cc_start: 0.7774 (t0) cc_final: 0.7520 (m-30) REVERT: I 112 LYS cc_start: 0.8518 (mttp) cc_final: 0.8206 (mttm) REVERT: I 117 VAL cc_start: 0.8384 (m) cc_final: 0.8174 (p) REVERT: I 130 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7407 (m-30) REVERT: I 145 LYS cc_start: 0.8298 (mtmt) cc_final: 0.8070 (mtmm) REVERT: I 195 ASN cc_start: 0.8262 (p0) cc_final: 0.7901 (t0) REVERT: J 35 ASP cc_start: 0.7328 (p0) cc_final: 0.6890 (p0) REVERT: J 117 VAL cc_start: 0.8216 (m) cc_final: 0.8011 (p) REVERT: J 130 ASP cc_start: 0.7743 (OUTLIER) cc_final: 0.7287 (m-30) REVERT: J 167 ASN cc_start: 0.8095 (t0) cc_final: 0.7888 (m110) REVERT: J 176 MET cc_start: 0.8632 (mmm) cc_final: 0.8399 (mmm) REVERT: K 40 TYR cc_start: 0.7698 (m-80) cc_final: 0.7477 (m-80) REVERT: K 103 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8477 (mt) REVERT: K 167 ASN cc_start: 0.8194 (t0) cc_final: 0.7862 (m-40) REVERT: K 261 ARG cc_start: 0.7246 (ttt180) cc_final: 0.7037 (ttm110) REVERT: L 67 LYS cc_start: 0.8342 (ttmt) cc_final: 0.8057 (ttpt) REVERT: L 100 ASP cc_start: 0.7716 (p0) cc_final: 0.7466 (p0) REVERT: L 145 LYS cc_start: 0.8471 (mtmt) cc_final: 0.8030 (mtmm) REVERT: L 167 ASN cc_start: 0.8351 (t0) cc_final: 0.7924 (m-40) REVERT: L 195 ASN cc_start: 0.8097 (p0) cc_final: 0.7776 (t0) REVERT: a 55 MET cc_start: 0.8476 (mtm) cc_final: 0.8014 (mtt) REVERT: b 93 ASP cc_start: 0.7709 (m-30) cc_final: 0.7355 (m-30) REVERT: c 34 SER cc_start: 0.8441 (t) cc_final: 0.8231 (m) REVERT: d 55 MET cc_start: 0.8559 (mtm) cc_final: 0.8216 (mtp) REVERT: d 105 GLU cc_start: 0.7501 (tp30) cc_final: 0.7130 (tp30) REVERT: e 93 ASP cc_start: 0.7523 (m-30) cc_final: 0.7225 (m-30) REVERT: g 88 GLN cc_start: 0.8358 (mt0) cc_final: 0.8075 (mt0) REVERT: g 143 ARG cc_start: 0.7370 (ttt-90) cc_final: 0.6454 (ttt180) REVERT: i 6 SER cc_start: 0.8811 (p) cc_final: 0.8524 (t) REVERT: i 143 ARG cc_start: 0.7244 (ttt-90) cc_final: 0.6367 (ttt180) REVERT: l 6 SER cc_start: 0.8821 (p) cc_final: 0.8563 (t) REVERT: l 88 GLN cc_start: 0.8330 (mt0) cc_final: 0.8001 (mt0) REVERT: l 143 ARG cc_start: 0.7283 (ttt-90) cc_final: 0.6380 (ttt180) outliers start: 204 outliers final: 34 residues processed: 1612 average time/residue: 1.3934 time to fit residues: 2832.3985 Evaluate side-chains 927 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 885 time to evaluate : 5.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 202 LEU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain l residue 16 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 496 optimal weight: 3.9990 chunk 445 optimal weight: 2.9990 chunk 247 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 300 optimal weight: 8.9990 chunk 238 optimal weight: 0.9990 chunk 460 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 280 optimal weight: 20.0000 chunk 343 optimal weight: 1.9990 chunk 533 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 289 ASN A 296 GLN B 16 ASN B 213 GLN B 289 ASN B 296 GLN C 289 ASN C 296 GLN C 321 GLN D 16 ASN D 167 ASN D 289 ASN D 296 GLN D 321 GLN E 16 ASN E 78 ASN E 167 ASN E 289 ASN E 296 GLN E 321 GLN F 213 GLN F 289 ASN F 296 GLN F 321 GLN G 16 ASN G 195 ASN G 213 GLN G 289 ASN G 296 GLN H 16 ASN H 78 ASN H 213 GLN H 289 ASN H 296 GLN H 321 GLN I 37 GLN I 78 ASN I 213 GLN I 289 ASN I 296 GLN I 321 GLN J 16 ASN J 78 ASN J 146 GLN J 213 GLN J 230 ASN J 289 ASN J 296 GLN ** J 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN K 78 ASN K 195 ASN K 213 GLN K 289 ASN K 296 GLN K 321 GLN L 16 ASN L 78 ASN L 213 GLN L 289 ASN L 296 GLN L 321 GLN a 7 GLN a 114 ASN b 7 GLN b 60 GLN b 114 ASN c 7 GLN c 58 GLN c 114 ASN d 7 GLN d 111 ASN d 114 ASN e 7 GLN e 60 GLN e 114 ASN f 7 GLN f 60 GLN f 114 ASN g 31 ASN g 58 GLN g 60 GLN g 130 ASN h 7 GLN h 31 ASN h 60 GLN h 130 ASN h 147 GLN i 7 GLN i 31 ASN i 60 GLN i 130 ASN j 31 ASN j 58 GLN j 60 GLN j 63 ASN j 130 ASN k 7 GLN k 60 GLN k 130 ASN l 31 ASN l 60 GLN l 130 ASN Total number of N/Q/H flips: 103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 47784 Z= 0.180 Angle : 0.615 10.537 65136 Z= 0.315 Chirality : 0.045 0.216 7428 Planarity : 0.004 0.033 8424 Dihedral : 6.319 48.001 6489 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.26 % Favored : 96.64 % Rotamer: Outliers : 5.86 % Allowed : 19.81 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.09), residues: 5952 helix: -2.01 (0.10), residues: 1512 sheet: -0.10 (0.14), residues: 1344 loop : -2.10 (0.08), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP H 190 PHE 0.025 0.002 PHE E 269 TYR 0.011 0.001 TYR G 157 ARG 0.007 0.001 ARG A 187 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 974 time to evaluate : 5.543 Fit side-chains revert: symmetry clash REVERT: A 212 LEU cc_start: 0.8918 (tt) cc_final: 0.8704 (tm) REVERT: B 24 ASN cc_start: 0.8116 (m-40) cc_final: 0.7834 (m-40) REVERT: B 54 ASP cc_start: 0.7924 (t0) cc_final: 0.7450 (m-30) REVERT: B 112 LYS cc_start: 0.8306 (mttp) cc_final: 0.8018 (ttmt) REVERT: B 130 ASP cc_start: 0.7731 (OUTLIER) cc_final: 0.7133 (m-30) REVERT: B 325 ASP cc_start: 0.7590 (m-30) cc_final: 0.6904 (m-30) REVERT: C 130 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7291 (m-30) REVERT: C 146 GLN cc_start: 0.7862 (tp40) cc_final: 0.7600 (tp40) REVERT: C 195 ASN cc_start: 0.7678 (p0) cc_final: 0.7420 (t0) REVERT: C 325 ASP cc_start: 0.7302 (m-30) cc_final: 0.6608 (m-30) REVERT: D 195 ASN cc_start: 0.7585 (p0) cc_final: 0.7110 (t0) REVERT: D 212 LEU cc_start: 0.8855 (tt) cc_final: 0.8612 (tm) REVERT: D 281 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7449 (mm-30) REVERT: E 24 ASN cc_start: 0.8172 (m-40) cc_final: 0.7847 (m-40) REVERT: E 54 ASP cc_start: 0.7967 (t0) cc_final: 0.7466 (m-30) REVERT: E 212 LEU cc_start: 0.8818 (tt) cc_final: 0.8590 (tm) REVERT: E 321 GLN cc_start: 0.8097 (tp40) cc_final: 0.7794 (tp40) REVERT: E 325 ASP cc_start: 0.7334 (m-30) cc_final: 0.6873 (m-30) REVERT: F 203 GLU cc_start: 0.7678 (pt0) cc_final: 0.7306 (mt-10) REVERT: F 212 LEU cc_start: 0.8648 (tt) cc_final: 0.8400 (tm) REVERT: F 325 ASP cc_start: 0.7459 (m-30) cc_final: 0.6791 (m-30) REVERT: G 100 ASP cc_start: 0.7733 (p0) cc_final: 0.7341 (p0) REVERT: G 130 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7123 (m-30) REVERT: G 142 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: G 167 ASN cc_start: 0.7934 (t0) cc_final: 0.7693 (m-40) REVERT: G 195 ASN cc_start: 0.8048 (OUTLIER) cc_final: 0.7531 (t0) REVERT: G 226 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8279 (ptm-80) REVERT: H 40 TYR cc_start: 0.7707 (m-80) cc_final: 0.7459 (m-80) REVERT: H 53 MET cc_start: 0.8440 (ttp) cc_final: 0.8215 (ttp) REVERT: H 130 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7295 (m-30) REVERT: H 136 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6079 (pp) REVERT: H 176 MET cc_start: 0.8453 (mmm) cc_final: 0.8237 (mmm) REVERT: H 195 ASN cc_start: 0.8255 (p0) cc_final: 0.7777 (t0) REVERT: H 211 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: I 54 ASP cc_start: 0.7685 (t0) cc_final: 0.7441 (m-30) REVERT: I 130 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7262 (m-30) REVERT: I 136 LEU cc_start: 0.5953 (OUTLIER) cc_final: 0.5343 (pp) REVERT: I 182 SER cc_start: 0.8870 (t) cc_final: 0.8575 (p) REVERT: I 195 ASN cc_start: 0.7977 (p0) cc_final: 0.7695 (t0) REVERT: I 211 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7558 (pm20) REVERT: I 224 MET cc_start: 0.8363 (mtt) cc_final: 0.7732 (mtt) REVERT: I 312 GLN cc_start: 0.8814 (mt0) cc_final: 0.8498 (mt0) REVERT: J 130 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7353 (m-30) REVERT: J 182 SER cc_start: 0.8924 (t) cc_final: 0.8484 (p) REVERT: K 40 TYR cc_start: 0.7670 (m-80) cc_final: 0.7365 (m-80) REVERT: K 167 ASN cc_start: 0.8239 (t0) cc_final: 0.7981 (m-40) REVERT: K 195 ASN cc_start: 0.8183 (OUTLIER) cc_final: 0.7390 (t0) REVERT: K 261 ARG cc_start: 0.7088 (ttt180) cc_final: 0.6811 (ttm110) REVERT: K 282 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7674 (mtp85) REVERT: L 136 LEU cc_start: 0.6314 (OUTLIER) cc_final: 0.5831 (pp) REVERT: L 149 THR cc_start: 0.6950 (OUTLIER) cc_final: 0.6371 (p) REVERT: L 167 ASN cc_start: 0.8369 (t0) cc_final: 0.8014 (m-40) REVERT: L 211 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7297 (pm20) REVERT: L 212 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8896 (tm) REVERT: L 244 LYS cc_start: 0.8033 (mmmm) cc_final: 0.7776 (mmmm) REVERT: a 64 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7930 (tt) REVERT: b 93 ASP cc_start: 0.7697 (m-30) cc_final: 0.7341 (m-30) REVERT: b 126 ASP cc_start: 0.8225 (t0) cc_final: 0.7945 (t0) REVERT: b 147 GLN cc_start: 0.7550 (mm-40) cc_final: 0.7306 (tp-100) REVERT: c 58 GLN cc_start: 0.8565 (tt0) cc_final: 0.8344 (mt0) REVERT: c 88 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7757 (mt0) REVERT: e 11 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7112 (mp0) REVERT: e 90 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: e 93 ASP cc_start: 0.7612 (m-30) cc_final: 0.7329 (m-30) REVERT: j 6 SER cc_start: 0.8849 (p) cc_final: 0.8570 (t) REVERT: j 58 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8296 (mm-40) REVERT: l 6 SER cc_start: 0.8759 (p) cc_final: 0.8486 (t) REVERT: l 126 ASP cc_start: 0.8231 (t0) cc_final: 0.7923 (t0) outliers start: 298 outliers final: 107 residues processed: 1169 average time/residue: 1.2743 time to fit residues: 1921.1571 Evaluate side-chains 906 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 776 time to evaluate : 4.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain F residue 4 VAL Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 93 LYS Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 146 GLN Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 209 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 282 ARG Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 149 THR Chi-restraints excluded: chain L residue 169 ASP Chi-restraints excluded: chain L residue 211 GLU Chi-restraints excluded: chain L residue 212 LEU Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 305 GLU Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 75 THR Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 90 GLU Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 49 VAL Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 140 MET Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 58 GLN Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 95 THR Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain k residue 3 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 296 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 444 optimal weight: 10.0000 chunk 363 optimal weight: 20.0000 chunk 147 optimal weight: 10.0000 chunk 534 optimal weight: 0.9990 chunk 577 optimal weight: 8.9990 chunk 476 optimal weight: 9.9990 chunk 530 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 429 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 213 GLN D 321 GLN E 16 ASN E 78 ASN E 213 GLN G 16 ASN G 195 ASN G 227 ASN G 230 ASN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 296 GLN I 296 GLN I 321 GLN J 16 ASN ** J 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN J 230 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 296 GLN K 321 GLN L 16 ASN L 37 GLN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 321 GLN a 60 GLN b 60 GLN c 31 ASN c 60 GLN d 31 ASN e 60 GLN f 31 ASN g 31 ASN g 114 ASN h 7 GLN h 114 ASN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 114 ASN j 114 ASN k 63 ASN k 114 ASN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 114 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.079 47784 Z= 0.499 Angle : 0.722 13.755 65136 Z= 0.373 Chirality : 0.052 0.245 7428 Planarity : 0.005 0.048 8424 Dihedral : 6.541 53.500 6476 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.88 % Favored : 95.83 % Rotamer: Outliers : 7.45 % Allowed : 20.03 % Favored : 72.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.09), residues: 5952 helix: -0.74 (0.12), residues: 1464 sheet: -0.02 (0.13), residues: 1452 loop : -2.08 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 190 PHE 0.029 0.003 PHE B 129 TYR 0.013 0.002 TYR D 82 ARG 0.008 0.001 ARG a 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 379 poor density : 863 time to evaluate : 5.425 Fit side-chains REVERT: A 87 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.8151 (tppt) REVERT: A 129 PHE cc_start: 0.8070 (OUTLIER) cc_final: 0.7323 (p90) REVERT: A 130 ASP cc_start: 0.8370 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: A 229 SER cc_start: 0.8267 (p) cc_final: 0.8037 (m) REVERT: B 24 ASN cc_start: 0.8146 (m-40) cc_final: 0.7897 (m-40) REVERT: B 54 ASP cc_start: 0.8050 (t0) cc_final: 0.7801 (m-30) REVERT: B 112 LYS cc_start: 0.8334 (mttp) cc_final: 0.8083 (ttmt) REVERT: B 130 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.7913 (m-30) REVERT: B 224 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (mtt) REVERT: B 269 PHE cc_start: 0.8645 (p90) cc_final: 0.8411 (p90) REVERT: B 273 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: B 325 ASP cc_start: 0.7503 (m-30) cc_final: 0.7062 (m-30) REVERT: C 15 LEU cc_start: 0.8423 (OUTLIER) cc_final: 0.8196 (pt) REVERT: C 43 GLU cc_start: 0.7582 (mp0) cc_final: 0.7226 (mp0) REVERT: C 112 LYS cc_start: 0.8397 (mttp) cc_final: 0.7943 (ttmt) REVERT: C 146 GLN cc_start: 0.7945 (tp40) cc_final: 0.7729 (tp40) REVERT: C 195 ASN cc_start: 0.7999 (p0) cc_final: 0.7468 (t0) REVERT: C 242 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7357 (tp30) REVERT: C 244 LYS cc_start: 0.8141 (mtmm) cc_final: 0.7852 (mtpt) REVERT: C 325 ASP cc_start: 0.7348 (m-30) cc_final: 0.6928 (m-30) REVERT: D 67 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.7772 (ttpt) REVERT: D 129 PHE cc_start: 0.8050 (OUTLIER) cc_final: 0.7189 (p90) REVERT: D 224 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.7566 (mtt) REVERT: D 281 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7630 (mm-30) REVERT: E 24 ASN cc_start: 0.8228 (m-40) cc_final: 0.7963 (m-40) REVERT: E 54 ASP cc_start: 0.7929 (t0) cc_final: 0.7691 (m-30) REVERT: E 129 PHE cc_start: 0.8109 (OUTLIER) cc_final: 0.7341 (p90) REVERT: F 203 GLU cc_start: 0.7744 (pt0) cc_final: 0.7363 (mt-10) REVERT: F 242 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: F 269 PHE cc_start: 0.8611 (p90) cc_final: 0.8344 (p90) REVERT: F 282 ARG cc_start: 0.8770 (OUTLIER) cc_final: 0.7900 (mtp85) REVERT: F 325 ASP cc_start: 0.7357 (m-30) cc_final: 0.6926 (m-30) REVERT: G 66 ASP cc_start: 0.7693 (t0) cc_final: 0.7416 (t0) REVERT: G 130 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: G 146 GLN cc_start: 0.8122 (tt0) cc_final: 0.7887 (mm-40) REVERT: G 167 ASN cc_start: 0.8010 (t0) cc_final: 0.7775 (m110) REVERT: G 224 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.7406 (mtt) REVERT: G 226 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8412 (ptm160) REVERT: G 244 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7826 (mmmm) REVERT: G 269 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.8512 (p90) REVERT: H 40 TYR cc_start: 0.7714 (m-80) cc_final: 0.7339 (m-80) REVERT: H 53 MET cc_start: 0.8276 (ttp) cc_final: 0.8037 (ttp) REVERT: H 66 ASP cc_start: 0.7712 (t0) cc_final: 0.7356 (t70) REVERT: H 130 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8077 (m-30) REVERT: H 176 MET cc_start: 0.8556 (mmm) cc_final: 0.8338 (mmm) REVERT: H 195 ASN cc_start: 0.8262 (p0) cc_final: 0.7827 (t0) REVERT: H 203 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6695 (mp0) REVERT: H 211 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7341 (pm20) REVERT: H 224 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7112 (mtt) REVERT: H 226 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8116 (ptm160) REVERT: I 66 ASP cc_start: 0.7940 (t0) cc_final: 0.7632 (t0) REVERT: I 130 ASP cc_start: 0.8369 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: I 136 LEU cc_start: 0.6886 (OUTLIER) cc_final: 0.6236 (pp) REVERT: I 195 ASN cc_start: 0.7979 (p0) cc_final: 0.7679 (t0) REVERT: I 211 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: J 54 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7549 (t0) REVERT: J 66 ASP cc_start: 0.7604 (t0) cc_final: 0.7353 (t0) REVERT: J 129 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7572 (p90) REVERT: J 130 ASP cc_start: 0.8444 (OUTLIER) cc_final: 0.7803 (m-30) REVERT: K 40 TYR cc_start: 0.7764 (m-80) cc_final: 0.7503 (m-80) REVERT: K 66 ASP cc_start: 0.7745 (t0) cc_final: 0.7424 (t70) REVERT: K 167 ASN cc_start: 0.8215 (t0) cc_final: 0.7896 (m-40) REVERT: K 195 ASN cc_start: 0.8102 (p0) cc_final: 0.7880 (t0) REVERT: K 224 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7171 (mtt) REVERT: K 261 ARG cc_start: 0.7078 (ttt180) cc_final: 0.6843 (ttm110) REVERT: K 282 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8085 (mtp85) REVERT: L 136 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6647 (pp) REVERT: L 167 ASN cc_start: 0.8314 (t0) cc_final: 0.7993 (m-40) REVERT: L 211 GLU cc_start: 0.7677 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: L 224 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7711 (mtt) REVERT: L 304 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7768 (ttmm) REVERT: a 90 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: a 126 ASP cc_start: 0.8289 (t0) cc_final: 0.7996 (t0) REVERT: b 93 ASP cc_start: 0.7709 (m-30) cc_final: 0.7376 (m-30) REVERT: c 28 ILE cc_start: 0.8266 (OUTLIER) cc_final: 0.7696 (mt) REVERT: c 140 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7932 (tpp) REVERT: d 11 GLU cc_start: 0.7481 (mt-10) cc_final: 0.7187 (mp0) REVERT: e 11 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7297 (mp0) REVERT: e 93 ASP cc_start: 0.7712 (m-30) cc_final: 0.7377 (m-30) REVERT: f 28 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7678 (mt) REVERT: f 44 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: g 143 ARG cc_start: 0.7664 (ttt-90) cc_final: 0.6554 (ttt180) REVERT: h 28 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7917 (pt) REVERT: i 142 ASP cc_start: 0.7840 (OUTLIER) cc_final: 0.7545 (p0) REVERT: i 143 ARG cc_start: 0.7571 (ttt-90) cc_final: 0.6458 (ttt180) REVERT: j 143 ARG cc_start: 0.7594 (ttt-90) cc_final: 0.6575 (ttt180) REVERT: k 51 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.7963 (p0) REVERT: l 142 ASP cc_start: 0.7830 (OUTLIER) cc_final: 0.7543 (p0) REVERT: l 143 ARG cc_start: 0.7650 (ttt-90) cc_final: 0.6509 (ttt180) outliers start: 379 outliers final: 194 residues processed: 1121 average time/residue: 1.2799 time to fit residues: 1846.4290 Evaluate side-chains 1000 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 761 time to evaluate : 5.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 87 LYS Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 319 MET Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 185 LEU Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain C residue 16 ASN Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 224 MET Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 319 MET Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 185 LEU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 313 ILE Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 13 GLU Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 224 MET Chi-restraints excluded: chain G residue 226 ARG Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 269 PHE Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 93 LYS Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 185 LEU Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 226 ARG Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 185 LEU Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 282 ARG Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 211 GLU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 320 THR Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain a residue 90 GLU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 101 ASP Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 75 THR Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 140 MET Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 20 ILE Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 119 SER Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 75 THR Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 88 GLN Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 28 ILE Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 49 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain i residue 142 ASP Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 95 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 51 ASN Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 49 VAL Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 142 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 528 optimal weight: 4.9990 chunk 402 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 255 optimal weight: 5.9990 chunk 359 optimal weight: 5.9990 chunk 536 optimal weight: 1.9990 chunk 568 optimal weight: 2.9990 chunk 280 optimal weight: 7.9990 chunk 508 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN G 230 ASN G 296 GLN ** H 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN J 230 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN a 31 ASN a 111 ASN b 31 ASN e 60 GLN f 60 GLN g 31 ASN h 7 GLN h 147 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 58 GLN j 31 ASN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 47784 Z= 0.294 Angle : 0.624 11.381 65136 Z= 0.318 Chirality : 0.047 0.240 7428 Planarity : 0.004 0.042 8424 Dihedral : 6.119 53.895 6476 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer: Outliers : 6.92 % Allowed : 21.56 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 5952 helix: -0.17 (0.13), residues: 1464 sheet: 0.12 (0.13), residues: 1452 loop : -2.04 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 165 PHE 0.019 0.002 PHE E 269 TYR 0.011 0.001 TYR H 82 ARG 0.009 0.001 ARG K 265 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1182 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 830 time to evaluate : 5.587 Fit side-chains REVERT: A 129 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7182 (p90) REVERT: A 130 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: A 136 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6650 (pp) REVERT: A 148 TYR cc_start: 0.8058 (m-80) cc_final: 0.7840 (m-80) REVERT: A 212 LEU cc_start: 0.8859 (tt) cc_final: 0.8657 (tp) REVERT: B 24 ASN cc_start: 0.8141 (m-40) cc_final: 0.7843 (m-40) REVERT: B 112 LYS cc_start: 0.8316 (mttp) cc_final: 0.8029 (ttmt) REVERT: B 129 PHE cc_start: 0.8003 (OUTLIER) cc_final: 0.7386 (p90) REVERT: B 130 ASP cc_start: 0.8442 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: B 224 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8109 (mtt) REVERT: B 269 PHE cc_start: 0.8560 (p90) cc_final: 0.8216 (p90) REVERT: B 273 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.6898 (mp0) REVERT: B 325 ASP cc_start: 0.7445 (m-30) cc_final: 0.7121 (m-30) REVERT: C 43 GLU cc_start: 0.7606 (mp0) cc_final: 0.7287 (mp0) REVERT: C 146 GLN cc_start: 0.7966 (tp40) cc_final: 0.7754 (tp40) REVERT: C 195 ASN cc_start: 0.7973 (p0) cc_final: 0.7648 (t0) REVERT: C 242 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7371 (tp30) REVERT: C 244 LYS cc_start: 0.8081 (mtmm) cc_final: 0.7789 (mtpt) REVERT: C 325 ASP cc_start: 0.7349 (m-30) cc_final: 0.6908 (m-30) REVERT: D 43 GLU cc_start: 0.7607 (mp0) cc_final: 0.7396 (mt-10) REVERT: D 67 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7738 (ttmt) REVERT: D 129 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7428 (p90) REVERT: D 195 ASN cc_start: 0.7539 (p0) cc_final: 0.7221 (t0) REVERT: D 229 SER cc_start: 0.8294 (p) cc_final: 0.8060 (m) REVERT: E 24 ASN cc_start: 0.8236 (m-40) cc_final: 0.7944 (m-40) REVERT: E 54 ASP cc_start: 0.7789 (t0) cc_final: 0.7583 (m-30) REVERT: E 129 PHE cc_start: 0.8061 (OUTLIER) cc_final: 0.7334 (p90) REVERT: E 224 MET cc_start: 0.8388 (OUTLIER) cc_final: 0.8138 (mtt) REVERT: E 325 ASP cc_start: 0.7479 (m-30) cc_final: 0.7159 (m-30) REVERT: F 203 GLU cc_start: 0.7660 (pt0) cc_final: 0.7314 (mt-10) REVERT: F 242 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: F 271 MET cc_start: 0.8945 (mmm) cc_final: 0.8705 (mmm) REVERT: F 273 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6960 (mp0) REVERT: F 325 ASP cc_start: 0.7377 (m-30) cc_final: 0.6963 (m-30) REVERT: G 66 ASP cc_start: 0.7873 (t0) cc_final: 0.7548 (t0) REVERT: G 118 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8150 (tt) REVERT: G 130 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7539 (m-30) REVERT: G 146 GLN cc_start: 0.8156 (tt0) cc_final: 0.7906 (mm-40) REVERT: G 167 ASN cc_start: 0.7960 (t0) cc_final: 0.7759 (m110) REVERT: G 244 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7733 (mmmm) REVERT: H 40 TYR cc_start: 0.7582 (m-80) cc_final: 0.7246 (m-80) REVERT: H 66 ASP cc_start: 0.7734 (t0) cc_final: 0.7393 (t70) REVERT: H 130 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: H 176 MET cc_start: 0.8571 (mmm) cc_final: 0.8338 (mmm) REVERT: H 195 ASN cc_start: 0.8064 (p0) cc_final: 0.7829 (t0) REVERT: H 203 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: H 211 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7417 (pm20) REVERT: H 224 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7025 (mtt) REVERT: I 66 ASP cc_start: 0.8006 (t0) cc_final: 0.7668 (t0) REVERT: I 130 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: I 136 LEU cc_start: 0.7216 (OUTLIER) cc_final: 0.6436 (pp) REVERT: I 182 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8787 (p) REVERT: I 211 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7533 (pm20) REVERT: I 224 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: J 54 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7588 (t0) REVERT: J 66 ASP cc_start: 0.7625 (t0) cc_final: 0.7378 (t0) REVERT: J 130 ASP cc_start: 0.8307 (OUTLIER) cc_final: 0.7589 (m-30) REVERT: K 40 TYR cc_start: 0.7626 (m-80) cc_final: 0.7393 (m-80) REVERT: K 66 ASP cc_start: 0.7793 (t0) cc_final: 0.7493 (t70) REVERT: K 149 THR cc_start: 0.7606 (t) cc_final: 0.7333 (m) REVERT: K 224 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7035 (mtt) REVERT: K 261 ARG cc_start: 0.7165 (ttt180) cc_final: 0.6911 (ttm110) REVERT: L 42 SER cc_start: 0.8063 (OUTLIER) cc_final: 0.7728 (p) REVERT: L 130 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: L 136 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6633 (pp) REVERT: L 167 ASN cc_start: 0.8299 (t0) cc_final: 0.8058 (m-40) REVERT: L 211 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7306 (pm20) REVERT: L 224 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7742 (mtt) REVERT: L 304 LYS cc_start: 0.8136 (OUTLIER) cc_final: 0.7779 (ttmm) REVERT: a 90 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7367 (tt0) REVERT: b 93 ASP cc_start: 0.7717 (m-30) cc_final: 0.7413 (m-30) REVERT: c 28 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7746 (mt) REVERT: d 11 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7102 (mp0) REVERT: e 93 ASP cc_start: 0.7719 (m-30) cc_final: 0.7413 (m-30) REVERT: f 28 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7844 (mt) REVERT: g 27 LYS cc_start: 0.8663 (ptmm) cc_final: 0.8158 (pttm) REVERT: g 140 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.7807 (ttm) REVERT: i 58 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8362 (mt0) REVERT: j 140 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7690 (ttm) REVERT: k 51 ASN cc_start: 0.8321 (OUTLIER) cc_final: 0.7951 (p0) REVERT: l 58 GLN cc_start: 0.8700 (mm110) cc_final: 0.8296 (mt0) outliers start: 352 outliers final: 176 residues processed: 1077 average time/residue: 1.3137 time to fit residues: 1815.3405 Evaluate side-chains 974 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 756 time to evaluate : 5.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 186 SER Chi-restraints excluded: chain B residue 209 THR Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 234 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 185 LEU Chi-restraints excluded: chain D residue 209 THR Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 234 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 16 ASN Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 61 ASN Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 71 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 134 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 13 GLU Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 134 THR Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 203 GLU Chi-restraints excluded: chain H residue 211 GLU Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 134 THR Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 189 VAL Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 130 ASP Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 169 ASP Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 211 GLU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 90 GLU Chi-restraints excluded: chain b residue 5 THR Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 75 THR Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 88 GLN Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 58 GLN Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 49 VAL Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 95 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 51 ASN Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 473 optimal weight: 0.6980 chunk 322 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 423 optimal weight: 3.9990 chunk 234 optimal weight: 0.0670 chunk 485 optimal weight: 0.5980 chunk 392 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 290 optimal weight: 4.9990 chunk 510 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.0720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 16 ASN G 227 ASN G 230 ASN G 296 GLN I 146 GLN J 195 ASN J 230 ASN ** J 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN b 60 GLN c 60 GLN e 60 GLN f 60 GLN g 31 ASN h 7 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 47784 Z= 0.157 Angle : 0.562 10.091 65136 Z= 0.283 Chirality : 0.044 0.193 7428 Planarity : 0.004 0.045 8424 Dihedral : 5.561 54.934 6476 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.82 % Allowed : 23.82 % Favored : 71.36 % 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: -1.19 (0.10), residues: 5952 helix: 0.29 (0.14), residues: 1464 sheet: 0.32 (0.14), residues: 1452 loop : -1.96 (0.09), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 165 PHE 0.022 0.001 PHE F 269 TYR 0.009 0.001 TYR H 157 ARG 0.010 0.000 ARG K 265 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 844 time to evaluate : 5.240 Fit side-chains REVERT: A 47 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.8094 (mm) REVERT: A 129 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7223 (p90) REVERT: A 212 LEU cc_start: 0.8743 (tt) cc_final: 0.8543 (tp) REVERT: B 24 ASN cc_start: 0.8151 (m-40) cc_final: 0.7851 (m-40) REVERT: B 130 ASP cc_start: 0.8240 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: B 224 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8111 (mtt) REVERT: B 325 ASP cc_start: 0.7374 (m-30) cc_final: 0.7015 (m-30) REVERT: C 43 GLU cc_start: 0.7474 (mp0) cc_final: 0.7226 (mp0) REVERT: C 66 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6516 (t0) REVERT: C 244 LYS cc_start: 0.7997 (mtmm) cc_final: 0.7730 (mtpt) REVERT: C 325 ASP cc_start: 0.7311 (m-30) cc_final: 0.6845 (m-30) REVERT: D 94 ILE cc_start: 0.8101 (mp) cc_final: 0.7862 (mm) REVERT: D 129 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7418 (p90) REVERT: D 229 SER cc_start: 0.8239 (p) cc_final: 0.8032 (m) REVERT: E 24 ASN cc_start: 0.8224 (m-40) cc_final: 0.7892 (m-40) REVERT: E 117 VAL cc_start: 0.8212 (m) cc_final: 0.7957 (p) REVERT: E 129 PHE cc_start: 0.7885 (OUTLIER) cc_final: 0.7001 (p90) REVERT: E 212 LEU cc_start: 0.8744 (tt) cc_final: 0.8498 (tm) REVERT: E 224 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8138 (mtt) REVERT: E 325 ASP cc_start: 0.7493 (m-30) cc_final: 0.7163 (m-30) REVERT: F 203 GLU cc_start: 0.7748 (pt0) cc_final: 0.7482 (mt-10) REVERT: F 242 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: F 271 MET cc_start: 0.8959 (mmm) cc_final: 0.8654 (mmm) REVERT: F 273 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: F 325 ASP cc_start: 0.7363 (m-30) cc_final: 0.6941 (m-30) REVERT: G 66 ASP cc_start: 0.7849 (t0) cc_final: 0.7490 (t0) REVERT: G 130 ASP cc_start: 0.8117 (OUTLIER) cc_final: 0.7416 (m-30) REVERT: G 146 GLN cc_start: 0.8151 (tt0) cc_final: 0.7847 (mm-40) REVERT: G 269 PHE cc_start: 0.8645 (p90) cc_final: 0.8345 (p90) REVERT: G 315 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7781 (tmmt) REVERT: H 40 TYR cc_start: 0.7559 (m-80) cc_final: 0.7239 (m-80) REVERT: H 130 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7664 (m-30) REVERT: H 211 GLU cc_start: 0.7681 (mp0) cc_final: 0.7449 (pm20) REVERT: I 54 ASP cc_start: 0.7768 (t0) cc_final: 0.7547 (t0) REVERT: I 66 ASP cc_start: 0.7977 (t0) cc_final: 0.7625 (t0) REVERT: I 130 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: I 136 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6240 (pp) REVERT: I 211 GLU cc_start: 0.7720 (mp0) cc_final: 0.7455 (pm20) REVERT: I 224 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.7634 (mtt) REVERT: J 54 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7595 (t0) REVERT: J 129 PHE cc_start: 0.7807 (OUTLIER) cc_final: 0.7326 (p90) REVERT: J 130 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: J 169 ASP cc_start: 0.7976 (m-30) cc_final: 0.7717 (m-30) REVERT: K 40 TYR cc_start: 0.7559 (m-80) cc_final: 0.7336 (m-80) REVERT: K 224 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: K 245 ASP cc_start: 0.7700 (m-30) cc_final: 0.7424 (m-30) REVERT: K 261 ARG cc_start: 0.7064 (ttt180) cc_final: 0.6860 (ttm110) REVERT: L 42 SER cc_start: 0.7984 (OUTLIER) cc_final: 0.7650 (p) REVERT: L 130 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7465 (m-30) REVERT: L 136 LEU cc_start: 0.7260 (OUTLIER) cc_final: 0.6538 (pp) REVERT: L 211 GLU cc_start: 0.7676 (mp0) cc_final: 0.7307 (pm20) REVERT: L 224 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7799 (mtt) REVERT: L 226 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8288 (ptm160) REVERT: L 304 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7813 (ttmm) REVERT: d 11 GLU cc_start: 0.7291 (mt-10) cc_final: 0.6832 (mp0) REVERT: f 44 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: g 140 MET cc_start: 0.8027 (OUTLIER) cc_final: 0.7526 (ttm) REVERT: i 140 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.7428 (ttm) REVERT: j 140 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7509 (ttm) REVERT: l 58 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8222 (mt0) REVERT: l 140 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7501 (ttm) outliers start: 245 outliers final: 121 residues processed: 1019 average time/residue: 1.3059 time to fit residues: 1716.5063 Evaluate side-chains 918 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 765 time to evaluate : 5.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ILE Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 130 ASP Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 273 GLU Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 322 GLU Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 226 ARG Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 64 ILE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain j residue 140 MET Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 58 GLN Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 191 optimal weight: 9.9990 chunk 511 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 333 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 568 optimal weight: 0.2980 chunk 472 optimal weight: 9.9990 chunk 263 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 188 optimal weight: 0.0770 chunk 298 optimal weight: 2.9990 overall best weight: 2.8744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 195 ASN G 16 ASN G 227 ASN G 230 ASN G 296 GLN H 78 ASN H 296 GLN I 146 GLN J 230 ASN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 58 GLN c 60 GLN e 60 GLN f 60 GLN g 31 ASN h 7 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN k 63 ASN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 47784 Z= 0.277 Angle : 0.610 11.348 65136 Z= 0.306 Chirality : 0.046 0.233 7428 Planarity : 0.004 0.033 8424 Dihedral : 5.711 56.520 6475 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.85 % Favored : 96.05 % Rotamer: Outliers : 5.70 % Allowed : 23.35 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.10), residues: 5952 helix: 0.51 (0.14), residues: 1440 sheet: 0.45 (0.14), residues: 1380 loop : -1.85 (0.09), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 165 PHE 0.021 0.002 PHE E 269 TYR 0.011 0.001 TYR e 17 ARG 0.007 0.000 ARG a 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 776 time to evaluate : 5.721 Fit side-chains REVERT: A 129 PHE cc_start: 0.8044 (OUTLIER) cc_final: 0.7426 (p90) REVERT: A 130 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7858 (m-30) REVERT: B 24 ASN cc_start: 0.8191 (m-40) cc_final: 0.7865 (m-40) REVERT: B 65 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6949 (mt-10) REVERT: B 129 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7410 (p90) REVERT: B 224 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8137 (mtt) REVERT: B 271 MET cc_start: 0.8889 (mmm) cc_final: 0.8686 (mmt) REVERT: C 43 GLU cc_start: 0.7507 (mp0) cc_final: 0.7231 (mp0) REVERT: C 129 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7218 (p90) REVERT: C 244 LYS cc_start: 0.8038 (mtmm) cc_final: 0.7791 (mtpt) REVERT: C 325 ASP cc_start: 0.7293 (m-30) cc_final: 0.6834 (m-30) REVERT: D 67 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7739 (ttmt) REVERT: D 129 PHE cc_start: 0.8115 (OUTLIER) cc_final: 0.7332 (p90) REVERT: E 24 ASN cc_start: 0.8223 (m-40) cc_final: 0.7894 (m-40) REVERT: E 65 GLU cc_start: 0.7318 (mm-30) cc_final: 0.6951 (mt-10) REVERT: E 129 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7120 (p90) REVERT: E 224 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.8137 (mtt) REVERT: E 271 MET cc_start: 0.8817 (mmm) cc_final: 0.8611 (mmt) REVERT: E 325 ASP cc_start: 0.7513 (m-30) cc_final: 0.7179 (m-30) REVERT: F 129 PHE cc_start: 0.7804 (OUTLIER) cc_final: 0.7358 (p90) REVERT: F 203 GLU cc_start: 0.7730 (pt0) cc_final: 0.7454 (mt-10) REVERT: F 242 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7467 (tt0) REVERT: F 269 PHE cc_start: 0.8676 (p90) cc_final: 0.8207 (p90) REVERT: F 282 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7517 (mtp85) REVERT: F 325 ASP cc_start: 0.7399 (m-30) cc_final: 0.6950 (m-30) REVERT: G 66 ASP cc_start: 0.7932 (t0) cc_final: 0.7569 (t0) REVERT: G 129 PHE cc_start: 0.7872 (OUTLIER) cc_final: 0.7414 (p90) REVERT: G 130 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: G 146 GLN cc_start: 0.8177 (tt0) cc_final: 0.7874 (mm-40) REVERT: G 315 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.7738 (tmmt) REVERT: H 40 TYR cc_start: 0.7563 (m-80) cc_final: 0.7257 (m-80) REVERT: H 99 ASP cc_start: 0.6868 (OUTLIER) cc_final: 0.6647 (p0) REVERT: H 130 ASP cc_start: 0.8358 (OUTLIER) cc_final: 0.7815 (m-30) REVERT: H 211 GLU cc_start: 0.7646 (mp0) cc_final: 0.7389 (pm20) REVERT: I 130 ASP cc_start: 0.8306 (OUTLIER) cc_final: 0.7500 (m-30) REVERT: I 136 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.6658 (pp) REVERT: I 182 SER cc_start: 0.9137 (OUTLIER) cc_final: 0.8744 (p) REVERT: I 211 GLU cc_start: 0.7738 (mp0) cc_final: 0.7480 (pm20) REVERT: I 224 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.7641 (mtt) REVERT: J 54 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7539 (t0) REVERT: J 129 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7434 (p90) REVERT: J 130 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: K 40 TYR cc_start: 0.7544 (m-80) cc_final: 0.7320 (m-80) REVERT: K 149 THR cc_start: 0.7813 (t) cc_final: 0.7526 (m) REVERT: K 182 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8503 (m) REVERT: K 224 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7119 (mtt) REVERT: K 245 ASP cc_start: 0.7621 (m-30) cc_final: 0.7330 (m-30) REVERT: K 261 ARG cc_start: 0.7111 (ttt180) cc_final: 0.6899 (ttm110) REVERT: L 130 ASP cc_start: 0.8226 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: L 136 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.6783 (pp) REVERT: L 211 GLU cc_start: 0.7677 (mp0) cc_final: 0.7279 (pm20) REVERT: L 224 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.7728 (mtt) REVERT: L 226 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.8322 (ptm160) REVERT: L 304 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7773 (ttmm) REVERT: a 37 ASP cc_start: 0.8107 (p0) cc_final: 0.7878 (p0) REVERT: b 93 ASP cc_start: 0.7744 (m-30) cc_final: 0.7444 (m-30) REVERT: c 28 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7908 (mp) REVERT: d 11 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7064 (mp0) REVERT: e 93 ASP cc_start: 0.7707 (m-30) cc_final: 0.7415 (m-30) REVERT: f 28 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.7936 (mp) REVERT: l 58 GLN cc_start: 0.8733 (mm110) cc_final: 0.8368 (mt0) outliers start: 290 outliers final: 169 residues processed: 977 average time/residue: 1.2834 time to fit residues: 1619.2914 Evaluate side-chains 941 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 739 time to evaluate : 5.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 61 ASN Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 138 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 17 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 136 LEU Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 202 LEU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 226 ARG Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 101 ASP Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 55 MET Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 55 MET Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 548 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 324 optimal weight: 5.9990 chunk 415 optimal weight: 6.9990 chunk 321 optimal weight: 8.9990 chunk 478 optimal weight: 1.9990 chunk 317 optimal weight: 0.4980 chunk 566 optimal weight: 3.9990 chunk 354 optimal weight: 6.9990 chunk 345 optimal weight: 5.9990 chunk 261 optimal weight: 8.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 321 GLN G 16 ASN G 227 ASN G 230 ASN G 296 GLN I 146 GLN J 78 ASN J 230 ASN J 296 GLN ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 296 GLN c 60 GLN e 60 GLN f 60 GLN g 31 ASN h 7 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN k 60 GLN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 47784 Z= 0.289 Angle : 0.612 9.065 65136 Z= 0.309 Chirality : 0.046 0.208 7428 Planarity : 0.004 0.037 8424 Dihedral : 5.792 58.260 6475 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.60 % Favored : 96.30 % Rotamer: Outliers : 6.25 % Allowed : 23.23 % Favored : 70.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.10), residues: 5952 helix: 0.41 (0.14), residues: 1476 sheet: 0.35 (0.14), residues: 1452 loop : -1.91 (0.09), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 280 PHE 0.018 0.002 PHE B 269 TYR 0.010 0.001 TYR H 82 ARG 0.009 0.000 ARG K 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 318 poor density : 756 time to evaluate : 5.422 Fit side-chains REVERT: A 129 PHE cc_start: 0.8076 (OUTLIER) cc_final: 0.7378 (p90) REVERT: A 130 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7942 (m-30) REVERT: A 224 MET cc_start: 0.8652 (OUTLIER) cc_final: 0.7985 (mpt) REVERT: B 24 ASN cc_start: 0.8188 (m-40) cc_final: 0.7862 (m-40) REVERT: B 129 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7417 (p90) REVERT: B 224 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.8135 (mtt) REVERT: C 43 GLU cc_start: 0.7491 (mp0) cc_final: 0.7222 (mp0) REVERT: C 93 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.8174 (mtpm) REVERT: C 129 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7256 (p90) REVERT: C 242 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7389 (tp30) REVERT: C 244 LYS cc_start: 0.8017 (mtmm) cc_final: 0.7743 (mtpt) REVERT: C 315 LYS cc_start: 0.8566 (tppp) cc_final: 0.8339 (tptp) REVERT: C 325 ASP cc_start: 0.7334 (m-30) cc_final: 0.6908 (m-30) REVERT: D 67 LYS cc_start: 0.7965 (OUTLIER) cc_final: 0.7742 (ttmt) REVERT: D 129 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7291 (p90) REVERT: E 24 ASN cc_start: 0.8208 (m-40) cc_final: 0.7877 (m-40) REVERT: E 129 PHE cc_start: 0.8007 (OUTLIER) cc_final: 0.7291 (p90) REVERT: E 224 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.8130 (mtt) REVERT: E 271 MET cc_start: 0.8809 (mmm) cc_final: 0.8593 (mmt) REVERT: F 43 GLU cc_start: 0.7573 (mp0) cc_final: 0.7194 (mp0) REVERT: F 129 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7452 (p90) REVERT: F 203 GLU cc_start: 0.7715 (pt0) cc_final: 0.7438 (mt-10) REVERT: F 242 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7419 (tt0) REVERT: F 269 PHE cc_start: 0.8685 (p90) cc_final: 0.7995 (p90) REVERT: F 282 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7464 (mtp85) REVERT: G 66 ASP cc_start: 0.7968 (t0) cc_final: 0.7644 (t70) REVERT: G 129 PHE cc_start: 0.7921 (OUTLIER) cc_final: 0.7442 (p90) REVERT: G 130 ASP cc_start: 0.8371 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: G 146 GLN cc_start: 0.8175 (tt0) cc_final: 0.7893 (mm-40) REVERT: G 244 LYS cc_start: 0.7889 (OUTLIER) cc_final: 0.7674 (mmmm) REVERT: G 315 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.7712 (tmmt) REVERT: H 40 TYR cc_start: 0.7575 (m-80) cc_final: 0.7274 (m-80) REVERT: H 99 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6840 (p0) REVERT: H 130 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.7842 (m-30) REVERT: H 211 GLU cc_start: 0.7649 (mp0) cc_final: 0.7382 (pm20) REVERT: H 265 ARG cc_start: 0.7441 (mtt90) cc_final: 0.7172 (mtt-85) REVERT: I 130 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: I 136 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.6805 (pp) REVERT: I 211 GLU cc_start: 0.7733 (mp0) cc_final: 0.7452 (pm20) REVERT: I 224 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.7631 (mtt) REVERT: J 54 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7527 (t0) REVERT: J 129 PHE cc_start: 0.7925 (OUTLIER) cc_final: 0.7419 (p90) REVERT: J 130 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7744 (m-30) REVERT: K 149 THR cc_start: 0.7867 (t) cc_final: 0.7599 (m) REVERT: K 164 ASP cc_start: 0.7217 (OUTLIER) cc_final: 0.6846 (m-30) REVERT: K 224 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7099 (mtt) REVERT: K 245 ASP cc_start: 0.7670 (m-30) cc_final: 0.7346 (m-30) REVERT: L 118 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7849 (tt) REVERT: L 130 ASP cc_start: 0.8274 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: L 136 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.6993 (pp) REVERT: L 211 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7316 (pm20) REVERT: L 224 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7663 (mtt) REVERT: L 304 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7878 (mtpp) REVERT: a 106 LEU cc_start: 0.8747 (mp) cc_final: 0.8483 (mp) REVERT: b 93 ASP cc_start: 0.7741 (m-30) cc_final: 0.7440 (m-30) REVERT: c 28 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8109 (mp) REVERT: c 44 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7379 (mt-10) REVERT: d 11 GLU cc_start: 0.7398 (mt-10) cc_final: 0.7074 (mp0) REVERT: e 93 ASP cc_start: 0.7774 (m-30) cc_final: 0.7509 (m-30) REVERT: f 28 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8226 (mp) REVERT: f 51 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.8181 (p0) REVERT: g 140 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7820 (ttm) REVERT: k 130 ASN cc_start: 0.8561 (OUTLIER) cc_final: 0.8245 (t0) REVERT: l 58 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8389 (mt0) outliers start: 318 outliers final: 189 residues processed: 979 average time/residue: 1.2509 time to fit residues: 1586.2187 Evaluate side-chains 947 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 717 time to evaluate : 5.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 224 MET Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 93 LYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 242 GLU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 229 SER Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 99 ASP Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 134 THR Chi-restraints excluded: chain J residue 136 LEU Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 118 LEU Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 211 GLU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 55 MET Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 101 ASP Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 28 ILE Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 44 GLU Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 55 MET Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 64 ILE Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 28 ILE Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 51 ASN Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 88 GLN Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 34 SER Chi-restraints excluded: chain g residue 55 MET Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 64 ILE Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain k residue 130 ASN Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 75 THR Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 350 optimal weight: 10.0000 chunk 226 optimal weight: 10.0000 chunk 338 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 360 optimal weight: 8.9990 chunk 386 optimal weight: 3.9990 chunk 280 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 445 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 ASN G 230 ASN ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN L 323 GLN ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 60 GLN c 60 GLN e 60 GLN g 31 ASN h 7 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN k 60 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 47784 Z= 0.446 Angle : 0.686 11.790 65136 Z= 0.349 Chirality : 0.050 0.230 7428 Planarity : 0.005 0.040 8424 Dihedral : 6.083 58.302 6475 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.28 % Favored : 95.61 % Rotamer: Outliers : 6.49 % Allowed : 23.15 % Favored : 70.36 % 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: -1.18 (0.10), residues: 5952 helix: 0.41 (0.14), residues: 1440 sheet: 0.26 (0.14), residues: 1452 loop : -1.97 (0.09), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 165 PHE 0.025 0.002 PHE F 129 TYR 0.013 0.002 TYR B 82 ARG 0.006 0.001 ARG a 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 736 time to evaluate : 5.372 Fit side-chains REVERT: A 129 PHE cc_start: 0.8008 (OUTLIER) cc_final: 0.6913 (p90) REVERT: A 130 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.8214 (m-30) REVERT: A 145 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8420 (mttt) REVERT: B 24 ASN cc_start: 0.8146 (m-40) cc_final: 0.7810 (m-40) REVERT: B 129 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7634 (p90) REVERT: B 224 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8146 (mtt) REVERT: C 43 GLU cc_start: 0.7521 (mp0) cc_final: 0.7238 (mp0) REVERT: C 112 LYS cc_start: 0.8391 (mttp) cc_final: 0.7956 (ttmt) REVERT: C 129 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7572 (p90) REVERT: C 148 TYR cc_start: 0.8034 (m-80) cc_final: 0.7766 (m-80) REVERT: C 224 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.6505 (mpt) REVERT: C 242 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7470 (tp30) REVERT: C 244 LYS cc_start: 0.7986 (mtmm) cc_final: 0.7727 (mtpt) REVERT: C 269 PHE cc_start: 0.8786 (p90) cc_final: 0.8363 (p90) REVERT: C 273 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.6968 (mp0) REVERT: C 315 LYS cc_start: 0.8481 (tppp) cc_final: 0.8247 (tptp) REVERT: C 325 ASP cc_start: 0.7226 (m-30) cc_final: 0.6786 (m-30) REVERT: D 15 LEU cc_start: 0.8487 (pp) cc_final: 0.8251 (pt) REVERT: D 67 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7725 (ttmt) REVERT: D 129 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.6964 (p90) REVERT: D 205 LYS cc_start: 0.8345 (OUTLIER) cc_final: 0.8127 (ttpp) REVERT: E 24 ASN cc_start: 0.8226 (m-40) cc_final: 0.7898 (m-40) REVERT: E 129 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.7532 (p90) REVERT: E 224 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8165 (mtt) REVERT: F 43 GLU cc_start: 0.7531 (mp0) cc_final: 0.7201 (mp0) REVERT: F 112 LYS cc_start: 0.8397 (mttp) cc_final: 0.7932 (ttmt) REVERT: F 129 PHE cc_start: 0.7959 (OUTLIER) cc_final: 0.7679 (p90) REVERT: F 203 GLU cc_start: 0.7698 (pt0) cc_final: 0.7401 (mt-10) REVERT: F 269 PHE cc_start: 0.8714 (p90) cc_final: 0.7956 (p90) REVERT: F 271 MET cc_start: 0.8860 (mmm) cc_final: 0.8610 (mmt) REVERT: F 282 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7444 (mtp85) REVERT: G 66 ASP cc_start: 0.7922 (t0) cc_final: 0.7647 (t70) REVERT: G 129 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7530 (p90) REVERT: G 130 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: G 146 GLN cc_start: 0.8344 (tt0) cc_final: 0.7988 (mm-40) REVERT: G 244 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7661 (mmmm) REVERT: G 315 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.7700 (tmmt) REVERT: H 99 ASP cc_start: 0.7117 (p0) cc_final: 0.6758 (p0) REVERT: H 130 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.8012 (m-30) REVERT: H 164 ASP cc_start: 0.7224 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: I 130 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.7779 (m-30) REVERT: I 136 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7081 (pp) REVERT: I 211 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7433 (pm20) REVERT: I 224 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.7714 (mtt) REVERT: J 54 ASP cc_start: 0.7791 (OUTLIER) cc_final: 0.7541 (t0) REVERT: J 129 PHE cc_start: 0.8063 (OUTLIER) cc_final: 0.7490 (p90) REVERT: J 130 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.7928 (m-30) REVERT: K 149 THR cc_start: 0.8093 (t) cc_final: 0.7840 (m) REVERT: K 164 ASP cc_start: 0.7209 (OUTLIER) cc_final: 0.6822 (m-30) REVERT: K 182 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8513 (m) REVERT: K 224 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7104 (mtt) REVERT: K 265 ARG cc_start: 0.7351 (mtt-85) cc_final: 0.7068 (mtt-85) REVERT: L 42 SER cc_start: 0.7877 (OUTLIER) cc_final: 0.7512 (p) REVERT: L 136 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7168 (pp) REVERT: L 211 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: L 224 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.7781 (mtt) REVERT: L 304 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7895 (mtpp) REVERT: a 126 ASP cc_start: 0.8296 (t0) cc_final: 0.8018 (t0) REVERT: b 90 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7438 (tt0) REVERT: b 93 ASP cc_start: 0.7709 (m-30) cc_final: 0.7425 (m-30) REVERT: e 11 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7284 (mp0) REVERT: e 93 ASP cc_start: 0.7720 (m-30) cc_final: 0.7442 (m-30) REVERT: f 44 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7377 (mt-10) REVERT: f 51 ASN cc_start: 0.8409 (OUTLIER) cc_final: 0.8057 (p0) REVERT: g 46 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7406 (ttt-90) REVERT: i 142 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7301 (p0) REVERT: i 143 ARG cc_start: 0.7635 (ttt-90) cc_final: 0.6450 (ttt180) REVERT: l 58 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8533 (mt0) REVERT: l 142 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7290 (p0) REVERT: l 143 ARG cc_start: 0.7636 (ttt-90) cc_final: 0.6453 (ttt180) outliers start: 330 outliers final: 209 residues processed: 973 average time/residue: 1.3024 time to fit residues: 1660.6185 Evaluate side-chains 954 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 701 time to evaluate : 5.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 224 MET Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 242 GLU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 67 LYS Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 129 PHE Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 17 SER Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 234 THR Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 282 ARG Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 136 LEU Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 169 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 202 LEU Chi-restraints excluded: chain G residue 235 VAL Chi-restraints excluded: chain G residue 244 LYS Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 91 LEU Chi-restraints excluded: chain H residue 114 THR Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain H residue 224 MET Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 27 THR Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 182 SER Chi-restraints excluded: chain I residue 211 GLU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 54 ASP Chi-restraints excluded: chain J residue 71 SER Chi-restraints excluded: chain J residue 114 THR Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 182 SER Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 267 MET Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 114 THR Chi-restraints excluded: chain K residue 118 LEU Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 13 GLU Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 134 THR Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain L residue 211 GLU Chi-restraints excluded: chain L residue 224 MET Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 338 VAL Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 20 ILE Chi-restraints excluded: chain b residue 34 SER Chi-restraints excluded: chain b residue 90 GLU Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 101 ASP Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 5 THR Chi-restraints excluded: chain c residue 34 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 20 ILE Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 55 MET Chi-restraints excluded: chain d residue 58 GLN Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 5 THR Chi-restraints excluded: chain e residue 20 ILE Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 101 ASP Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 5 THR Chi-restraints excluded: chain f residue 34 SER Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 51 ASN Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain g residue 55 MET Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 75 THR Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain i residue 142 ASP Chi-restraints excluded: chain j residue 22 SER Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 64 ILE Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain k residue 5 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 28 ILE Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 22 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 58 GLN Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 140 MET Chi-restraints excluded: chain l residue 142 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 515 optimal weight: 0.9990 chunk 542 optimal weight: 0.9990 chunk 495 optimal weight: 0.9990 chunk 528 optimal weight: 0.6980 chunk 317 optimal weight: 0.6980 chunk 230 optimal weight: 0.0670 chunk 414 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 477 optimal weight: 3.9990 chunk 499 optimal weight: 3.9990 chunk 526 optimal weight: 1.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 GLN F 321 GLN G 16 ASN G 227 ASN I 146 GLN K 61 ASN c 60 GLN e 31 ASN e 60 GLN g 7 GLN g 31 ASN h 7 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN k 60 GLN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 47784 Z= 0.152 Angle : 0.571 9.660 65136 Z= 0.285 Chirality : 0.044 0.180 7428 Planarity : 0.004 0.029 8424 Dihedral : 5.393 59.590 6471 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.11 % Allowed : 25.67 % Favored : 70.22 % 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: -0.96 (0.10), residues: 5952 helix: 0.55 (0.14), residues: 1476 sheet: 0.44 (0.14), residues: 1452 loop : -1.86 (0.09), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 165 PHE 0.024 0.001 PHE C 269 TYR 0.011 0.001 TYR f 17 ARG 0.005 0.000 ARG L 265 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 780 time to evaluate : 5.713 Fit side-chains REVERT: A 129 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7232 (p90) REVERT: A 136 LEU cc_start: 0.7377 (OUTLIER) cc_final: 0.6943 (pp) REVERT: B 24 ASN cc_start: 0.8229 (m-40) cc_final: 0.7881 (m-40) REVERT: B 130 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: B 224 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.8076 (mtt) REVERT: B 325 ASP cc_start: 0.7354 (m-30) cc_final: 0.6928 (m-30) REVERT: C 43 GLU cc_start: 0.7347 (mp0) cc_final: 0.7085 (mp0) REVERT: C 57 ASN cc_start: 0.7796 (m-40) cc_final: 0.7473 (m-40) REVERT: C 244 LYS cc_start: 0.7873 (mtmm) cc_final: 0.7663 (mtpt) REVERT: C 325 ASP cc_start: 0.7349 (m-30) cc_final: 0.6849 (m-30) REVERT: D 15 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8242 (pt) REVERT: E 24 ASN cc_start: 0.8245 (m-40) cc_final: 0.7887 (m-40) REVERT: E 129 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.6987 (p90) REVERT: E 146 GLN cc_start: 0.8100 (tp40) cc_final: 0.7873 (mp10) REVERT: E 224 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.8080 (mtt) REVERT: E 271 MET cc_start: 0.7297 (mmt) cc_final: 0.7041 (mmm) REVERT: F 43 GLU cc_start: 0.7491 (mp0) cc_final: 0.7154 (mp0) REVERT: F 203 GLU cc_start: 0.7754 (pt0) cc_final: 0.7439 (mt-10) REVERT: F 271 MET cc_start: 0.8862 (mmm) cc_final: 0.8587 (mmt) REVERT: G 66 ASP cc_start: 0.7990 (t0) cc_final: 0.7674 (t70) REVERT: G 129 PHE cc_start: 0.7809 (OUTLIER) cc_final: 0.7397 (p90) REVERT: G 130 ASP cc_start: 0.8148 (OUTLIER) cc_final: 0.7456 (m-30) REVERT: G 146 GLN cc_start: 0.8266 (tt0) cc_final: 0.7837 (mm-40) REVERT: G 315 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7716 (tmmt) REVERT: H 99 ASP cc_start: 0.6946 (p0) cc_final: 0.6708 (p0) REVERT: H 130 ASP cc_start: 0.8177 (OUTLIER) cc_final: 0.7628 (m-30) REVERT: H 245 ASP cc_start: 0.7647 (m-30) cc_final: 0.7437 (m-30) REVERT: H 265 ARG cc_start: 0.7489 (mtt90) cc_final: 0.7265 (mtt-85) REVERT: I 130 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: I 136 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.6758 (pp) REVERT: I 211 GLU cc_start: 0.7693 (mp0) cc_final: 0.7325 (pm20) REVERT: I 224 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.7592 (mtt) REVERT: J 129 PHE cc_start: 0.7880 (OUTLIER) cc_final: 0.7447 (p90) REVERT: J 130 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: J 142 GLU cc_start: 0.7517 (tp30) cc_final: 0.7301 (mm-30) REVERT: K 149 THR cc_start: 0.7874 (t) cc_final: 0.7654 (m) REVERT: K 224 MET cc_start: 0.8293 (OUTLIER) cc_final: 0.7955 (mtt) REVERT: K 245 ASP cc_start: 0.7629 (m-30) cc_final: 0.7406 (m-30) REVERT: L 136 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.6769 (pp) REVERT: L 211 GLU cc_start: 0.7668 (mp0) cc_final: 0.7313 (pm20) REVERT: L 304 LYS cc_start: 0.7955 (OUTLIER) cc_final: 0.7728 (ttmm) REVERT: d 11 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6858 (mp0) REVERT: f 44 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7316 (mt-10) REVERT: i 140 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7269 (ttm) REVERT: l 58 GLN cc_start: 0.8660 (OUTLIER) cc_final: 0.8367 (mt0) REVERT: l 140 MET cc_start: 0.7885 (OUTLIER) cc_final: 0.7312 (ttm) outliers start: 209 outliers final: 137 residues processed: 935 average time/residue: 1.2606 time to fit residues: 1523.8430 Evaluate side-chains 878 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 718 time to evaluate : 5.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 136 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 186 SER Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 129 PHE Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 55 MET Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 108 MET Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 44 GLU Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 108 MET Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 58 GLN Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 346 optimal weight: 5.9990 chunk 558 optimal weight: 2.9990 chunk 340 optimal weight: 0.8980 chunk 264 optimal weight: 5.9990 chunk 388 optimal weight: 7.9990 chunk 585 optimal weight: 0.0870 chunk 539 optimal weight: 3.9990 chunk 466 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 360 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 ASN G 296 GLN K 61 ASN K 78 ASN L 146 GLN c 60 GLN e 88 GLN g 7 GLN g 31 ASN h 7 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN k 60 GLN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 47784 Z= 0.276 Angle : 0.621 10.509 65136 Z= 0.311 Chirality : 0.046 0.274 7428 Planarity : 0.004 0.042 8424 Dihedral : 5.532 59.828 6470 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 3.97 % Allowed : 26.06 % Favored : 69.97 % 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: -0.90 (0.10), residues: 5952 helix: 0.73 (0.14), residues: 1440 sheet: 0.52 (0.14), residues: 1380 loop : -1.84 (0.09), residues: 3132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 190 PHE 0.024 0.002 PHE D 269 TYR 0.013 0.001 TYR c 17 ARG 0.011 0.000 ARG K 265 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11904 Ramachandran restraints generated. 5952 Oldfield, 0 Emsley, 5952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 739 time to evaluate : 5.355 Fit side-chains REVERT: A 129 PHE cc_start: 0.8058 (OUTLIER) cc_final: 0.7373 (p90) REVERT: A 130 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7917 (m-30) REVERT: A 136 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7061 (pp) REVERT: B 24 ASN cc_start: 0.8230 (m-40) cc_final: 0.7889 (m-40) REVERT: B 224 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8141 (mtt) REVERT: C 43 GLU cc_start: 0.7304 (mp0) cc_final: 0.7047 (mp0) REVERT: C 57 ASN cc_start: 0.7822 (m-40) cc_final: 0.7485 (m-40) REVERT: C 129 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7308 (p90) REVERT: C 244 LYS cc_start: 0.7916 (mtmm) cc_final: 0.7713 (mtpt) REVERT: C 271 MET cc_start: 0.8908 (mmm) cc_final: 0.8647 (mmt) REVERT: C 325 ASP cc_start: 0.7247 (m-30) cc_final: 0.6819 (m-30) REVERT: D 15 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8195 (pt) REVERT: D 42 SER cc_start: 0.8486 (t) cc_final: 0.8164 (p) REVERT: D 205 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.8037 (ttpp) REVERT: E 24 ASN cc_start: 0.8248 (m-40) cc_final: 0.7890 (m-40) REVERT: E 129 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7226 (p90) REVERT: E 224 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8140 (mtt) REVERT: F 43 GLU cc_start: 0.7494 (mp0) cc_final: 0.7166 (mp0) REVERT: F 129 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7554 (p90) REVERT: F 203 GLU cc_start: 0.7779 (pt0) cc_final: 0.7436 (mt-10) REVERT: F 271 MET cc_start: 0.8903 (mmm) cc_final: 0.8638 (mmt) REVERT: G 130 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7819 (m-30) REVERT: G 146 GLN cc_start: 0.8270 (tt0) cc_final: 0.7841 (mm-40) REVERT: G 315 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7674 (tmmt) REVERT: H 99 ASP cc_start: 0.6901 (p0) cc_final: 0.6669 (p0) REVERT: H 130 ASP cc_start: 0.8377 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: H 265 ARG cc_start: 0.7545 (mtt90) cc_final: 0.7309 (mtt-85) REVERT: I 130 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.7697 (m-30) REVERT: I 136 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.6882 (pp) REVERT: I 211 GLU cc_start: 0.7714 (mp0) cc_final: 0.7427 (pm20) REVERT: I 224 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.7645 (mtt) REVERT: J 129 PHE cc_start: 0.7989 (OUTLIER) cc_final: 0.7438 (p90) REVERT: J 130 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7685 (m-30) REVERT: K 149 THR cc_start: 0.8018 (t) cc_final: 0.7784 (m) REVERT: K 164 ASP cc_start: 0.7172 (OUTLIER) cc_final: 0.6789 (m-30) REVERT: K 224 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7040 (mtt) REVERT: L 136 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.6942 (pp) REVERT: L 211 GLU cc_start: 0.7686 (mp0) cc_final: 0.7293 (pm20) REVERT: L 304 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7850 (mtpp) REVERT: a 106 LEU cc_start: 0.8726 (mp) cc_final: 0.8472 (mp) REVERT: a 126 ASP cc_start: 0.8260 (t0) cc_final: 0.7961 (t0) REVERT: b 90 GLU cc_start: 0.7557 (tm-30) cc_final: 0.7182 (tt0) REVERT: b 93 ASP cc_start: 0.7803 (m-30) cc_final: 0.7553 (m-30) REVERT: d 11 GLU cc_start: 0.7377 (mt-10) cc_final: 0.7051 (mp0) REVERT: e 44 GLU cc_start: 0.7776 (mp0) cc_final: 0.7497 (mm-30) REVERT: e 93 ASP cc_start: 0.7763 (m-30) cc_final: 0.7520 (m-30) REVERT: g 140 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7586 (ttm) REVERT: l 58 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.8432 (mt0) outliers start: 202 outliers final: 156 residues processed: 893 average time/residue: 1.2833 time to fit residues: 1484.5489 Evaluate side-chains 900 residues out of total 5088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 720 time to evaluate : 5.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 VAL Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 224 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 235 VAL Chi-restraints excluded: chain B residue 250 VAL Chi-restraints excluded: chain B residue 273 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 129 PHE Chi-restraints excluded: chain C residue 130 ASP Chi-restraints excluded: chain C residue 175 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 10 VAL Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 17 SER Chi-restraints excluded: chain D residue 27 THR Chi-restraints excluded: chain D residue 128 VAL Chi-restraints excluded: chain D residue 130 ASP Chi-restraints excluded: chain D residue 175 VAL Chi-restraints excluded: chain D residue 186 SER Chi-restraints excluded: chain D residue 205 LYS Chi-restraints excluded: chain D residue 235 VAL Chi-restraints excluded: chain D residue 250 VAL Chi-restraints excluded: chain D residue 338 VAL Chi-restraints excluded: chain D residue 349 THR Chi-restraints excluded: chain E residue 17 SER Chi-restraints excluded: chain E residue 27 THR Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 129 PHE Chi-restraints excluded: chain E residue 130 ASP Chi-restraints excluded: chain E residue 175 VAL Chi-restraints excluded: chain E residue 224 MET Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 235 VAL Chi-restraints excluded: chain E residue 250 VAL Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 338 VAL Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 128 VAL Chi-restraints excluded: chain F residue 129 PHE Chi-restraints excluded: chain F residue 175 VAL Chi-restraints excluded: chain F residue 235 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain F residue 338 VAL Chi-restraints excluded: chain G residue 21 SER Chi-restraints excluded: chain G residue 114 THR Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain G residue 130 ASP Chi-restraints excluded: chain G residue 175 VAL Chi-restraints excluded: chain G residue 250 VAL Chi-restraints excluded: chain G residue 315 LYS Chi-restraints excluded: chain G residue 338 VAL Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 22 VAL Chi-restraints excluded: chain H residue 118 LEU Chi-restraints excluded: chain H residue 128 VAL Chi-restraints excluded: chain H residue 130 ASP Chi-restraints excluded: chain H residue 231 THR Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain H residue 250 VAL Chi-restraints excluded: chain H residue 268 SER Chi-restraints excluded: chain H residue 338 VAL Chi-restraints excluded: chain H residue 349 THR Chi-restraints excluded: chain H residue 352 VAL Chi-restraints excluded: chain I residue 21 SER Chi-restraints excluded: chain I residue 22 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 128 VAL Chi-restraints excluded: chain I residue 130 ASP Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain I residue 161 LEU Chi-restraints excluded: chain I residue 224 MET Chi-restraints excluded: chain I residue 235 VAL Chi-restraints excluded: chain I residue 250 VAL Chi-restraints excluded: chain I residue 338 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain J residue 27 THR Chi-restraints excluded: chain J residue 53 MET Chi-restraints excluded: chain J residue 118 LEU Chi-restraints excluded: chain J residue 128 VAL Chi-restraints excluded: chain J residue 129 PHE Chi-restraints excluded: chain J residue 130 ASP Chi-restraints excluded: chain J residue 137 THR Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 233 THR Chi-restraints excluded: chain J residue 235 VAL Chi-restraints excluded: chain J residue 250 VAL Chi-restraints excluded: chain J residue 338 VAL Chi-restraints excluded: chain J residue 349 THR Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 128 VAL Chi-restraints excluded: chain K residue 136 LEU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 164 ASP Chi-restraints excluded: chain K residue 224 MET Chi-restraints excluded: chain K residue 233 THR Chi-restraints excluded: chain K residue 235 VAL Chi-restraints excluded: chain K residue 250 VAL Chi-restraints excluded: chain K residue 338 VAL Chi-restraints excluded: chain K residue 349 THR Chi-restraints excluded: chain K residue 352 VAL Chi-restraints excluded: chain L residue 21 SER Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 128 VAL Chi-restraints excluded: chain L residue 130 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 235 VAL Chi-restraints excluded: chain L residue 250 VAL Chi-restraints excluded: chain L residue 304 LYS Chi-restraints excluded: chain L residue 349 THR Chi-restraints excluded: chain a residue 5 THR Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 64 ILE Chi-restraints excluded: chain a residue 75 THR Chi-restraints excluded: chain a residue 122 SER Chi-restraints excluded: chain b residue 95 THR Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain c residue 64 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain d residue 5 THR Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain d residue 64 ILE Chi-restraints excluded: chain d residue 122 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain e residue 34 SER Chi-restraints excluded: chain e residue 95 THR Chi-restraints excluded: chain e residue 122 SER Chi-restraints excluded: chain f residue 64 ILE Chi-restraints excluded: chain f residue 122 SER Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 128 THR Chi-restraints excluded: chain g residue 140 MET Chi-restraints excluded: chain h residue 16 VAL Chi-restraints excluded: chain h residue 34 SER Chi-restraints excluded: chain h residue 47 ASP Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain i residue 16 VAL Chi-restraints excluded: chain i residue 32 SER Chi-restraints excluded: chain i residue 34 SER Chi-restraints excluded: chain i residue 132 ILE Chi-restraints excluded: chain i residue 140 MET Chi-restraints excluded: chain j residue 34 SER Chi-restraints excluded: chain j residue 75 THR Chi-restraints excluded: chain j residue 122 SER Chi-restraints excluded: chain j residue 128 THR Chi-restraints excluded: chain k residue 16 VAL Chi-restraints excluded: chain k residue 22 SER Chi-restraints excluded: chain k residue 34 SER Chi-restraints excluded: chain k residue 47 ASP Chi-restraints excluded: chain k residue 122 SER Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 32 SER Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 58 GLN Chi-restraints excluded: chain l residue 128 THR Chi-restraints excluded: chain l residue 132 ILE Chi-restraints excluded: chain l residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 588 random chunks: chunk 370 optimal weight: 7.9990 chunk 496 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 430 optimal weight: 8.9990 chunk 68 optimal weight: 50.0000 chunk 129 optimal weight: 7.9990 chunk 467 optimal weight: 0.0980 chunk 195 optimal weight: 7.9990 chunk 479 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 227 ASN ** I 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 146 GLN K 61 ASN ** L 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 60 GLN ** d 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 60 GLN g 7 GLN g 31 ASN h 7 GLN ** i 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 31 ASN k 60 GLN ** l 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.135467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.108661 restraints weight = 56315.663| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 1.71 r_work: 0.3088 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 47784 Z= 0.331 Angle : 0.647 11.154 65136 Z= 0.326 Chirality : 0.048 0.255 7428 Planarity : 0.004 0.049 8424 Dihedral : 5.735 59.735 6470 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.76 % Favored : 96.14 % Rotamer: Outliers : 4.70 % Allowed : 25.39 % Favored : 69.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.10), residues: 5952 helix: 0.65 (0.14), residues: 1440 sheet: 0.35 (0.14), residues: 1452 loop : -1.92 (0.09), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 190 PHE 0.023 0.002 PHE C 269 TYR 0.013 0.001 TYR b 17 ARG 0.011 0.001 ARG K 265 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23024.59 seconds wall clock time: 404 minutes 6.92 seconds (24246.92 seconds total)