Starting phenix.real_space_refine on Sat Mar 16 21:45:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/03_2024/8fnv_29327.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/03_2024/8fnv_29327.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/03_2024/8fnv_29327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/03_2024/8fnv_29327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/03_2024/8fnv_29327.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/03_2024/8fnv_29327.pdb" } resolution = 2.11 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= 0.142 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 12 6.06 5 S 408 5.16 5 C 48011 2.51 5 N 12980 2.21 5 O 13517 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 27": "OE1" <-> "OE2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A ASP 167": "OD1" <-> "OD2" Residue "A GLU 173": "OE1" <-> "OE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 262": "OD1" <-> "OD2" Residue "A TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "A ASP 362": "OD1" <-> "OD2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A ASP 451": "OD1" <-> "OD2" Residue "A GLU 456": "OE1" <-> "OE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A ASP 502": "OD1" <-> "OD2" Residue "A GLU 608": "OE1" <-> "OE2" Residue "A GLU 615": "OE1" <-> "OE2" Residue "A GLU 638": "OE1" <-> "OE2" Residue "A ASP 663": "OD1" <-> "OD2" Residue "A GLU 678": "OE1" <-> "OE2" Residue "A GLU 733": "OE1" <-> "OE2" Residue "A ASP 756": "OD1" <-> "OD2" Residue "A ASP 778": "OD1" <-> "OD2" Residue "A GLU 788": "OE1" <-> "OE2" Residue "A ASP 797": "OD1" <-> "OD2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 162": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 262": "OD1" <-> "OD2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B GLU 286": "OE1" <-> "OE2" Residue "B ASP 362": "OD1" <-> "OD2" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B ASP 451": "OD1" <-> "OD2" Residue "B GLU 456": "OE1" <-> "OE2" Residue "B GLU 501": "OE1" <-> "OE2" Residue "B ASP 502": "OD1" <-> "OD2" Residue "B GLU 608": "OE1" <-> "OE2" Residue "B GLU 615": "OE1" <-> "OE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B GLU 678": "OE1" <-> "OE2" Residue "B GLU 733": "OE1" <-> "OE2" Residue "B ASP 756": "OD1" <-> "OD2" Residue "B ASP 778": "OD1" <-> "OD2" Residue "B GLU 788": "OE1" <-> "OE2" Residue "B ASP 797": "OD1" <-> "OD2" Residue "C GLU 27": "OE1" <-> "OE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 91": "OD1" <-> "OD2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 162": "OE1" <-> "OE2" Residue "C GLU 163": "OE1" <-> "OE2" Residue "C ASP 167": "OD1" <-> "OD2" Residue "C GLU 173": "OE1" <-> "OE2" Residue "C PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 262": "OD1" <-> "OD2" Residue "C TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C ASP 362": "OD1" <-> "OD2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C ASP 451": "OD1" <-> "OD2" Residue "C GLU 456": "OE1" <-> "OE2" Residue "C GLU 501": "OE1" <-> "OE2" Residue "C ASP 502": "OD1" <-> "OD2" Residue "C GLU 608": "OE1" <-> "OE2" Residue "C GLU 615": "OE1" <-> "OE2" Residue "C GLU 638": "OE1" <-> "OE2" Residue "C ASP 663": "OD1" <-> "OD2" Residue "C GLU 678": "OE1" <-> "OE2" Residue "C GLU 733": "OE1" <-> "OE2" Residue "C ASP 756": "OD1" <-> "OD2" Residue "C ASP 778": "OD1" <-> "OD2" Residue "C GLU 788": "OE1" <-> "OE2" Residue "C ASP 797": "OD1" <-> "OD2" Residue "D GLU 27": "OE1" <-> "OE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 91": "OD1" <-> "OD2" Residue "D GLU 146": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "D PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 262": "OD1" <-> "OD2" Residue "D TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 267": "OE1" <-> "OE2" Residue "D GLU 286": "OE1" <-> "OE2" Residue "D ASP 362": "OD1" <-> "OD2" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 415": "OE1" <-> "OE2" Residue "D ASP 451": "OD1" <-> "OD2" Residue "D GLU 456": "OE1" <-> "OE2" Residue "D GLU 501": "OE1" <-> "OE2" Residue "D ASP 502": "OD1" <-> "OD2" Residue "D GLU 608": "OE1" <-> "OE2" Residue "D GLU 615": "OE1" <-> "OE2" Residue "D GLU 638": "OE1" <-> "OE2" Residue "D ASP 663": "OD1" <-> "OD2" Residue "D GLU 678": "OE1" <-> "OE2" Residue "D GLU 733": "OE1" <-> "OE2" Residue "D ASP 756": "OD1" <-> "OD2" Residue "D ASP 778": "OD1" <-> "OD2" Residue "D GLU 788": "OE1" <-> "OE2" Residue "D ASP 797": "OD1" <-> "OD2" Residue "E GLU 27": "OE1" <-> "OE2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 91": "OD1" <-> "OD2" Residue "E GLU 146": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "E ASP 167": "OD1" <-> "OD2" Residue "E GLU 173": "OE1" <-> "OE2" Residue "E PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 262": "OD1" <-> "OD2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 267": "OE1" <-> "OE2" Residue "E GLU 286": "OE1" <-> "OE2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E GLU 392": "OE1" <-> "OE2" Residue "E GLU 415": "OE1" <-> "OE2" Residue "E ASP 451": "OD1" <-> "OD2" Residue "E GLU 456": "OE1" <-> "OE2" Residue "E GLU 501": "OE1" <-> "OE2" Residue "E ASP 502": "OD1" <-> "OD2" Residue "E GLU 608": "OE1" <-> "OE2" Residue "E GLU 615": "OE1" <-> "OE2" Residue "E GLU 638": "OE1" <-> "OE2" Residue "E ASP 663": "OD1" <-> "OD2" Residue "E GLU 678": "OE1" <-> "OE2" Residue "E GLU 733": "OE1" <-> "OE2" Residue "E ASP 756": "OD1" <-> "OD2" Residue "E ASP 778": "OD1" <-> "OD2" Residue "E GLU 788": "OE1" <-> "OE2" Residue "E ASP 797": "OD1" <-> "OD2" Residue "F GLU 27": "OE1" <-> "OE2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 91": "OD1" <-> "OD2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 150": "OE1" <-> "OE2" Residue "F GLU 162": "OE1" <-> "OE2" Residue "F GLU 163": "OE1" <-> "OE2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "F GLU 173": "OE1" <-> "OE2" Residue "F PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 262": "OD1" <-> "OD2" Residue "F TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 267": "OE1" <-> "OE2" Residue "F GLU 286": "OE1" <-> "OE2" Residue "F ASP 362": "OD1" <-> "OD2" Residue "F GLU 392": "OE1" <-> "OE2" Residue "F GLU 415": "OE1" <-> "OE2" Residue "F ASP 451": "OD1" <-> "OD2" Residue "F GLU 456": "OE1" <-> "OE2" Residue "F GLU 501": "OE1" <-> "OE2" Residue "F ASP 502": "OD1" <-> "OD2" Residue "F GLU 608": "OE1" <-> "OE2" Residue "F GLU 615": "OE1" <-> "OE2" Residue "F GLU 638": "OE1" <-> "OE2" Residue "F ASP 663": "OD1" <-> "OD2" Residue "F GLU 678": "OE1" <-> "OE2" Residue "F GLU 733": "OE1" <-> "OE2" Residue "F ASP 756": "OD1" <-> "OD2" Residue "F ASP 778": "OD1" <-> "OD2" Residue "F GLU 788": "OE1" <-> "OE2" Residue "F ASP 797": "OD1" <-> "OD2" Residue "G GLU 27": "OE1" <-> "OE2" Residue "G TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "G GLU 150": "OE1" <-> "OE2" Residue "G GLU 162": "OE1" <-> "OE2" Residue "G GLU 163": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "G GLU 173": "OE1" <-> "OE2" Residue "G PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 262": "OD1" <-> "OD2" Residue "G TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G GLU 286": "OE1" <-> "OE2" Residue "G ASP 362": "OD1" <-> "OD2" Residue "G GLU 392": "OE1" <-> "OE2" Residue "G GLU 415": "OE1" <-> "OE2" Residue "G ASP 451": "OD1" <-> "OD2" Residue "G GLU 456": "OE1" <-> "OE2" Residue "G GLU 501": "OE1" <-> "OE2" Residue "G ASP 502": "OD1" <-> "OD2" Residue "G GLU 608": "OE1" <-> "OE2" Residue "G GLU 615": "OE1" <-> "OE2" Residue "G GLU 638": "OE1" <-> "OE2" Residue "G ASP 663": "OD1" <-> "OD2" Residue "G GLU 678": "OE1" <-> "OE2" Residue "G GLU 733": "OE1" <-> "OE2" Residue "G ASP 756": "OD1" <-> "OD2" Residue "G ASP 778": "OD1" <-> "OD2" Residue "G GLU 788": "OE1" <-> "OE2" Residue "G ASP 797": "OD1" <-> "OD2" Residue "H GLU 27": "OE1" <-> "OE2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "H GLU 146": "OE1" <-> "OE2" Residue "H GLU 150": "OE1" <-> "OE2" Residue "H GLU 162": "OE1" <-> "OE2" Residue "H GLU 163": "OE1" <-> "OE2" Residue "H ASP 167": "OD1" <-> "OD2" Residue "H GLU 173": "OE1" <-> "OE2" Residue "H PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 262": "OD1" <-> "OD2" Residue "H TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 267": "OE1" <-> "OE2" Residue "H GLU 286": "OE1" <-> "OE2" Residue "H ASP 362": "OD1" <-> "OD2" Residue "H GLU 392": "OE1" <-> "OE2" Residue "H GLU 415": "OE1" <-> "OE2" Residue "H ASP 451": "OD1" <-> "OD2" Residue "H GLU 456": "OE1" <-> "OE2" Residue "H GLU 501": "OE1" <-> "OE2" Residue "H ASP 502": "OD1" <-> "OD2" Residue "H GLU 608": "OE1" <-> "OE2" Residue "H GLU 615": "OE1" <-> "OE2" Residue "H GLU 638": "OE1" <-> "OE2" Residue "H ASP 663": "OD1" <-> "OD2" Residue "H GLU 678": "OE1" <-> "OE2" Residue "H GLU 733": "OE1" <-> "OE2" Residue "H ASP 756": "OD1" <-> "OD2" Residue "H ASP 778": "OD1" <-> "OD2" Residue "H GLU 788": "OE1" <-> "OE2" Residue "H ASP 797": "OD1" <-> "OD2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 91": "OD1" <-> "OD2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I GLU 150": "OE1" <-> "OE2" Residue "I GLU 162": "OE1" <-> "OE2" Residue "I GLU 163": "OE1" <-> "OE2" Residue "I ASP 167": "OD1" <-> "OD2" Residue "I GLU 173": "OE1" <-> "OE2" Residue "I PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 262": "OD1" <-> "OD2" Residue "I TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 267": "OE1" <-> "OE2" Residue "I GLU 286": "OE1" <-> "OE2" Residue "I ASP 362": "OD1" <-> "OD2" Residue "I GLU 392": "OE1" <-> "OE2" Residue "I GLU 415": "OE1" <-> "OE2" Residue "I ASP 451": "OD1" <-> "OD2" Residue "I GLU 456": "OE1" <-> "OE2" Residue "I GLU 501": "OE1" <-> "OE2" Residue "I ASP 502": "OD1" <-> "OD2" Residue "I GLU 608": "OE1" <-> "OE2" Residue "I GLU 615": "OE1" <-> "OE2" Residue "I GLU 638": "OE1" <-> "OE2" Residue "I ASP 663": "OD1" <-> "OD2" Residue "I GLU 678": "OE1" <-> "OE2" Residue "I GLU 733": "OE1" <-> "OE2" Residue "I ASP 756": "OD1" <-> "OD2" Residue "I ASP 778": "OD1" <-> "OD2" Residue "I GLU 788": "OE1" <-> "OE2" Residue "I ASP 797": "OD1" <-> "OD2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 91": "OD1" <-> "OD2" Residue "J GLU 146": "OE1" <-> "OE2" Residue "J GLU 150": "OE1" <-> "OE2" Residue "J GLU 162": "OE1" <-> "OE2" Residue "J GLU 163": "OE1" <-> "OE2" Residue "J ASP 167": "OD1" <-> "OD2" Residue "J GLU 173": "OE1" <-> "OE2" Residue "J PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 262": "OD1" <-> "OD2" Residue "J TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 267": "OE1" <-> "OE2" Residue "J GLU 286": "OE1" <-> "OE2" Residue "J ASP 362": "OD1" <-> "OD2" Residue "J GLU 392": "OE1" <-> "OE2" Residue "J GLU 415": "OE1" <-> "OE2" Residue "J ASP 451": "OD1" <-> "OD2" Residue "J GLU 456": "OE1" <-> "OE2" Residue "J GLU 501": "OE1" <-> "OE2" Residue "J ASP 502": "OD1" <-> "OD2" Residue "J GLU 608": "OE1" <-> "OE2" Residue "J GLU 615": "OE1" <-> "OE2" Residue "J GLU 638": "OE1" <-> "OE2" Residue "J ASP 663": "OD1" <-> "OD2" Residue "J GLU 678": "OE1" <-> "OE2" Residue "J GLU 733": "OE1" <-> "OE2" Residue "J ASP 756": "OD1" <-> "OD2" Residue "J ASP 778": "OD1" <-> "OD2" Residue "J GLU 788": "OE1" <-> "OE2" Residue "J ASP 797": "OD1" <-> "OD2" Residue "K GLU 27": "OE1" <-> "OE2" Residue "K TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 91": "OD1" <-> "OD2" Residue "K GLU 146": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K GLU 163": "OE1" <-> "OE2" Residue "K ASP 167": "OD1" <-> "OD2" Residue "K GLU 173": "OE1" <-> "OE2" Residue "K PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 262": "OD1" <-> "OD2" Residue "K TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 267": "OE1" <-> "OE2" Residue "K GLU 286": "OE1" <-> "OE2" Residue "K ASP 362": "OD1" <-> "OD2" Residue "K GLU 392": "OE1" <-> "OE2" Residue "K GLU 415": "OE1" <-> "OE2" Residue "K ASP 451": "OD1" <-> "OD2" Residue "K GLU 456": "OE1" <-> "OE2" Residue "K GLU 501": "OE1" <-> "OE2" Residue "K ASP 502": "OD1" <-> "OD2" Residue "K GLU 608": "OE1" <-> "OE2" Residue "K GLU 615": "OE1" <-> "OE2" Residue "K GLU 638": "OE1" <-> "OE2" Residue "K ASP 663": "OD1" <-> "OD2" Residue "K GLU 678": "OE1" <-> "OE2" Residue "K GLU 733": "OE1" <-> "OE2" Residue "K ASP 756": "OD1" <-> "OD2" Residue "K ASP 778": "OD1" <-> "OD2" Residue "K GLU 788": "OE1" <-> "OE2" Residue "K ASP 797": "OD1" <-> "OD2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 91": "OD1" <-> "OD2" Residue "L GLU 146": "OE1" <-> "OE2" Residue "L GLU 150": "OE1" <-> "OE2" Residue "L GLU 162": "OE1" <-> "OE2" Residue "L GLU 163": "OE1" <-> "OE2" Residue "L ASP 167": "OD1" <-> "OD2" Residue "L GLU 173": "OE1" <-> "OE2" Residue "L PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 262": "OD1" <-> "OD2" Residue "L TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 267": "OE1" <-> "OE2" Residue "L GLU 286": "OE1" <-> "OE2" Residue "L ASP 362": "OD1" <-> "OD2" Residue "L GLU 392": "OE1" <-> "OE2" Residue "L GLU 415": "OE1" <-> "OE2" Residue "L ASP 451": "OD1" <-> "OD2" Residue "L GLU 456": "OE1" <-> "OE2" Residue "L GLU 501": "OE1" <-> "OE2" Residue "L ASP 502": "OD1" <-> "OD2" Residue "L GLU 608": "OE1" <-> "OE2" Residue "L GLU 615": "OE1" <-> "OE2" Residue "L GLU 638": "OE1" <-> "OE2" Residue "L ASP 663": "OD1" <-> "OD2" Residue "L GLU 678": "OE1" <-> "OE2" Residue "L GLU 733": "OE1" <-> "OE2" Residue "L ASP 756": "OD1" <-> "OD2" Residue "L ASP 778": "OD1" <-> "OD2" Residue "L GLU 788": "OE1" <-> "OE2" Residue "L ASP 797": "OD1" <-> "OD2" 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: 74928 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "B" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "C" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "D" Number of atoms: 6221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 767, 6221 Classifications: {'peptide': 767} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 725} Chain breaks: 4 Chain: "E" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "F" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "G" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "H" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "I" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "J" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "K" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "L" Number of atoms: 6245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 770, 6245 Classifications: {'peptide': 770} Link IDs: {'PCIS': 1, 'PTRANS': 40, 'TRANS': 728} Chain breaks: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 28.17, per 1000 atoms: 0.38 Number of scatterers: 74928 At special positions: 0 Unit cell: (197.175, 200.475, 165.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 12 29.99 S 408 16.00 O 13517 8.00 N 12980 7.00 C 48011 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: 22.85 Conformation dependent library (CDL) restraints added in 9.8 seconds 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17634 Finding SS restraints... Secondary structure from input PDB file: 492 helices and 72 sheets defined 64.3% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.94 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 removed outlier: 3.661A pdb=" N LEU A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 18 Processing helix chain 'A' and resid 25 through 41 Processing helix chain 'A' and resid 47 through 63 Processing helix chain 'A' and resid 68 through 80 Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 147 Processing helix chain 'A' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS A 164 " --> pdb=" O SER A 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU A 166 " --> pdb=" O GLU A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 184 removed outlier: 3.749A pdb=" N GLY A 182 " --> pdb=" O ASP A 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 184 " --> pdb=" O GLU A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 196 Processing helix chain 'A' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 236 through 242 removed outlier: 3.838A pdb=" N ASN A 242 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 280 Processing helix chain 'A' and resid 285 through 309 Processing helix chain 'A' and resid 323 through 327 Processing helix chain 'A' and resid 332 through 342 Processing helix chain 'A' and resid 362 through 383 Processing helix chain 'A' and resid 396 through 405 Processing helix chain 'A' and resid 435 through 456 Processing helix chain 'A' and resid 457 through 462 Processing helix chain 'A' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS A 474 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 479 Processing helix chain 'A' and resid 480 through 491 Processing helix chain 'A' and resid 505 through 520 Processing helix chain 'A' and resid 531 through 535 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS A 542 " --> pdb=" O SER A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 568 Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 573 through 592 Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 633 through 638 Processing helix chain 'A' and resid 638 through 646 removed outlier: 4.106A pdb=" N GLU A 642 " --> pdb=" O GLU A 638 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU A 643 " --> pdb=" O ARG A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 681 through 700 Processing helix chain 'A' and resid 718 through 721 Processing helix chain 'A' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG A 726 " --> pdb=" O HIS A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 772 Processing helix chain 'A' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL A 786 " --> pdb=" O LYS A 782 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG A 791 " --> pdb=" O ASN A 787 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 removed outlier: 3.661A pdb=" N LEU B 6 " --> pdb=" O GLU B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 18 Processing helix chain 'B' and resid 25 through 41 Processing helix chain 'B' and resid 47 through 63 Processing helix chain 'B' and resid 68 through 80 Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE B 110 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 147 Processing helix chain 'B' and resid 160 through 171 removed outlier: 3.893A pdb=" N CYS B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 166 " --> pdb=" O GLU B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 184 " --> pdb=" O GLU B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 196 Processing helix chain 'B' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 232 Processing helix chain 'B' and resid 236 through 242 removed outlier: 3.839A pdb=" N ASN B 242 " --> pdb=" O GLN B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 280 Processing helix chain 'B' and resid 285 through 309 Processing helix chain 'B' and resid 323 through 327 Processing helix chain 'B' and resid 332 through 342 Processing helix chain 'B' and resid 362 through 383 Processing helix chain 'B' and resid 396 through 405 Processing helix chain 'B' and resid 435 through 456 Processing helix chain 'B' and resid 457 through 462 Processing helix chain 'B' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS B 474 " --> pdb=" O ASN B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 479 Processing helix chain 'B' and resid 480 through 491 Processing helix chain 'B' and resid 505 through 520 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS B 542 " --> pdb=" O SER B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 568 Processing helix chain 'B' and resid 570 through 572 No H-bonds generated for 'chain 'B' and resid 570 through 572' Processing helix chain 'B' and resid 573 through 592 Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 633 through 638 Processing helix chain 'B' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU B 642 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU B 643 " --> pdb=" O ARG B 639 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 662 Processing helix chain 'B' and resid 662 through 671 Processing helix chain 'B' and resid 681 through 700 Processing helix chain 'B' and resid 718 through 721 Processing helix chain 'B' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG B 726 " --> pdb=" O HIS B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 772 Processing helix chain 'B' and resid 775 through 793 removed outlier: 3.641A pdb=" N VAL B 786 " --> pdb=" O LYS B 782 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG B 791 " --> pdb=" O ASN B 787 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU C 6 " --> pdb=" O GLU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 Processing helix chain 'C' and resid 25 through 41 Processing helix chain 'C' and resid 47 through 63 Processing helix chain 'C' and resid 68 through 80 Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE C 110 " --> pdb=" O SER C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 147 Processing helix chain 'C' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS C 164 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP C 165 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 166 " --> pdb=" O GLU C 162 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 removed outlier: 3.749A pdb=" N GLY C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA C 184 " --> pdb=" O GLU C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 196 Processing helix chain 'C' and resid 199 through 224 removed outlier: 3.658A pdb=" N ILE C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 236 through 242 removed outlier: 3.838A pdb=" N ASN C 242 " --> pdb=" O GLN C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 280 Processing helix chain 'C' and resid 285 through 309 Processing helix chain 'C' and resid 323 through 327 Processing helix chain 'C' and resid 332 through 342 Processing helix chain 'C' and resid 362 through 383 Processing helix chain 'C' and resid 396 through 405 Processing helix chain 'C' and resid 435 through 456 Processing helix chain 'C' and resid 457 through 462 Processing helix chain 'C' and resid 471 through 475 removed outlier: 3.634A pdb=" N HIS C 474 " --> pdb=" O ASN C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 479 Processing helix chain 'C' and resid 480 through 491 Processing helix chain 'C' and resid 505 through 520 Processing helix chain 'C' and resid 531 through 535 Processing helix chain 'C' and resid 538 through 542 removed outlier: 3.769A pdb=" N LYS C 542 " --> pdb=" O SER C 539 " (cutoff:3.500A) Processing helix chain 'C' and resid 553 through 568 Processing helix chain 'C' and resid 570 through 572 No H-bonds generated for 'chain 'C' and resid 570 through 572' Processing helix chain 'C' and resid 573 through 592 Processing helix chain 'C' and resid 599 through 608 Processing helix chain 'C' and resid 633 through 638 Processing helix chain 'C' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU C 642 " --> pdb=" O GLU C 638 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU C 643 " --> pdb=" O ARG C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 662 Processing helix chain 'C' and resid 662 through 671 Processing helix chain 'C' and resid 681 through 700 Processing helix chain 'C' and resid 718 through 721 Processing helix chain 'C' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG C 726 " --> pdb=" O HIS C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 772 Processing helix chain 'C' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL C 786 " --> pdb=" O LYS C 782 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG C 791 " --> pdb=" O ASN C 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 removed outlier: 3.661A pdb=" N LEU D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 25 through 41 Processing helix chain 'D' and resid 47 through 63 Processing helix chain 'D' and resid 68 through 80 Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE D 110 " --> pdb=" O SER D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 147 Processing helix chain 'D' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS D 164 " --> pdb=" O SER D 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU D 166 " --> pdb=" O GLU D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA D 184 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 185 through 196 Processing helix chain 'D' and resid 199 through 224 removed outlier: 3.658A pdb=" N ILE D 203 " --> pdb=" O LEU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 232 Processing helix chain 'D' and resid 236 through 242 removed outlier: 3.838A pdb=" N ASN D 242 " --> pdb=" O GLN D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 280 Processing helix chain 'D' and resid 285 through 309 Processing helix chain 'D' and resid 323 through 327 Processing helix chain 'D' and resid 332 through 342 Processing helix chain 'D' and resid 362 through 383 Processing helix chain 'D' and resid 396 through 405 Processing helix chain 'D' and resid 435 through 456 Processing helix chain 'D' and resid 457 through 462 Processing helix chain 'D' and resid 471 through 475 removed outlier: 3.634A pdb=" N HIS D 474 " --> pdb=" O ASN D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 479 Processing helix chain 'D' and resid 480 through 491 Processing helix chain 'D' and resid 505 through 520 Processing helix chain 'D' and resid 531 through 535 Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS D 542 " --> pdb=" O SER D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 568 Processing helix chain 'D' and resid 570 through 572 No H-bonds generated for 'chain 'D' and resid 570 through 572' Processing helix chain 'D' and resid 573 through 592 Processing helix chain 'D' and resid 599 through 608 Processing helix chain 'D' and resid 633 through 638 Processing helix chain 'D' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU D 642 " --> pdb=" O GLU D 638 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU D 643 " --> pdb=" O ARG D 639 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 662 Processing helix chain 'D' and resid 662 through 671 Processing helix chain 'D' and resid 681 through 700 Processing helix chain 'D' and resid 718 through 721 Processing helix chain 'D' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG D 726 " --> pdb=" O HIS D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 756 through 772 Processing helix chain 'D' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL D 786 " --> pdb=" O LYS D 782 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG D 791 " --> pdb=" O ASN D 787 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU E 6 " --> pdb=" O GLU E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 18 Processing helix chain 'E' and resid 25 through 41 Processing helix chain 'E' and resid 47 through 63 Processing helix chain 'E' and resid 68 through 80 Processing helix chain 'E' and resid 94 through 103 Processing helix chain 'E' and resid 106 through 118 removed outlier: 4.506A pdb=" N ILE E 110 " --> pdb=" O SER E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 147 Processing helix chain 'E' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS E 164 " --> pdb=" O SER E 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP E 165 " --> pdb=" O ALA E 161 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA E 184 " --> pdb=" O GLU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 196 Processing helix chain 'E' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 236 through 242 removed outlier: 3.838A pdb=" N ASN E 242 " --> pdb=" O GLN E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 280 Processing helix chain 'E' and resid 285 through 309 Processing helix chain 'E' and resid 323 through 327 Processing helix chain 'E' and resid 332 through 342 Processing helix chain 'E' and resid 362 through 383 Processing helix chain 'E' and resid 396 through 405 Processing helix chain 'E' and resid 435 through 456 Processing helix chain 'E' and resid 457 through 462 Processing helix chain 'E' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS E 474 " --> pdb=" O ASN E 471 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 479 Processing helix chain 'E' and resid 480 through 491 Processing helix chain 'E' and resid 505 through 520 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS E 542 " --> pdb=" O SER E 539 " (cutoff:3.500A) Processing helix chain 'E' and resid 553 through 568 Processing helix chain 'E' and resid 570 through 572 No H-bonds generated for 'chain 'E' and resid 570 through 572' Processing helix chain 'E' and resid 573 through 592 Processing helix chain 'E' and resid 599 through 608 Processing helix chain 'E' and resid 633 through 638 Processing helix chain 'E' and resid 638 through 646 removed outlier: 4.106A pdb=" N GLU E 642 " --> pdb=" O GLU E 638 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU E 643 " --> pdb=" O ARG E 639 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 662 Processing helix chain 'E' and resid 662 through 671 Processing helix chain 'E' and resid 681 through 700 Processing helix chain 'E' and resid 718 through 721 Processing helix chain 'E' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG E 726 " --> pdb=" O HIS E 722 " (cutoff:3.500A) Processing helix chain 'E' and resid 756 through 772 Processing helix chain 'E' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL E 786 " --> pdb=" O LYS E 782 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG E 791 " --> pdb=" O ASN E 787 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU F 6 " --> pdb=" O GLU F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 18 Processing helix chain 'F' and resid 25 through 41 Processing helix chain 'F' and resid 47 through 63 Processing helix chain 'F' and resid 68 through 80 Processing helix chain 'F' and resid 94 through 103 Processing helix chain 'F' and resid 106 through 118 removed outlier: 4.506A pdb=" N ILE F 110 " --> pdb=" O SER F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 147 Processing helix chain 'F' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS F 164 " --> pdb=" O SER F 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP F 165 " --> pdb=" O ALA F 161 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU F 166 " --> pdb=" O GLU F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY F 182 " --> pdb=" O ASP F 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA F 184 " --> pdb=" O GLU F 180 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 196 Processing helix chain 'F' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE F 203 " --> pdb=" O LEU F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 228 through 232 Processing helix chain 'F' and resid 236 through 242 removed outlier: 3.838A pdb=" N ASN F 242 " --> pdb=" O GLN F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 280 Processing helix chain 'F' and resid 285 through 309 Processing helix chain 'F' and resid 323 through 327 Processing helix chain 'F' and resid 332 through 342 Processing helix chain 'F' and resid 362 through 383 Processing helix chain 'F' and resid 396 through 405 Processing helix chain 'F' and resid 435 through 456 Processing helix chain 'F' and resid 457 through 462 Processing helix chain 'F' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS F 474 " --> pdb=" O ASN F 471 " (cutoff:3.500A) Processing helix chain 'F' and resid 476 through 479 Processing helix chain 'F' and resid 480 through 491 Processing helix chain 'F' and resid 505 through 520 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS F 542 " --> pdb=" O SER F 539 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 568 Processing helix chain 'F' and resid 570 through 572 No H-bonds generated for 'chain 'F' and resid 570 through 572' Processing helix chain 'F' and resid 573 through 592 Processing helix chain 'F' and resid 599 through 608 Processing helix chain 'F' and resid 633 through 638 Processing helix chain 'F' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU F 642 " --> pdb=" O GLU F 638 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU F 643 " --> pdb=" O ARG F 639 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 662 Processing helix chain 'F' and resid 662 through 671 Processing helix chain 'F' and resid 681 through 700 Processing helix chain 'F' and resid 718 through 721 Processing helix chain 'F' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG F 726 " --> pdb=" O HIS F 722 " (cutoff:3.500A) Processing helix chain 'F' and resid 756 through 772 Processing helix chain 'F' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL F 786 " --> pdb=" O LYS F 782 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG F 791 " --> pdb=" O ASN F 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU G 6 " --> pdb=" O GLU G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 18 Processing helix chain 'G' and resid 25 through 41 Processing helix chain 'G' and resid 47 through 63 Processing helix chain 'G' and resid 68 through 80 Processing helix chain 'G' and resid 94 through 103 Processing helix chain 'G' and resid 106 through 118 removed outlier: 4.506A pdb=" N ILE G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 147 Processing helix chain 'G' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS G 164 " --> pdb=" O SER G 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP G 165 " --> pdb=" O ALA G 161 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU G 166 " --> pdb=" O GLU G 162 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY G 182 " --> pdb=" O ASP G 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA G 184 " --> pdb=" O GLU G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 185 through 196 Processing helix chain 'G' and resid 199 through 224 removed outlier: 3.658A pdb=" N ILE G 203 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 236 through 242 removed outlier: 3.839A pdb=" N ASN G 242 " --> pdb=" O GLN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 280 Processing helix chain 'G' and resid 285 through 309 Processing helix chain 'G' and resid 323 through 327 Processing helix chain 'G' and resid 332 through 342 Processing helix chain 'G' and resid 362 through 383 Processing helix chain 'G' and resid 396 through 405 Processing helix chain 'G' and resid 435 through 456 Processing helix chain 'G' and resid 457 through 462 Processing helix chain 'G' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS G 474 " --> pdb=" O ASN G 471 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 479 Processing helix chain 'G' and resid 480 through 491 Processing helix chain 'G' and resid 505 through 520 Processing helix chain 'G' and resid 531 through 535 Processing helix chain 'G' and resid 538 through 542 removed outlier: 3.769A pdb=" N LYS G 542 " --> pdb=" O SER G 539 " (cutoff:3.500A) Processing helix chain 'G' and resid 553 through 568 Processing helix chain 'G' and resid 570 through 572 No H-bonds generated for 'chain 'G' and resid 570 through 572' Processing helix chain 'G' and resid 573 through 592 Processing helix chain 'G' and resid 599 through 608 Processing helix chain 'G' and resid 633 through 638 Processing helix chain 'G' and resid 638 through 646 removed outlier: 4.106A pdb=" N GLU G 642 " --> pdb=" O GLU G 638 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU G 643 " --> pdb=" O ARG G 639 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 662 Processing helix chain 'G' and resid 662 through 671 Processing helix chain 'G' and resid 681 through 700 Processing helix chain 'G' and resid 718 through 721 Processing helix chain 'G' and resid 722 through 729 removed outlier: 4.159A pdb=" N ARG G 726 " --> pdb=" O HIS G 722 " (cutoff:3.500A) Processing helix chain 'G' and resid 756 through 772 Processing helix chain 'G' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL G 786 " --> pdb=" O LYS G 782 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG G 791 " --> pdb=" O ASN G 787 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 removed outlier: 3.661A pdb=" N LEU H 6 " --> pdb=" O GLU H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 18 Processing helix chain 'H' and resid 25 through 41 Processing helix chain 'H' and resid 47 through 63 Processing helix chain 'H' and resid 68 through 80 Processing helix chain 'H' and resid 94 through 103 Processing helix chain 'H' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE H 110 " --> pdb=" O SER H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 147 Processing helix chain 'H' and resid 160 through 171 removed outlier: 3.891A pdb=" N CYS H 164 " --> pdb=" O SER H 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP H 165 " --> pdb=" O ALA H 161 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU H 166 " --> pdb=" O GLU H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 184 removed outlier: 3.751A pdb=" N GLY H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA H 184 " --> pdb=" O GLU H 180 " (cutoff:3.500A) Processing helix chain 'H' and resid 185 through 196 Processing helix chain 'H' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE H 203 " --> pdb=" O LEU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 232 Processing helix chain 'H' and resid 236 through 242 removed outlier: 3.838A pdb=" N ASN H 242 " --> pdb=" O GLN H 239 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 280 Processing helix chain 'H' and resid 285 through 309 Processing helix chain 'H' and resid 323 through 327 Processing helix chain 'H' and resid 332 through 342 Processing helix chain 'H' and resid 362 through 383 Processing helix chain 'H' and resid 396 through 405 Processing helix chain 'H' and resid 435 through 456 Processing helix chain 'H' and resid 457 through 462 Processing helix chain 'H' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS H 474 " --> pdb=" O ASN H 471 " (cutoff:3.500A) Processing helix chain 'H' and resid 476 through 479 Processing helix chain 'H' and resid 480 through 491 Processing helix chain 'H' and resid 505 through 520 Processing helix chain 'H' and resid 531 through 535 Processing helix chain 'H' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS H 542 " --> pdb=" O SER H 539 " (cutoff:3.500A) Processing helix chain 'H' and resid 553 through 568 Processing helix chain 'H' and resid 570 through 572 No H-bonds generated for 'chain 'H' and resid 570 through 572' Processing helix chain 'H' and resid 573 through 592 Processing helix chain 'H' and resid 599 through 608 Processing helix chain 'H' and resid 633 through 638 Processing helix chain 'H' and resid 638 through 646 removed outlier: 4.104A pdb=" N GLU H 642 " --> pdb=" O GLU H 638 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU H 643 " --> pdb=" O ARG H 639 " (cutoff:3.500A) Processing helix chain 'H' and resid 649 through 662 Processing helix chain 'H' and resid 662 through 671 Processing helix chain 'H' and resid 681 through 700 Processing helix chain 'H' and resid 718 through 721 Processing helix chain 'H' and resid 722 through 729 removed outlier: 4.159A pdb=" N ARG H 726 " --> pdb=" O HIS H 722 " (cutoff:3.500A) Processing helix chain 'H' and resid 756 through 772 Processing helix chain 'H' and resid 775 through 793 removed outlier: 3.641A pdb=" N VAL H 786 " --> pdb=" O LYS H 782 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG H 791 " --> pdb=" O ASN H 787 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU I 6 " --> pdb=" O GLU I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 18 Processing helix chain 'I' and resid 25 through 41 Processing helix chain 'I' and resid 47 through 63 Processing helix chain 'I' and resid 68 through 80 Processing helix chain 'I' and resid 94 through 103 Processing helix chain 'I' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 136 through 147 Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.893A pdb=" N CYS I 164 " --> pdb=" O SER I 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU I 166 " --> pdb=" O GLU I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA I 184 " --> pdb=" O GLU I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 185 through 196 Processing helix chain 'I' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE I 203 " --> pdb=" O LEU I 199 " (cutoff:3.500A) Processing helix chain 'I' and resid 228 through 232 Processing helix chain 'I' and resid 236 through 242 removed outlier: 3.839A pdb=" N ASN I 242 " --> pdb=" O GLN I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 280 Processing helix chain 'I' and resid 285 through 309 Processing helix chain 'I' and resid 323 through 327 Processing helix chain 'I' and resid 332 through 342 Processing helix chain 'I' and resid 362 through 383 Processing helix chain 'I' and resid 396 through 405 Processing helix chain 'I' and resid 435 through 456 Processing helix chain 'I' and resid 457 through 462 Processing helix chain 'I' and resid 471 through 475 removed outlier: 3.634A pdb=" N HIS I 474 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 479 Processing helix chain 'I' and resid 480 through 491 Processing helix chain 'I' and resid 505 through 520 Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS I 542 " --> pdb=" O SER I 539 " (cutoff:3.500A) Processing helix chain 'I' and resid 553 through 568 Processing helix chain 'I' and resid 570 through 572 No H-bonds generated for 'chain 'I' and resid 570 through 572' Processing helix chain 'I' and resid 573 through 592 Processing helix chain 'I' and resid 599 through 608 Processing helix chain 'I' and resid 633 through 638 Processing helix chain 'I' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU I 642 " --> pdb=" O GLU I 638 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU I 643 " --> pdb=" O ARG I 639 " (cutoff:3.500A) Processing helix chain 'I' and resid 649 through 662 Processing helix chain 'I' and resid 662 through 671 Processing helix chain 'I' and resid 681 through 700 Processing helix chain 'I' and resid 718 through 721 Processing helix chain 'I' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG I 726 " --> pdb=" O HIS I 722 " (cutoff:3.500A) Processing helix chain 'I' and resid 756 through 772 Processing helix chain 'I' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL I 786 " --> pdb=" O LYS I 782 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG I 791 " --> pdb=" O ASN I 787 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU J 6 " --> pdb=" O GLU J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 18 Processing helix chain 'J' and resid 25 through 41 Processing helix chain 'J' and resid 47 through 63 Processing helix chain 'J' and resid 68 through 80 Processing helix chain 'J' and resid 94 through 103 Processing helix chain 'J' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE J 110 " --> pdb=" O SER J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 147 Processing helix chain 'J' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS J 164 " --> pdb=" O SER J 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP J 165 " --> pdb=" O ALA J 161 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY J 182 " --> pdb=" O ASP J 178 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA J 184 " --> pdb=" O GLU J 180 " (cutoff:3.500A) Processing helix chain 'J' and resid 185 through 196 Processing helix chain 'J' and resid 199 through 224 removed outlier: 3.658A pdb=" N ILE J 203 " --> pdb=" O LEU J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 228 through 232 Processing helix chain 'J' and resid 236 through 242 removed outlier: 3.839A pdb=" N ASN J 242 " --> pdb=" O GLN J 239 " (cutoff:3.500A) Processing helix chain 'J' and resid 265 through 280 Processing helix chain 'J' and resid 285 through 309 Processing helix chain 'J' and resid 323 through 327 Processing helix chain 'J' and resid 332 through 342 Processing helix chain 'J' and resid 362 through 383 Processing helix chain 'J' and resid 396 through 405 Processing helix chain 'J' and resid 435 through 456 Processing helix chain 'J' and resid 457 through 462 Processing helix chain 'J' and resid 471 through 475 removed outlier: 3.634A pdb=" N HIS J 474 " --> pdb=" O ASN J 471 " (cutoff:3.500A) Processing helix chain 'J' and resid 476 through 479 Processing helix chain 'J' and resid 480 through 491 Processing helix chain 'J' and resid 505 through 520 Processing helix chain 'J' and resid 531 through 535 Processing helix chain 'J' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS J 542 " --> pdb=" O SER J 539 " (cutoff:3.500A) Processing helix chain 'J' and resid 553 through 568 Processing helix chain 'J' and resid 570 through 572 No H-bonds generated for 'chain 'J' and resid 570 through 572' Processing helix chain 'J' and resid 573 through 592 Processing helix chain 'J' and resid 599 through 608 Processing helix chain 'J' and resid 633 through 638 Processing helix chain 'J' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU J 642 " --> pdb=" O GLU J 638 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU J 643 " --> pdb=" O ARG J 639 " (cutoff:3.500A) Processing helix chain 'J' and resid 649 through 662 Processing helix chain 'J' and resid 662 through 671 Processing helix chain 'J' and resid 681 through 700 Processing helix chain 'J' and resid 718 through 721 Processing helix chain 'J' and resid 722 through 729 removed outlier: 4.159A pdb=" N ARG J 726 " --> pdb=" O HIS J 722 " (cutoff:3.500A) Processing helix chain 'J' and resid 756 through 772 Processing helix chain 'J' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL J 786 " --> pdb=" O LYS J 782 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG J 791 " --> pdb=" O ASN J 787 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU K 6 " --> pdb=" O GLU K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 8 through 18 Processing helix chain 'K' and resid 25 through 41 Processing helix chain 'K' and resid 47 through 63 Processing helix chain 'K' and resid 68 through 80 Processing helix chain 'K' and resid 94 through 103 Processing helix chain 'K' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE K 110 " --> pdb=" O SER K 106 " (cutoff:3.500A) Processing helix chain 'K' and resid 136 through 147 Processing helix chain 'K' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS K 164 " --> pdb=" O SER K 160 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TRP K 165 " --> pdb=" O ALA K 161 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA K 184 " --> pdb=" O GLU K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 185 through 196 Processing helix chain 'K' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE K 203 " --> pdb=" O LEU K 199 " (cutoff:3.500A) Processing helix chain 'K' and resid 228 through 232 Processing helix chain 'K' and resid 236 through 242 removed outlier: 3.839A pdb=" N ASN K 242 " --> pdb=" O GLN K 239 " (cutoff:3.500A) Processing helix chain 'K' and resid 265 through 280 Processing helix chain 'K' and resid 285 through 309 Processing helix chain 'K' and resid 323 through 327 Processing helix chain 'K' and resid 332 through 342 Processing helix chain 'K' and resid 362 through 383 Processing helix chain 'K' and resid 396 through 405 Processing helix chain 'K' and resid 435 through 456 Processing helix chain 'K' and resid 457 through 462 Processing helix chain 'K' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS K 474 " --> pdb=" O ASN K 471 " (cutoff:3.500A) Processing helix chain 'K' and resid 476 through 479 Processing helix chain 'K' and resid 480 through 491 Processing helix chain 'K' and resid 505 through 520 Processing helix chain 'K' and resid 531 through 535 Processing helix chain 'K' and resid 538 through 542 removed outlier: 3.768A pdb=" N LYS K 542 " --> pdb=" O SER K 539 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 568 Processing helix chain 'K' and resid 570 through 572 No H-bonds generated for 'chain 'K' and resid 570 through 572' Processing helix chain 'K' and resid 573 through 592 Processing helix chain 'K' and resid 599 through 608 Processing helix chain 'K' and resid 633 through 638 Processing helix chain 'K' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU K 642 " --> pdb=" O GLU K 638 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU K 643 " --> pdb=" O ARG K 639 " (cutoff:3.500A) Processing helix chain 'K' and resid 649 through 662 Processing helix chain 'K' and resid 662 through 671 Processing helix chain 'K' and resid 681 through 700 Processing helix chain 'K' and resid 718 through 721 Processing helix chain 'K' and resid 722 through 729 removed outlier: 4.159A pdb=" N ARG K 726 " --> pdb=" O HIS K 722 " (cutoff:3.500A) Processing helix chain 'K' and resid 756 through 772 Processing helix chain 'K' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL K 786 " --> pdb=" O LYS K 782 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG K 791 " --> pdb=" O ASN K 787 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 3.662A pdb=" N LEU L 6 " --> pdb=" O GLU L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 8 through 18 Processing helix chain 'L' and resid 25 through 41 Processing helix chain 'L' and resid 47 through 63 Processing helix chain 'L' and resid 68 through 80 Processing helix chain 'L' and resid 94 through 103 Processing helix chain 'L' and resid 106 through 118 removed outlier: 4.507A pdb=" N ILE L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 147 Processing helix chain 'L' and resid 160 through 171 removed outlier: 3.892A pdb=" N CYS L 164 " --> pdb=" O SER L 160 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP L 165 " --> pdb=" O ALA L 161 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU L 166 " --> pdb=" O GLU L 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 171 through 184 removed outlier: 3.750A pdb=" N GLY L 182 " --> pdb=" O ASP L 178 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA L 184 " --> pdb=" O GLU L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 196 Processing helix chain 'L' and resid 199 through 224 removed outlier: 3.657A pdb=" N ILE L 203 " --> pdb=" O LEU L 199 " (cutoff:3.500A) Processing helix chain 'L' and resid 228 through 232 Processing helix chain 'L' and resid 236 through 242 removed outlier: 3.838A pdb=" N ASN L 242 " --> pdb=" O GLN L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 265 through 280 Processing helix chain 'L' and resid 285 through 309 Processing helix chain 'L' and resid 323 through 327 Processing helix chain 'L' and resid 332 through 342 Processing helix chain 'L' and resid 362 through 383 Processing helix chain 'L' and resid 396 through 405 Processing helix chain 'L' and resid 435 through 456 Processing helix chain 'L' and resid 457 through 462 Processing helix chain 'L' and resid 471 through 475 removed outlier: 3.633A pdb=" N HIS L 474 " --> pdb=" O ASN L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 476 through 479 Processing helix chain 'L' and resid 480 through 491 Processing helix chain 'L' and resid 505 through 520 Processing helix chain 'L' and resid 531 through 535 Processing helix chain 'L' and resid 538 through 542 removed outlier: 3.769A pdb=" N LYS L 542 " --> pdb=" O SER L 539 " (cutoff:3.500A) Processing helix chain 'L' and resid 553 through 568 Processing helix chain 'L' and resid 570 through 572 No H-bonds generated for 'chain 'L' and resid 570 through 572' Processing helix chain 'L' and resid 573 through 592 Processing helix chain 'L' and resid 599 through 608 Processing helix chain 'L' and resid 633 through 638 Processing helix chain 'L' and resid 638 through 646 removed outlier: 4.105A pdb=" N GLU L 642 " --> pdb=" O GLU L 638 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LEU L 643 " --> pdb=" O ARG L 639 " (cutoff:3.500A) Processing helix chain 'L' and resid 649 through 662 Processing helix chain 'L' and resid 662 through 671 Processing helix chain 'L' and resid 681 through 700 Processing helix chain 'L' and resid 718 through 721 Processing helix chain 'L' and resid 722 through 729 removed outlier: 4.160A pdb=" N ARG L 726 " --> pdb=" O HIS L 722 " (cutoff:3.500A) Processing helix chain 'L' and resid 756 through 772 Processing helix chain 'L' and resid 775 through 793 removed outlier: 3.642A pdb=" N VAL L 786 " --> pdb=" O LYS L 782 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG L 791 " --> pdb=" O ASN L 787 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AA2, first strand: chain 'A' and resid 148 through 150 removed outlier: 7.514A pdb=" N LEU A 148 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU A 353 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU A 150 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLY A 355 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG A 351 " --> pdb=" O GLU A 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA A 417 " --> pdb=" O ARG A 351 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU A 353 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL A 419 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY A 355 " --> pdb=" O VAL A 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 246 Processing sheet with id=AA4, first strand: chain 'A' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL A 466 " --> pdb=" O THR A 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 548 through 552 Processing sheet with id=AA6, first strand: chain 'A' and resid 703 through 705 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AA8, first strand: chain 'B' and resid 148 through 150 removed outlier: 7.514A pdb=" N LEU B 148 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU B 353 " --> pdb=" O LEU B 148 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU B 150 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLY B 355 " --> pdb=" O GLU B 150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG B 351 " --> pdb=" O GLU B 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA B 417 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 353 " --> pdb=" O ALA B 417 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL B 419 " --> pdb=" O LEU B 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY B 355 " --> pdb=" O VAL B 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 244 through 246 Processing sheet with id=AB1, first strand: chain 'B' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL B 466 " --> pdb=" O THR B 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 548 through 552 Processing sheet with id=AB3, first strand: chain 'B' and resid 703 through 705 removed outlier: 6.166A pdb=" N ILE B 703 " --> pdb=" O CYS B 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 81 through 83 Processing sheet with id=AB5, first strand: chain 'C' and resid 148 through 150 removed outlier: 7.514A pdb=" N LEU C 148 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU C 353 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU C 150 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY C 355 " --> pdb=" O GLU C 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG C 351 " --> pdb=" O GLU C 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA C 417 " --> pdb=" O ARG C 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU C 353 " --> pdb=" O ALA C 417 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL C 419 " --> pdb=" O LEU C 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY C 355 " --> pdb=" O VAL C 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 244 through 246 Processing sheet with id=AB7, first strand: chain 'C' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL C 466 " --> pdb=" O THR C 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'C' and resid 548 through 552 Processing sheet with id=AB9, first strand: chain 'C' and resid 703 through 705 removed outlier: 6.166A pdb=" N ILE C 703 " --> pdb=" O CYS C 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 81 through 83 Processing sheet with id=AC2, first strand: chain 'D' and resid 148 through 150 removed outlier: 7.514A pdb=" N LEU D 148 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU D 353 " --> pdb=" O LEU D 148 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU D 150 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY D 355 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG D 351 " --> pdb=" O GLU D 415 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA D 417 " --> pdb=" O ARG D 351 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU D 353 " --> pdb=" O ALA D 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL D 419 " --> pdb=" O LEU D 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY D 355 " --> pdb=" O VAL D 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'D' and resid 244 through 246 Processing sheet with id=AC4, first strand: chain 'D' and resid 466 through 468 removed outlier: 5.974A pdb=" N VAL D 466 " --> pdb=" O THR D 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'D' and resid 548 through 552 Processing sheet with id=AC6, first strand: chain 'D' and resid 703 through 705 removed outlier: 6.167A pdb=" N ILE D 703 " --> pdb=" O CYS D 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'E' and resid 81 through 83 Processing sheet with id=AC8, first strand: chain 'E' and resid 148 through 150 removed outlier: 7.513A pdb=" N LEU E 148 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU E 353 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU E 150 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY E 355 " --> pdb=" O GLU E 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG E 351 " --> pdb=" O GLU E 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA E 417 " --> pdb=" O ARG E 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU E 353 " --> pdb=" O ALA E 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL E 419 " --> pdb=" O LEU E 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY E 355 " --> pdb=" O VAL E 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'E' and resid 244 through 246 Processing sheet with id=AD1, first strand: chain 'E' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL E 466 " --> pdb=" O THR E 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 548 through 552 Processing sheet with id=AD3, first strand: chain 'E' and resid 703 through 705 Processing sheet with id=AD4, first strand: chain 'F' and resid 81 through 83 Processing sheet with id=AD5, first strand: chain 'F' and resid 148 through 150 removed outlier: 7.513A pdb=" N LEU F 148 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU F 353 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU F 150 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY F 355 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG F 351 " --> pdb=" O GLU F 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA F 417 " --> pdb=" O ARG F 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU F 353 " --> pdb=" O ALA F 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL F 419 " --> pdb=" O LEU F 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY F 355 " --> pdb=" O VAL F 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'F' and resid 244 through 246 Processing sheet with id=AD7, first strand: chain 'F' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL F 466 " --> pdb=" O THR F 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'F' and resid 548 through 552 Processing sheet with id=AD9, first strand: chain 'F' and resid 703 through 705 Processing sheet with id=AE1, first strand: chain 'G' and resid 81 through 83 Processing sheet with id=AE2, first strand: chain 'G' and resid 148 through 150 removed outlier: 7.513A pdb=" N LEU G 148 " --> pdb=" O ARG G 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU G 353 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU G 150 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY G 355 " --> pdb=" O GLU G 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG G 351 " --> pdb=" O GLU G 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA G 417 " --> pdb=" O ARG G 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU G 353 " --> pdb=" O ALA G 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL G 419 " --> pdb=" O LEU G 353 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLY G 355 " --> pdb=" O VAL G 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'G' and resid 244 through 246 Processing sheet with id=AE4, first strand: chain 'G' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL G 466 " --> pdb=" O THR G 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'G' and resid 548 through 552 Processing sheet with id=AE6, first strand: chain 'G' and resid 703 through 705 Processing sheet with id=AE7, first strand: chain 'H' and resid 81 through 83 Processing sheet with id=AE8, first strand: chain 'H' and resid 148 through 150 removed outlier: 7.515A pdb=" N LEU H 148 " --> pdb=" O ARG H 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU H 353 " --> pdb=" O LEU H 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU H 150 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLY H 355 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG H 351 " --> pdb=" O GLU H 415 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N ALA H 417 " --> pdb=" O ARG H 351 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU H 353 " --> pdb=" O ALA H 417 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL H 419 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY H 355 " --> pdb=" O VAL H 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'H' and resid 244 through 246 Processing sheet with id=AF1, first strand: chain 'H' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL H 466 " --> pdb=" O THR H 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'H' and resid 548 through 552 Processing sheet with id=AF3, first strand: chain 'H' and resid 703 through 705 removed outlier: 6.166A pdb=" N ILE H 703 " --> pdb=" O CYS H 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'I' and resid 81 through 83 Processing sheet with id=AF5, first strand: chain 'I' and resid 148 through 150 removed outlier: 7.513A pdb=" N LEU I 148 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU I 353 " --> pdb=" O LEU I 148 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU I 150 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY I 355 " --> pdb=" O GLU I 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG I 351 " --> pdb=" O GLU I 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA I 417 " --> pdb=" O ARG I 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU I 353 " --> pdb=" O ALA I 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL I 419 " --> pdb=" O LEU I 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY I 355 " --> pdb=" O VAL I 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'I' and resid 244 through 246 Processing sheet with id=AF7, first strand: chain 'I' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL I 466 " --> pdb=" O THR I 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'I' and resid 548 through 552 Processing sheet with id=AF9, first strand: chain 'I' and resid 703 through 705 removed outlier: 6.165A pdb=" N ILE I 703 " --> pdb=" O CYS I 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'J' and resid 81 through 83 Processing sheet with id=AG2, first strand: chain 'J' and resid 148 through 150 removed outlier: 7.513A pdb=" N LEU J 148 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU J 353 " --> pdb=" O LEU J 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU J 150 " --> pdb=" O LEU J 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY J 355 " --> pdb=" O GLU J 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG J 351 " --> pdb=" O GLU J 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA J 417 " --> pdb=" O ARG J 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU J 353 " --> pdb=" O ALA J 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL J 419 " --> pdb=" O LEU J 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY J 355 " --> pdb=" O VAL J 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'J' and resid 244 through 246 Processing sheet with id=AG4, first strand: chain 'J' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL J 466 " --> pdb=" O THR J 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'J' and resid 548 through 552 Processing sheet with id=AG6, first strand: chain 'J' and resid 703 through 705 removed outlier: 6.166A pdb=" N ILE J 703 " --> pdb=" O CYS J 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'K' and resid 81 through 83 Processing sheet with id=AG8, first strand: chain 'K' and resid 148 through 150 removed outlier: 7.514A pdb=" N LEU K 148 " --> pdb=" O ARG K 351 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU K 353 " --> pdb=" O LEU K 148 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU K 150 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY K 355 " --> pdb=" O GLU K 150 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ARG K 351 " --> pdb=" O GLU K 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA K 417 " --> pdb=" O ARG K 351 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU K 353 " --> pdb=" O ALA K 417 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N VAL K 419 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY K 355 " --> pdb=" O VAL K 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'K' and resid 244 through 246 Processing sheet with id=AH1, first strand: chain 'K' and resid 466 through 468 removed outlier: 5.974A pdb=" N VAL K 466 " --> pdb=" O THR K 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'K' and resid 548 through 552 Processing sheet with id=AH3, first strand: chain 'K' and resid 703 through 705 removed outlier: 6.166A pdb=" N ILE K 703 " --> pdb=" O CYS K 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'L' and resid 81 through 83 Processing sheet with id=AH5, first strand: chain 'L' and resid 148 through 150 removed outlier: 7.513A pdb=" N LEU L 148 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU L 353 " --> pdb=" O LEU L 148 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLU L 150 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLY L 355 " --> pdb=" O GLU L 150 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG L 351 " --> pdb=" O GLU L 415 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ALA L 417 " --> pdb=" O ARG L 351 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU L 353 " --> pdb=" O ALA L 417 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL L 419 " --> pdb=" O LEU L 353 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N GLY L 355 " --> pdb=" O VAL L 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'L' and resid 244 through 246 Processing sheet with id=AH7, first strand: chain 'L' and resid 466 through 468 removed outlier: 5.975A pdb=" N VAL L 466 " --> pdb=" O THR L 496 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'L' and resid 548 through 552 Processing sheet with id=AH9, first strand: chain 'L' and resid 703 through 705 removed outlier: 6.166A pdb=" N ILE L 703 " --> pdb=" O CYS L 744 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 3992 hydrogen bonds defined for protein. 11472 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: 31.84 Time building geometry restraints manager: 25.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 12295 1.31 - 1.44: 20638 1.44 - 1.57: 43170 1.57 - 1.69: 24 1.69 - 1.82: 648 Bond restraints: 76775 Sorted by residual: bond pdb=" CD2 TYR G 13 " pdb=" CE2 TYR G 13 " ideal model delta sigma weight residual 1.382 1.548 -0.166 3.00e-02 1.11e+03 3.08e+01 bond pdb=" CD2 TYR I 13 " pdb=" CE2 TYR I 13 " ideal model delta sigma weight residual 1.382 1.548 -0.166 3.00e-02 1.11e+03 3.07e+01 bond pdb=" CD2 TYR F 13 " pdb=" CE2 TYR F 13 " ideal model delta sigma weight residual 1.382 1.548 -0.166 3.00e-02 1.11e+03 3.07e+01 bond pdb=" CD2 TYR C 13 " pdb=" CE2 TYR C 13 " ideal model delta sigma weight residual 1.382 1.548 -0.166 3.00e-02 1.11e+03 3.07e+01 bond pdb=" CD2 TYR J 13 " pdb=" CE2 TYR J 13 " ideal model delta sigma weight residual 1.382 1.548 -0.166 3.00e-02 1.11e+03 3.06e+01 ... (remaining 76770 not shown) Histogram of bond angle deviations from ideal: 93.54 - 103.94: 1195 103.94 - 114.35: 44826 114.35 - 124.76: 55799 124.76 - 135.17: 2149 135.17 - 145.58: 60 Bond angle restraints: 104029 Sorted by residual: angle pdb=" CG ARG F 129 " pdb=" CD ARG F 129 " pdb=" NE ARG F 129 " ideal model delta sigma weight residual 112.00 142.11 -30.11 2.20e+00 2.07e-01 1.87e+02 angle pdb=" CG ARG H 129 " pdb=" CD ARG H 129 " pdb=" NE ARG H 129 " ideal model delta sigma weight residual 112.00 142.11 -30.11 2.20e+00 2.07e-01 1.87e+02 angle pdb=" CG ARG E 129 " pdb=" CD ARG E 129 " pdb=" NE ARG E 129 " ideal model delta sigma weight residual 112.00 142.10 -30.10 2.20e+00 2.07e-01 1.87e+02 angle pdb=" CG ARG D 129 " pdb=" CD ARG D 129 " pdb=" NE ARG D 129 " ideal model delta sigma weight residual 112.00 142.09 -30.09 2.20e+00 2.07e-01 1.87e+02 angle pdb=" CG ARG K 129 " pdb=" CD ARG K 129 " pdb=" NE ARG K 129 " ideal model delta sigma weight residual 112.00 142.08 -30.08 2.20e+00 2.07e-01 1.87e+02 ... (remaining 104024 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 39502 17.75 - 35.49: 4897 35.49 - 53.24: 1323 53.24 - 70.99: 395 70.99 - 88.73: 258 Dihedral angle restraints: 46375 sinusoidal: 19241 harmonic: 27134 Sorted by residual: dihedral pdb=" CD ARG C 586 " pdb=" NE ARG C 586 " pdb=" CZ ARG C 586 " pdb=" NH1 ARG C 586 " ideal model delta sinusoidal sigma weight residual 0.00 80.45 -80.45 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CD ARG G 586 " pdb=" NE ARG G 586 " pdb=" CZ ARG G 586 " pdb=" NH1 ARG G 586 " ideal model delta sinusoidal sigma weight residual 0.00 80.44 -80.44 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CD ARG I 586 " pdb=" NE ARG I 586 " pdb=" CZ ARG I 586 " pdb=" NH1 ARG I 586 " ideal model delta sinusoidal sigma weight residual 0.00 80.44 -80.44 1 1.00e+01 1.00e-02 8.01e+01 ... (remaining 46372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.181: 11092 0.181 - 0.363: 197 0.363 - 0.544: 48 0.544 - 0.726: 0 0.726 - 0.907: 12 Chirality restraints: 11349 Sorted by residual: chirality pdb=" CG LEU G 653 " pdb=" CB LEU G 653 " pdb=" CD1 LEU G 653 " pdb=" CD2 LEU G 653 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.06e+01 chirality pdb=" CG LEU K 653 " pdb=" CB LEU K 653 " pdb=" CD1 LEU K 653 " pdb=" CD2 LEU K 653 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.05e+01 chirality pdb=" CG LEU B 653 " pdb=" CB LEU B 653 " pdb=" CD1 LEU B 653 " pdb=" CD2 LEU B 653 " both_signs ideal model delta sigma weight residual False -2.59 -1.68 -0.91 2.00e-01 2.50e+01 2.05e+01 ... (remaining 11346 not shown) Planarity restraints: 13302 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG L 586 " 0.884 9.50e-02 1.11e+02 3.97e-01 1.08e+02 pdb=" NE ARG L 586 " -0.076 2.00e-02 2.50e+03 pdb=" CZ ARG L 586 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG L 586 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG L 586 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 586 " 0.883 9.50e-02 1.11e+02 3.97e-01 1.08e+02 pdb=" NE ARG B 586 " -0.076 2.00e-02 2.50e+03 pdb=" CZ ARG B 586 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG B 586 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 586 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 586 " -0.883 9.50e-02 1.11e+02 3.97e-01 1.08e+02 pdb=" NE ARG C 586 " 0.076 2.00e-02 2.50e+03 pdb=" CZ ARG C 586 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG C 586 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 586 " 0.001 2.00e-02 2.50e+03 ... (remaining 13299 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 972 2.59 - 3.17: 64147 3.17 - 3.75: 124133 3.75 - 4.32: 176332 4.32 - 4.90: 282734 Nonbonded interactions: 648318 Sorted by model distance: nonbonded pdb=" O THR F 100 " pdb=" OG SER F 103 " model vdw 2.014 2.440 nonbonded pdb=" O THR J 100 " pdb=" OG SER J 103 " model vdw 2.014 2.440 nonbonded pdb=" O THR B 100 " pdb=" OG SER B 103 " model vdw 2.015 2.440 nonbonded pdb=" O THR I 100 " pdb=" OG SER I 103 " model vdw 2.015 2.440 nonbonded pdb=" O THR C 100 " pdb=" OG SER C 103 " model vdw 2.015 2.440 ... (remaining 648313 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'B' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'C' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = chain 'D' selection = (chain 'E' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'F' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'G' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'H' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'I' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'J' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'K' and (resid 1 through 122 or resid 126 through 798 or resid 801)) selection = (chain 'L' and (resid 1 through 122 or resid 126 through 798 or resid 801)) } 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: 4.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 24.550 Check model and map are aligned: 0.810 Set scattering table: 0.510 Process input model: 155.950 Find NCS groups from input model: 4.720 Set up NCS constraints: 0.290 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 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 : 0.007 0.166 76775 Z= 0.464 Angle : 1.362 33.681 104029 Z= 0.618 Chirality : 0.068 0.907 11349 Planarity : 0.018 0.397 13302 Dihedral : 18.515 88.733 28741 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.73 % Favored : 93.48 % Rotamer: Outliers : 3.84 % Allowed : 18.35 % Favored : 77.82 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 0.03 (0.09), residues: 9139 helix: 1.05 (0.07), residues: 5376 sheet: -2.51 (0.22), residues: 516 loop : -1.25 (0.10), residues: 3247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 130 HIS 0.021 0.002 HIS C 391 PHE 0.018 0.001 PHE C 439 TYR 0.109 0.004 TYR I 13 ARG 0.060 0.002 ARG B 586 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1327 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 1015 time to evaluate : 6.461 Fit side-chains REVERT: A 332 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7168 (tppt) REVERT: A 364 ASN cc_start: 0.7597 (OUTLIER) cc_final: 0.7293 (m110) REVERT: A 650 LYS cc_start: 0.6076 (OUTLIER) cc_final: 0.5469 (tppp) REVERT: A 664 ASN cc_start: 0.7696 (t0) cc_final: 0.7472 (t0) REVERT: B 323 MET cc_start: 0.5539 (tmt) cc_final: 0.5224 (tmt) REVERT: B 650 LYS cc_start: 0.5914 (OUTLIER) cc_final: 0.5500 (tppp) REVERT: C 309 ARG cc_start: 0.7244 (OUTLIER) cc_final: 0.7006 (mtm180) REVERT: C 364 ASN cc_start: 0.7443 (OUTLIER) cc_final: 0.7130 (m-40) REVERT: C 638 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6195 (mm-30) REVERT: C 649 MET cc_start: 0.6249 (mmm) cc_final: 0.6002 (mmm) REVERT: D 330 THR cc_start: 0.7536 (p) cc_final: 0.7185 (t) REVERT: D 638 GLU cc_start: 0.6470 (OUTLIER) cc_final: 0.6217 (mm-30) REVERT: D 650 LYS cc_start: 0.5896 (OUTLIER) cc_final: 0.5224 (tppp) REVERT: D 653 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7868 (tm) REVERT: E 332 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7310 (tppt) REVERT: E 450 MET cc_start: 0.7993 (mtm) cc_final: 0.7734 (mtm) REVERT: E 638 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6163 (mm-30) REVERT: E 650 LYS cc_start: 0.5920 (OUTLIER) cc_final: 0.5253 (tppp) REVERT: E 653 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7983 (tm) REVERT: F 25 LEU cc_start: 0.7268 (mt) cc_final: 0.7026 (mp) REVERT: F 332 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7310 (tppt) REVERT: F 572 GLU cc_start: 0.7207 (mp0) cc_final: 0.6984 (mp0) REVERT: F 650 LYS cc_start: 0.5777 (OUTLIER) cc_final: 0.5402 (tppp) REVERT: F 653 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7913 (tm) REVERT: G 173 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.6609 (tp30) REVERT: G 638 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.6096 (mm-30) REVERT: G 649 MET cc_start: 0.6190 (mmm) cc_final: 0.5946 (mmm) REVERT: H 364 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7231 (m-40) REVERT: H 650 LYS cc_start: 0.6011 (OUTLIER) cc_final: 0.5579 (tppp) REVERT: H 653 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8005 (tm) REVERT: I 173 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6665 (tp30) REVERT: I 203 ILE cc_start: 0.8581 (mt) cc_final: 0.8361 (mp) REVERT: I 332 LYS cc_start: 0.7666 (OUTLIER) cc_final: 0.7261 (tppt) REVERT: I 572 GLU cc_start: 0.7250 (mp0) cc_final: 0.6963 (mp0) REVERT: I 650 LYS cc_start: 0.5987 (OUTLIER) cc_final: 0.5561 (tppp) REVERT: I 653 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.8037 (tm) REVERT: I 654 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7457 (tttp) REVERT: J 27 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6320 (tp30) REVERT: J 332 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7251 (tppt) REVERT: J 366 MET cc_start: 0.8843 (tpt) cc_final: 0.8636 (tpt) REVERT: J 638 GLU cc_start: 0.6446 (OUTLIER) cc_final: 0.6162 (mm-30) REVERT: J 654 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7578 (tmmt) REVERT: K 102 MET cc_start: 0.8737 (mmp) cc_final: 0.8374 (mmp) REVERT: K 202 ARG cc_start: 0.7461 (tmm160) cc_final: 0.7197 (tmm-80) REVERT: K 452 MET cc_start: 0.8143 (mtp) cc_final: 0.7883 (mtp) REVERT: K 650 LYS cc_start: 0.5959 (OUTLIER) cc_final: 0.5598 (tppp) REVERT: K 653 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7929 (tm) REVERT: L 332 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7262 (tppt) REVERT: L 638 GLU cc_start: 0.6542 (OUTLIER) cc_final: 0.6326 (mm-30) outliers start: 312 outliers final: 67 residues processed: 1146 average time/residue: 1.9539 time to fit residues: 2809.5654 Evaluate side-chains 990 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 889 time to evaluate : 6.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 364 ASN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 490 SER Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 650 LYS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 490 SER Chi-restraints excluded: chain B residue 568 ARG Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 650 LYS Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 364 ASN Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 490 SER Chi-restraints excluded: chain C residue 568 ARG Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 638 GLU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 490 SER Chi-restraints excluded: chain D residue 568 ARG Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 638 GLU Chi-restraints excluded: chain D residue 650 LYS Chi-restraints excluded: chain D residue 653 LEU Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 332 LYS Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain E residue 601 THR Chi-restraints excluded: chain E residue 638 GLU Chi-restraints excluded: chain E residue 650 LYS Chi-restraints excluded: chain E residue 653 LEU Chi-restraints excluded: chain F residue 66 LYS Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 332 LYS Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 490 SER Chi-restraints excluded: chain F residue 568 ARG Chi-restraints excluded: chain F residue 601 THR Chi-restraints excluded: chain F residue 650 LYS Chi-restraints excluded: chain F residue 653 LEU Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 386 SER Chi-restraints excluded: chain G residue 568 ARG Chi-restraints excluded: chain G residue 601 THR Chi-restraints excluded: chain G residue 638 GLU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 364 ASN Chi-restraints excluded: chain H residue 386 SER Chi-restraints excluded: chain H residue 490 SER Chi-restraints excluded: chain H residue 568 ARG Chi-restraints excluded: chain H residue 601 THR Chi-restraints excluded: chain H residue 650 LYS Chi-restraints excluded: chain H residue 653 LEU Chi-restraints excluded: chain H residue 698 ASP Chi-restraints excluded: chain I residue 66 LYS Chi-restraints excluded: chain I residue 173 GLU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 332 LYS Chi-restraints excluded: chain I residue 386 SER Chi-restraints excluded: chain I residue 568 ARG Chi-restraints excluded: chain I residue 601 THR Chi-restraints excluded: chain I residue 650 LYS Chi-restraints excluded: chain I residue 653 LEU Chi-restraints excluded: chain I residue 654 LYS Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 332 LYS Chi-restraints excluded: chain J residue 386 SER Chi-restraints excluded: chain J residue 490 SER Chi-restraints excluded: chain J residue 568 ARG Chi-restraints excluded: chain J residue 601 THR Chi-restraints excluded: chain J residue 638 GLU Chi-restraints excluded: chain J residue 654 LYS Chi-restraints excluded: chain K residue 221 VAL Chi-restraints excluded: chain K residue 386 SER Chi-restraints excluded: chain K residue 568 ARG Chi-restraints excluded: chain K residue 601 THR Chi-restraints excluded: chain K residue 650 LYS Chi-restraints excluded: chain K residue 653 LEU Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 309 ARG Chi-restraints excluded: chain L residue 332 LYS Chi-restraints excluded: chain L residue 386 SER Chi-restraints excluded: chain L residue 490 SER Chi-restraints excluded: chain L residue 568 ARG Chi-restraints excluded: chain L residue 601 THR Chi-restraints excluded: chain L residue 638 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 779 optimal weight: 4.9990 chunk 699 optimal weight: 1.9990 chunk 388 optimal weight: 0.9980 chunk 238 optimal weight: 0.7980 chunk 471 optimal weight: 3.9990 chunk 373 optimal weight: 0.6980 chunk 723 optimal weight: 0.8980 chunk 279 optimal weight: 0.8980 chunk 439 optimal weight: 1.9990 chunk 538 optimal weight: 10.0000 chunk 838 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN ** B 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** F 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 156 ASN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN ** F 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 ASN H 156 ASN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** J 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 ASN ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 391 HIS ** K 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 83 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 76775 Z= 0.182 Angle : 0.582 11.754 104029 Z= 0.293 Chirality : 0.040 0.140 11349 Planarity : 0.005 0.061 13302 Dihedral : 5.883 59.331 10340 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.02 % Favored : 94.19 % Rotamer: Outliers : 2.23 % Allowed : 19.33 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % 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: 1.00 (0.09), residues: 9139 helix: 1.92 (0.07), residues: 5354 sheet: -2.17 (0.21), residues: 564 loop : -0.95 (0.11), residues: 3221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 659 HIS 0.010 0.001 HIS K 149 PHE 0.014 0.002 PHE J 725 TYR 0.012 0.002 TYR G 497 ARG 0.005 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 994 time to evaluate : 6.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 387 MET cc_start: 0.7158 (ptm) cc_final: 0.6726 (ptm) REVERT: A 489 LYS cc_start: 0.8083 (mttp) cc_final: 0.7761 (mptt) REVERT: A 595 GLU cc_start: 0.6614 (mm-30) cc_final: 0.6190 (tt0) REVERT: B 28 ARG cc_start: 0.7316 (mmm160) cc_final: 0.6824 (mtm180) REVERT: B 332 LYS cc_start: 0.7637 (mmpt) cc_final: 0.7199 (tppt) REVERT: B 489 LYS cc_start: 0.8027 (mttp) cc_final: 0.7602 (mppt) REVERT: B 664 ASN cc_start: 0.7509 (t0) cc_final: 0.7194 (t0) REVERT: C 364 ASN cc_start: 0.7828 (m-40) cc_final: 0.7462 (m-40) REVERT: C 415 GLU cc_start: 0.8034 (mt-10) cc_final: 0.7759 (mt-10) REVERT: C 664 ASN cc_start: 0.7321 (OUTLIER) cc_final: 0.6812 (p0) REVERT: D 28 ARG cc_start: 0.7185 (mmm160) cc_final: 0.6727 (mtm180) REVERT: D 330 THR cc_start: 0.7569 (p) cc_final: 0.7233 (t) REVERT: E 173 GLU cc_start: 0.7165 (pm20) cc_final: 0.6315 (tp30) REVERT: E 234 MET cc_start: 0.7699 (ttp) cc_final: 0.7473 (ttp) REVERT: E 387 MET cc_start: 0.7234 (ptm) cc_final: 0.6688 (ptm) REVERT: E 489 LYS cc_start: 0.8074 (mttp) cc_final: 0.7616 (mmtm) REVERT: E 575 ARG cc_start: 0.7526 (ttp-110) cc_final: 0.7258 (tpp-160) REVERT: F 27 GLU cc_start: 0.6787 (tm-30) cc_final: 0.6457 (tp30) REVERT: F 332 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7318 (tppt) REVERT: F 489 LYS cc_start: 0.8119 (mttp) cc_final: 0.7712 (mppt) REVERT: G 387 MET cc_start: 0.7174 (ptm) cc_final: 0.6922 (ptm) REVERT: H 187 GLU cc_start: 0.6499 (tm-30) cc_final: 0.5838 (tm-30) REVERT: H 489 LYS cc_start: 0.8144 (mttp) cc_final: 0.7812 (mppt) REVERT: I 173 GLU cc_start: 0.6876 (pm20) cc_final: 0.6450 (tp30) REVERT: I 187 GLU cc_start: 0.6385 (tm-30) cc_final: 0.5491 (tp30) REVERT: I 267 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: I 387 MET cc_start: 0.7161 (ptm) cc_final: 0.6657 (ptm) REVERT: I 450 MET cc_start: 0.8088 (mtm) cc_final: 0.7885 (mtm) REVERT: I 489 LYS cc_start: 0.8187 (mttp) cc_final: 0.7719 (mmtm) REVERT: I 654 LYS cc_start: 0.7926 (tmmt) cc_final: 0.7689 (ttmt) REVERT: J 27 GLU cc_start: 0.6855 (tm-30) cc_final: 0.6534 (tp30) REVERT: J 188 MET cc_start: 0.8115 (tpt) cc_final: 0.7875 (tpt) REVERT: J 323 MET cc_start: 0.5683 (tmt) cc_final: 0.5415 (tmt) REVERT: J 489 LYS cc_start: 0.8096 (mttp) cc_final: 0.7652 (mmtm) REVERT: J 649 MET cc_start: 0.6281 (mmm) cc_final: 0.6060 (mmm) REVERT: K 102 MET cc_start: 0.8815 (mmp) cc_final: 0.8486 (mmp) REVERT: K 267 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6971 (mp0) REVERT: K 325 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6571 (mp0) REVERT: K 452 MET cc_start: 0.8188 (mtp) cc_final: 0.7921 (mtp) REVERT: L 235 GLN cc_start: 0.7013 (mm110) cc_final: 0.6556 (mm-40) REVERT: L 387 MET cc_start: 0.7139 (ptm) cc_final: 0.6752 (ptm) REVERT: L 489 LYS cc_start: 0.8164 (mttp) cc_final: 0.7753 (mmtm) REVERT: L 583 GLU cc_start: 0.7325 (mt-10) cc_final: 0.7123 (mt-10) outliers start: 181 outliers final: 43 residues processed: 1118 average time/residue: 2.0031 time to fit residues: 2810.5007 Evaluate side-chains 925 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 879 time to evaluate : 6.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 664 ASN Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 698 ASP Chi-restraints excluded: chain E residue 718 ASN Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 756 ASP Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 267 GLU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain I residue 756 ASP Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 547 LEU Chi-restraints excluded: chain K residue 221 VAL Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain L residue 91 ASP Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 483 LEU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 718 ASN Chi-restraints excluded: chain L residue 756 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 465 optimal weight: 5.9990 chunk 260 optimal weight: 7.9990 chunk 697 optimal weight: 0.8980 chunk 570 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 839 optimal weight: 0.0020 chunk 907 optimal weight: 0.9990 chunk 747 optimal weight: 2.9990 chunk 832 optimal weight: 4.9990 chunk 286 optimal weight: 0.0770 chunk 673 optimal weight: 3.9990 overall best weight: 0.9950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 83 ASN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 403 ASN ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 GLN ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN B 589 HIS ** B 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN C 83 ASN C 236 ASN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN C 589 HIS D 62 GLN D 83 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 ASN D 664 ASN D 763 HIS E 62 GLN E 83 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 ASN E 589 HIS ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 GLN F 83 ASN F 124 GLN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 ASN F 589 HIS F 664 ASN G 62 GLN ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 403 ASN G 589 HIS ** G 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 403 ASN H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 62 GLN I 83 ASN ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 403 ASN I 589 HIS ** I 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 62 GLN J 83 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 403 ASN J 589 HIS ** J 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 763 HIS K 62 GLN K 83 ASN K 156 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 403 ASN K 589 HIS ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 GLN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 266 GLN L 403 ASN L 589 HIS ** L 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 76775 Z= 0.175 Angle : 0.561 9.536 104029 Z= 0.283 Chirality : 0.039 0.145 11349 Planarity : 0.004 0.049 13302 Dihedral : 4.577 30.507 10112 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.14 % Favored : 94.20 % Rotamer: Outliers : 1.76 % Allowed : 19.23 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.17 (0.09), residues: 9139 helix: 2.00 (0.07), residues: 5414 sheet: -2.16 (0.20), residues: 574 loop : -0.81 (0.11), residues: 3151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 659 HIS 0.010 0.001 HIS A 149 PHE 0.014 0.002 PHE G 725 TYR 0.015 0.002 TYR D 55 ARG 0.007 0.001 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 934 time to evaluate : 7.418 Fit side-chains REVERT: A 387 MET cc_start: 0.7296 (ptm) cc_final: 0.6811 (ptm) REVERT: A 473 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.7080 (mtt) REVERT: A 489 LYS cc_start: 0.8068 (mttp) cc_final: 0.7712 (mppt) REVERT: A 654 LYS cc_start: 0.7817 (OUTLIER) cc_final: 0.7522 (tmtm) REVERT: B 187 GLU cc_start: 0.6290 (OUTLIER) cc_final: 0.5598 (tp30) REVERT: B 489 LYS cc_start: 0.7956 (mttp) cc_final: 0.7603 (mppt) REVERT: B 664 ASN cc_start: 0.7534 (t0) cc_final: 0.7225 (t0) REVERT: C 187 GLU cc_start: 0.6137 (tm-30) cc_final: 0.5862 (tm-30) REVERT: C 375 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.7963 (ttt180) REVERT: C 664 ASN cc_start: 0.7368 (t0) cc_final: 0.7053 (t160) REVERT: C 718 ASN cc_start: 0.8063 (OUTLIER) cc_final: 0.7842 (p0) REVERT: D 28 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6741 (mtm180) REVERT: D 187 GLU cc_start: 0.6275 (tm-30) cc_final: 0.5384 (tm-30) REVERT: D 330 THR cc_start: 0.7575 (p) cc_final: 0.7231 (t) REVERT: E 309 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6992 (mtm-85) REVERT: E 387 MET cc_start: 0.7337 (ptm) cc_final: 0.6784 (ptm) REVERT: E 489 LYS cc_start: 0.8057 (mttp) cc_final: 0.7725 (mppt) REVERT: E 575 ARG cc_start: 0.7587 (ttp-110) cc_final: 0.7298 (tpp-160) REVERT: F 27 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6750 (tp30) REVERT: F 234 MET cc_start: 0.7613 (ttp) cc_final: 0.7272 (ttp) REVERT: F 325 GLU cc_start: 0.7001 (mm-30) cc_final: 0.6633 (mm-30) REVERT: F 489 LYS cc_start: 0.8074 (mttp) cc_final: 0.7754 (mppt) REVERT: F 654 LYS cc_start: 0.7955 (tmmm) cc_final: 0.7661 (tppt) REVERT: G 177 ARG cc_start: 0.7488 (ttp-110) cc_final: 0.7223 (ttp80) REVERT: G 187 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.6007 (tm-30) REVERT: G 387 MET cc_start: 0.7259 (ptm) cc_final: 0.7009 (ptm) REVERT: G 595 GLU cc_start: 0.6585 (tp30) cc_final: 0.6266 (mm-30) REVERT: H 187 GLU cc_start: 0.6263 (tm-30) cc_final: 0.5656 (tm-30) REVERT: H 267 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7007 (mp0) REVERT: H 450 MET cc_start: 0.8212 (mtm) cc_final: 0.8011 (mtm) REVERT: H 489 LYS cc_start: 0.8051 (mttp) cc_final: 0.7792 (mppt) REVERT: H 664 ASN cc_start: 0.7432 (t0) cc_final: 0.7160 (t0) REVERT: I 187 GLU cc_start: 0.6268 (tm-30) cc_final: 0.5555 (tp30) REVERT: I 235 GLN cc_start: 0.6839 (mm110) cc_final: 0.6223 (mm-40) REVERT: I 366 MET cc_start: 0.8878 (tpt) cc_final: 0.8515 (tpt) REVERT: I 387 MET cc_start: 0.7247 (ptm) cc_final: 0.6753 (ptm) REVERT: I 489 LYS cc_start: 0.8112 (mttp) cc_final: 0.7844 (mppt) REVERT: I 654 LYS cc_start: 0.7920 (tmmt) cc_final: 0.7665 (tttp) REVERT: I 664 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.7231 (t0) REVERT: J 27 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6851 (tp30) REVERT: J 325 GLU cc_start: 0.6953 (mm-30) cc_final: 0.6574 (mm-30) REVERT: J 489 LYS cc_start: 0.8055 (mttp) cc_final: 0.7734 (mmtm) REVERT: K 102 MET cc_start: 0.8821 (mmp) cc_final: 0.8535 (mmp) REVERT: K 267 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.6935 (mp0) REVERT: K 325 GLU cc_start: 0.6770 (mm-30) cc_final: 0.6522 (mp0) REVERT: K 452 MET cc_start: 0.8147 (mtp) cc_final: 0.7859 (mtp) REVERT: K 664 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.7113 (t0) REVERT: K 678 GLU cc_start: 0.7538 (mp0) cc_final: 0.7322 (pm20) REVERT: L 235 GLN cc_start: 0.6900 (mm110) cc_final: 0.6306 (mm-40) REVERT: L 387 MET cc_start: 0.7218 (ptm) cc_final: 0.6755 (ptm) REVERT: L 489 LYS cc_start: 0.8148 (mttp) cc_final: 0.7823 (mppt) REVERT: L 664 ASN cc_start: 0.7370 (t0) cc_final: 0.7162 (t0) outliers start: 143 outliers final: 44 residues processed: 1030 average time/residue: 1.9438 time to fit residues: 2515.6741 Evaluate side-chains 927 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 872 time to evaluate : 6.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 654 LYS Chi-restraints excluded: chain A residue 718 ASN Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain B residue 221 VAL Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain C residue 221 VAL Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain G residue 187 GLU Chi-restraints excluded: chain G residue 221 VAL Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 267 GLU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 664 ASN Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 221 VAL Chi-restraints excluded: chain J residue 309 ARG Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain K residue 221 VAL Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 664 ASN Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 308 GLN Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 718 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 829 optimal weight: 0.4980 chunk 631 optimal weight: 5.9990 chunk 435 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 400 optimal weight: 5.9990 chunk 563 optimal weight: 6.9990 chunk 842 optimal weight: 4.9990 chunk 892 optimal weight: 0.2980 chunk 440 optimal weight: 1.9990 chunk 798 optimal weight: 5.9990 chunk 240 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS ** B 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 763 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN E 236 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 589 HIS F 664 ASN F 763 HIS ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 HIS ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 763 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 124 GLN ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS I 763 HIS J 236 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS K 236 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 763 HIS L 124 GLN L 236 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 76775 Z= 0.224 Angle : 0.600 12.257 104029 Z= 0.307 Chirality : 0.041 0.156 11349 Planarity : 0.005 0.056 13302 Dihedral : 4.752 30.936 10112 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.66 % Allowed : 5.66 % Favored : 93.69 % Rotamer: Outliers : 1.93 % Allowed : 19.32 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.09), residues: 9139 helix: 1.95 (0.07), residues: 5423 sheet: -2.19 (0.20), residues: 564 loop : -0.69 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 541 HIS 0.010 0.001 HIS C 149 PHE 0.017 0.002 PHE K 725 TYR 0.018 0.002 TYR L 55 ARG 0.009 0.001 ARG G 586 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1083 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 926 time to evaluate : 6.578 Fit side-chains REVERT: A 173 GLU cc_start: 0.7114 (pm20) cc_final: 0.6707 (tp30) REVERT: A 308 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: A 387 MET cc_start: 0.7281 (ptm) cc_final: 0.6832 (ptm) REVERT: A 473 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7333 (mtt) REVERT: A 489 LYS cc_start: 0.8045 (mttp) cc_final: 0.7749 (mppt) REVERT: B 28 ARG cc_start: 0.7245 (mmm160) cc_final: 0.6762 (mtm180) REVERT: B 325 GLU cc_start: 0.7052 (mp0) cc_final: 0.6815 (mm-30) REVERT: B 489 LYS cc_start: 0.7953 (mttp) cc_final: 0.7675 (mppt) REVERT: B 641 ARG cc_start: 0.6520 (OUTLIER) cc_final: 0.5705 (mtt90) REVERT: B 664 ASN cc_start: 0.7517 (t0) cc_final: 0.7212 (t0) REVERT: C 187 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5925 (tm-30) REVERT: C 309 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7113 (mtm180) REVERT: C 375 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.8018 (ttt180) REVERT: C 664 ASN cc_start: 0.7393 (t0) cc_final: 0.7050 (t160) REVERT: C 718 ASN cc_start: 0.8128 (OUTLIER) cc_final: 0.7926 (p0) REVERT: D 28 ARG cc_start: 0.7212 (mmm160) cc_final: 0.6710 (mtm180) REVERT: D 63 ARG cc_start: 0.7943 (mmm-85) cc_final: 0.7588 (mtp-110) REVERT: D 330 THR cc_start: 0.7714 (p) cc_final: 0.7363 (t) REVERT: D 370 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8716 (mp) REVERT: E 309 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.7005 (mtm-85) REVERT: E 387 MET cc_start: 0.7360 (ptm) cc_final: 0.6816 (ptm) REVERT: E 452 MET cc_start: 0.8138 (mtp) cc_final: 0.7924 (mtp) REVERT: E 489 LYS cc_start: 0.7999 (mttp) cc_final: 0.7649 (mppt) REVERT: E 572 GLU cc_start: 0.7362 (mp0) cc_final: 0.7156 (mp0) REVERT: F 188 MET cc_start: 0.8228 (tpt) cc_final: 0.7715 (tpt) REVERT: F 234 MET cc_start: 0.7669 (ttp) cc_final: 0.7434 (ttp) REVERT: F 308 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: F 325 GLU cc_start: 0.6947 (mm-30) cc_final: 0.6617 (mm-30) REVERT: F 489 LYS cc_start: 0.8045 (mttp) cc_final: 0.7746 (mppt) REVERT: G 309 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.7098 (mtm180) REVERT: G 387 MET cc_start: 0.7256 (ptm) cc_final: 0.7019 (ptm) REVERT: G 405 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7419 (mt-10) REVERT: G 489 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7952 (mppt) REVERT: G 785 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: H 450 MET cc_start: 0.8383 (mtm) cc_final: 0.8155 (mtm) REVERT: H 489 LYS cc_start: 0.8058 (mttp) cc_final: 0.7826 (mppt) REVERT: H 590 LYS cc_start: 0.7960 (mttp) cc_final: 0.7713 (mttt) REVERT: H 595 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.6079 (tt0) REVERT: H 664 ASN cc_start: 0.7464 (t0) cc_final: 0.7184 (t0) REVERT: I 25 LEU cc_start: 0.7638 (mt) cc_final: 0.7329 (mp) REVERT: I 387 MET cc_start: 0.7287 (OUTLIER) cc_final: 0.6812 (ptm) REVERT: I 489 LYS cc_start: 0.8054 (mttp) cc_final: 0.7761 (mppt) REVERT: I 572 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6889 (mp0) REVERT: I 654 LYS cc_start: 0.7848 (tmmt) cc_final: 0.7562 (tttp) REVERT: I 664 ASN cc_start: 0.7535 (t0) cc_final: 0.7204 (t0) REVERT: J 27 GLU cc_start: 0.7217 (tm-30) cc_final: 0.6985 (tp30) REVERT: J 325 GLU cc_start: 0.6845 (mm-30) cc_final: 0.6595 (mm-30) REVERT: J 473 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7289 (mtt) REVERT: J 489 LYS cc_start: 0.8041 (mttp) cc_final: 0.7702 (mppt) REVERT: K 187 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5779 (tm-30) REVERT: K 267 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: K 452 MET cc_start: 0.8102 (mtp) cc_final: 0.7831 (mtp) REVERT: K 664 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.7118 (t0) REVERT: L 173 GLU cc_start: 0.7005 (pm20) cc_final: 0.6440 (tp30) REVERT: L 235 GLN cc_start: 0.7003 (mm110) cc_final: 0.6323 (mm-40) REVERT: L 267 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.6822 (mp0) REVERT: L 387 MET cc_start: 0.7182 (ptm) cc_final: 0.6720 (ptm) REVERT: L 489 LYS cc_start: 0.8127 (mttp) cc_final: 0.7808 (mppt) REVERT: L 664 ASN cc_start: 0.7367 (t0) cc_final: 0.7151 (t0) outliers start: 157 outliers final: 63 residues processed: 1017 average time/residue: 1.9705 time to fit residues: 2524.2034 Evaluate side-chains 947 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 864 time to evaluate : 6.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 202 ARG Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 221 VAL Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain E residue 221 VAL Chi-restraints excluded: chain E residue 235 GLN Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 698 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 221 VAL Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 718 ASN Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 594 LEU Chi-restraints excluded: chain G residue 653 LEU Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain H residue 221 VAL Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain I residue 221 VAL Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 572 GLU Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 594 LEU Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain K residue 187 GLU Chi-restraints excluded: chain K residue 235 GLN Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 308 GLN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 664 ASN Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 615 GLU Chi-restraints excluded: chain L residue 718 ASN Chi-restraints excluded: chain L residue 756 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 743 optimal weight: 8.9990 chunk 506 optimal weight: 8.9990 chunk 12 optimal weight: 0.6980 chunk 664 optimal weight: 2.9990 chunk 368 optimal weight: 0.5980 chunk 761 optimal weight: 1.9990 chunk 616 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 455 optimal weight: 9.9990 chunk 800 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 HIS A 763 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 763 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS G 124 GLN ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 589 HIS ** G 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 HIS ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS I 763 HIS J 124 GLN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 HIS J 589 HIS J 718 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 763 HIS ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 76775 Z= 0.172 Angle : 0.544 10.902 104029 Z= 0.277 Chirality : 0.039 0.141 11349 Planarity : 0.004 0.045 13302 Dihedral : 4.541 30.773 10107 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.31 % Favored : 94.17 % Rotamer: Outliers : 1.70 % Allowed : 19.96 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: 1.29 (0.09), residues: 9139 helix: 2.02 (0.07), residues: 5435 sheet: -2.00 (0.21), residues: 564 loop : -0.65 (0.11), residues: 3140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 659 HIS 0.007 0.001 HIS K 149 PHE 0.014 0.002 PHE G 725 TYR 0.016 0.002 TYR C 55 ARG 0.010 0.000 ARG I 586 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 910 time to evaluate : 6.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7117 (pm20) cc_final: 0.6714 (tp30) REVERT: A 308 GLN cc_start: 0.7854 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: A 387 MET cc_start: 0.7312 (ptm) cc_final: 0.6929 (ptm) REVERT: A 489 LYS cc_start: 0.7996 (mttp) cc_final: 0.7729 (mppt) REVERT: A 590 LYS cc_start: 0.7813 (mttp) cc_final: 0.7603 (mtmt) REVERT: A 594 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.8087 (mp) REVERT: B 325 GLU cc_start: 0.7091 (mp0) cc_final: 0.6848 (mm-30) REVERT: B 489 LYS cc_start: 0.7913 (mttp) cc_final: 0.7637 (mppt) REVERT: B 664 ASN cc_start: 0.7554 (t0) cc_final: 0.7263 (t0) REVERT: C 187 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5851 (tm-30) REVERT: C 309 ARG cc_start: 0.7311 (OUTLIER) cc_final: 0.7074 (mtm180) REVERT: C 375 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.7966 (ttt180) REVERT: C 664 ASN cc_start: 0.7380 (t0) cc_final: 0.7017 (t160) REVERT: C 718 ASN cc_start: 0.8113 (OUTLIER) cc_final: 0.7886 (p0) REVERT: D 28 ARG cc_start: 0.7237 (mmm160) cc_final: 0.6720 (mtm180) REVERT: D 63 ARG cc_start: 0.7910 (mmm-85) cc_final: 0.7614 (mtp-110) REVERT: D 187 GLU cc_start: 0.6261 (OUTLIER) cc_final: 0.5536 (tm-30) REVERT: D 370 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8715 (mp) REVERT: D 590 LYS cc_start: 0.7908 (mttt) cc_final: 0.7577 (mppt) REVERT: D 718 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7904 (p0) REVERT: E 177 ARG cc_start: 0.7738 (ttm110) cc_final: 0.7531 (ttp80) REVERT: E 387 MET cc_start: 0.7348 (ptm) cc_final: 0.6754 (ptm) REVERT: E 489 LYS cc_start: 0.7982 (mttp) cc_final: 0.7704 (mppt) REVERT: E 575 ARG cc_start: 0.7565 (ttp-110) cc_final: 0.7332 (tpp-160) REVERT: E 590 LYS cc_start: 0.7742 (mmtm) cc_final: 0.7391 (mttt) REVERT: F 188 MET cc_start: 0.8200 (tpt) cc_final: 0.7839 (tpt) REVERT: F 234 MET cc_start: 0.7676 (ttp) cc_final: 0.7476 (ttp) REVERT: F 308 GLN cc_start: 0.7841 (OUTLIER) cc_final: 0.7536 (mt0) REVERT: F 489 LYS cc_start: 0.8011 (mttp) cc_final: 0.7718 (mppt) REVERT: F 551 MET cc_start: 0.9060 (ptp) cc_final: 0.8844 (ptp) REVERT: G 186 GLN cc_start: 0.7118 (tp40) cc_final: 0.6793 (tp-100) REVERT: G 309 ARG cc_start: 0.7452 (OUTLIER) cc_final: 0.7175 (mtm180) REVERT: G 387 MET cc_start: 0.7281 (ptm) cc_final: 0.7056 (ptm) REVERT: G 654 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7509 (tppt) REVERT: H 450 MET cc_start: 0.8370 (mtm) cc_final: 0.8130 (mtm) REVERT: H 489 LYS cc_start: 0.7981 (mttp) cc_final: 0.7767 (mppt) REVERT: H 595 GLU cc_start: 0.6555 (OUTLIER) cc_final: 0.6033 (tt0) REVERT: H 664 ASN cc_start: 0.7440 (t0) cc_final: 0.7155 (t0) REVERT: I 25 LEU cc_start: 0.7617 (mt) cc_final: 0.7351 (mp) REVERT: I 91 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7274 (t0) REVERT: I 187 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5719 (tp30) REVERT: I 235 GLN cc_start: 0.6707 (mm110) cc_final: 0.6120 (mm-40) REVERT: I 387 MET cc_start: 0.7261 (ptm) cc_final: 0.6799 (ptm) REVERT: I 489 LYS cc_start: 0.8012 (mttp) cc_final: 0.7710 (mppt) REVERT: I 654 LYS cc_start: 0.7820 (tmmt) cc_final: 0.7541 (tttp) REVERT: I 664 ASN cc_start: 0.7491 (t0) cc_final: 0.7158 (t0) REVERT: J 27 GLU cc_start: 0.7221 (tm-30) cc_final: 0.6899 (tp30) REVERT: J 173 GLU cc_start: 0.6453 (tp30) cc_final: 0.6242 (tp30) REVERT: J 177 ARG cc_start: 0.7743 (ttp80) cc_final: 0.7510 (ttp80) REVERT: J 187 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5533 (tp30) REVERT: J 325 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6572 (mm-30) REVERT: K 186 GLN cc_start: 0.7086 (tp40) cc_final: 0.6703 (tp-100) REVERT: K 452 MET cc_start: 0.8082 (mtp) cc_final: 0.7799 (mtp) REVERT: K 489 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7856 (mppt) REVERT: K 664 ASN cc_start: 0.7361 (OUTLIER) cc_final: 0.7132 (t0) REVERT: L 267 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: L 387 MET cc_start: 0.7221 (ptm) cc_final: 0.6815 (ptm) REVERT: L 489 LYS cc_start: 0.8105 (mttp) cc_final: 0.7808 (mppt) REVERT: L 664 ASN cc_start: 0.7350 (t0) cc_final: 0.7131 (t0) outliers start: 138 outliers final: 60 residues processed: 985 average time/residue: 1.9578 time to fit residues: 2419.0328 Evaluate side-chains 956 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 878 time to evaluate : 6.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 547 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 718 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain C residue 187 GLU Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 235 GLN Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 698 ASP Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 483 LEU Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 602 THR Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 718 ASN Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain G residue 124 GLN Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 594 LEU Chi-restraints excluded: chain G residue 654 LYS Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 187 GLU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 718 ASN Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 235 GLN Chi-restraints excluded: chain K residue 308 GLN Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 664 ASN Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 615 GLU Chi-restraints excluded: chain L residue 718 ASN Chi-restraints excluded: chain L residue 780 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 300 optimal weight: 1.9990 chunk 803 optimal weight: 4.9990 chunk 176 optimal weight: 2.9990 chunk 523 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 893 optimal weight: 3.9990 chunk 741 optimal weight: 5.9990 chunk 413 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 295 optimal weight: 3.9990 chunk 468 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 ASN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN A 763 HIS ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 763 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 763 HIS ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 236 ASN ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS I 763 HIS ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS J 718 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 718 ASN K 763 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 236 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 76775 Z= 0.269 Angle : 0.631 11.602 104029 Z= 0.327 Chirality : 0.043 0.163 11349 Planarity : 0.005 0.071 13302 Dihedral : 4.875 32.547 10100 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.76 % Favored : 93.72 % Rotamer: Outliers : 1.93 % Allowed : 19.39 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.12 (0.09), residues: 9139 helix: 1.84 (0.07), residues: 5457 sheet: -2.04 (0.21), residues: 564 loop : -0.63 (0.11), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 541 HIS 0.012 0.002 HIS C 149 PHE 0.019 0.003 PHE K 725 TYR 0.019 0.002 TYR G 55 ARG 0.010 0.001 ARG J 586 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 899 time to evaluate : 6.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7134 (pm20) cc_final: 0.6685 (tp30) REVERT: A 308 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7354 (tt0) REVERT: A 325 GLU cc_start: 0.6952 (mp0) cc_final: 0.6709 (mm-30) REVERT: A 332 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7397 (mmmt) REVERT: A 387 MET cc_start: 0.7261 (ptm) cc_final: 0.6805 (ptm) REVERT: A 489 LYS cc_start: 0.8025 (mttp) cc_final: 0.7763 (mppt) REVERT: B 28 ARG cc_start: 0.7270 (mmm160) cc_final: 0.6785 (mtm180) REVERT: B 325 GLU cc_start: 0.7187 (mp0) cc_final: 0.6906 (mm-30) REVERT: B 489 LYS cc_start: 0.7939 (mttp) cc_final: 0.7676 (mppt) REVERT: B 641 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.5830 (mtt90) REVERT: B 664 ASN cc_start: 0.7525 (t0) cc_final: 0.7230 (t0) REVERT: C 187 GLU cc_start: 0.6235 (tm-30) cc_final: 0.5982 (tm-30) REVERT: C 309 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.7121 (mtm180) REVERT: C 664 ASN cc_start: 0.7434 (t0) cc_final: 0.7068 (t160) REVERT: C 718 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7909 (p0) REVERT: D 28 ARG cc_start: 0.7293 (mmm160) cc_final: 0.6750 (mtm180) REVERT: D 187 GLU cc_start: 0.6299 (OUTLIER) cc_final: 0.5595 (tm-30) REVERT: D 330 THR cc_start: 0.7793 (p) cc_final: 0.7431 (t) REVERT: D 370 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8707 (mp) REVERT: D 718 ASN cc_start: 0.8100 (OUTLIER) cc_final: 0.7855 (p0) REVERT: E 309 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.6976 (mtm-85) REVERT: E 387 MET cc_start: 0.7239 (ptm) cc_final: 0.6653 (ptm) REVERT: E 405 GLU cc_start: 0.7677 (mt-10) cc_final: 0.7363 (tt0) REVERT: E 450 MET cc_start: 0.8503 (mtm) cc_final: 0.8189 (mtm) REVERT: E 489 LYS cc_start: 0.8004 (mttp) cc_final: 0.7657 (mppt) REVERT: E 551 MET cc_start: 0.9157 (ptp) cc_final: 0.8851 (ptm) REVERT: E 572 GLU cc_start: 0.7428 (mp0) cc_final: 0.7191 (mp0) REVERT: E 594 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8004 (mp) REVERT: F 308 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7698 (mt0) REVERT: F 489 LYS cc_start: 0.7999 (mttp) cc_final: 0.7692 (mppt) REVERT: F 551 MET cc_start: 0.9165 (ptp) cc_final: 0.8682 (ptp) REVERT: G 186 GLN cc_start: 0.7186 (tp40) cc_final: 0.6969 (tp-100) REVERT: G 309 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7229 (mtm180) REVERT: G 387 MET cc_start: 0.7265 (ptm) cc_final: 0.7037 (ptm) REVERT: G 785 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7600 (tp30) REVERT: H 405 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7380 (tt0) REVERT: H 489 LYS cc_start: 0.8016 (mttp) cc_final: 0.7812 (mppt) REVERT: H 595 GLU cc_start: 0.6760 (OUTLIER) cc_final: 0.6204 (tt0) REVERT: H 664 ASN cc_start: 0.7479 (t0) cc_final: 0.7191 (t0) REVERT: I 25 LEU cc_start: 0.7674 (mt) cc_final: 0.7413 (mp) REVERT: I 186 GLN cc_start: 0.7011 (tp40) cc_final: 0.6712 (tp-100) REVERT: I 235 GLN cc_start: 0.6899 (mm110) cc_final: 0.6268 (mm-40) REVERT: I 387 MET cc_start: 0.7317 (ptm) cc_final: 0.6824 (ptm) REVERT: I 489 LYS cc_start: 0.8055 (mttp) cc_final: 0.7764 (mppt) REVERT: I 654 LYS cc_start: 0.7844 (tmmt) cc_final: 0.7641 (ttmt) REVERT: I 664 ASN cc_start: 0.7518 (t0) cc_final: 0.7186 (t0) REVERT: J 173 GLU cc_start: 0.6481 (tp30) cc_final: 0.6279 (tp30) REVERT: J 177 ARG cc_start: 0.7795 (ttp80) cc_final: 0.7575 (ttp80) REVERT: J 325 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6657 (mm-30) REVERT: J 664 ASN cc_start: 0.7518 (t0) cc_final: 0.7208 (t0) REVERT: K 186 GLN cc_start: 0.7035 (tp40) cc_final: 0.6642 (tp-100) REVERT: K 267 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7005 (mp0) REVERT: K 452 MET cc_start: 0.8082 (mtp) cc_final: 0.7821 (mtp) REVERT: K 664 ASN cc_start: 0.7379 (t0) cc_final: 0.7156 (t0) REVERT: L 235 GLN cc_start: 0.6994 (mm110) cc_final: 0.6274 (mm-40) REVERT: L 267 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.6847 (mp0) REVERT: L 387 MET cc_start: 0.7176 (ptm) cc_final: 0.6800 (ptm) REVERT: L 489 LYS cc_start: 0.8116 (mttp) cc_final: 0.7800 (mppt) REVERT: L 664 ASN cc_start: 0.7400 (t0) cc_final: 0.7180 (t0) outliers start: 157 outliers final: 85 residues processed: 1000 average time/residue: 2.0141 time to fit residues: 2518.8937 Evaluate side-chains 966 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 865 time to evaluate : 6.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 547 LEU Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 235 GLN Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain E residue 594 LEU Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 602 THR Chi-restraints excluded: chain F residue 718 ASN Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 594 LEU Chi-restraints excluded: chain G residue 602 THR Chi-restraints excluded: chain G residue 644 VAL Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 644 VAL Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 308 GLN Chi-restraints excluded: chain J residue 324 THR Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 594 LEU Chi-restraints excluded: chain J residue 602 THR Chi-restraints excluded: chain J residue 641 ARG Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 235 GLN Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 308 GLN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 483 LEU Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 594 LEU Chi-restraints excluded: chain K residue 602 THR Chi-restraints excluded: chain K residue 644 VAL Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 602 THR Chi-restraints excluded: chain L residue 615 GLU Chi-restraints excluded: chain L residue 644 VAL Chi-restraints excluded: chain L residue 718 ASN Chi-restraints excluded: chain L residue 756 ASP Chi-restraints excluded: chain L residue 780 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 861 optimal weight: 9.9990 chunk 100 optimal weight: 0.7980 chunk 508 optimal weight: 6.9990 chunk 652 optimal weight: 0.0970 chunk 505 optimal weight: 2.9990 chunk 751 optimal weight: 1.9990 chunk 498 optimal weight: 0.5980 chunk 889 optimal weight: 1.9990 chunk 556 optimal weight: 3.9990 chunk 542 optimal weight: 3.9990 chunk 410 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 236 ASN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 763 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 HIS E 664 ASN E 763 HIS ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 HIS H 124 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 763 HIS ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 76775 Z= 0.178 Angle : 0.550 10.730 104029 Z= 0.283 Chirality : 0.039 0.140 11349 Planarity : 0.004 0.055 13302 Dihedral : 4.635 31.480 10100 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.13 % Favored : 94.34 % Rotamer: Outliers : 1.81 % Allowed : 19.75 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.28 (0.09), residues: 9139 helix: 2.00 (0.07), residues: 5435 sheet: -1.83 (0.22), residues: 540 loop : -0.67 (0.11), residues: 3164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 659 HIS 0.007 0.001 HIS K 149 PHE 0.014 0.002 PHE G 725 TYR 0.017 0.002 TYR A 55 ARG 0.011 0.000 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 889 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7074 (pm20) cc_final: 0.6628 (tp30) REVERT: A 308 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7310 (tt0) REVERT: A 332 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7354 (mmmt) REVERT: A 387 MET cc_start: 0.7298 (ptm) cc_final: 0.6880 (ptm) REVERT: A 489 LYS cc_start: 0.7979 (mttp) cc_final: 0.7712 (mppt) REVERT: A 639 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7534 (ttp-110) REVERT: B 28 ARG cc_start: 0.7253 (mmm160) cc_final: 0.6804 (mtm180) REVERT: B 325 GLU cc_start: 0.7131 (mp0) cc_final: 0.6878 (mm-30) REVERT: B 489 LYS cc_start: 0.7924 (mttp) cc_final: 0.7663 (mppt) REVERT: B 641 ARG cc_start: 0.6513 (OUTLIER) cc_final: 0.5619 (mtt90) REVERT: B 664 ASN cc_start: 0.7528 (t0) cc_final: 0.7219 (t0) REVERT: C 309 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.7100 (mtm180) REVERT: C 375 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.8001 (ttt180) REVERT: C 664 ASN cc_start: 0.7425 (t0) cc_final: 0.7054 (t160) REVERT: C 718 ASN cc_start: 0.8106 (OUTLIER) cc_final: 0.7862 (p0) REVERT: D 28 ARG cc_start: 0.7209 (mmm160) cc_final: 0.6704 (mtm180) REVERT: D 186 GLN cc_start: 0.7144 (tp40) cc_final: 0.6823 (tp40) REVERT: D 187 GLU cc_start: 0.6262 (OUTLIER) cc_final: 0.5616 (tp30) REVERT: D 330 THR cc_start: 0.7652 (p) cc_final: 0.7314 (t) REVERT: D 370 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8709 (mp) REVERT: D 590 LYS cc_start: 0.7851 (mtmt) cc_final: 0.7600 (mppt) REVERT: D 718 ASN cc_start: 0.8130 (OUTLIER) cc_final: 0.7909 (p0) REVERT: E 177 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7446 (ttp80) REVERT: E 186 GLN cc_start: 0.6984 (tp40) cc_final: 0.6454 (tp-100) REVERT: E 309 ARG cc_start: 0.7437 (OUTLIER) cc_final: 0.7041 (mtm-85) REVERT: E 387 MET cc_start: 0.7306 (ptm) cc_final: 0.6789 (ptm) REVERT: E 405 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7356 (tt0) REVERT: E 489 LYS cc_start: 0.7994 (mttp) cc_final: 0.7710 (mppt) REVERT: E 590 LYS cc_start: 0.7738 (mmtm) cc_final: 0.7376 (mttt) REVERT: F 308 GLN cc_start: 0.7861 (OUTLIER) cc_final: 0.7627 (mt0) REVERT: F 489 LYS cc_start: 0.7997 (mttp) cc_final: 0.7709 (mppt) REVERT: F 551 MET cc_start: 0.9127 (ptp) cc_final: 0.8591 (ptp) REVERT: F 639 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6034 (ttp-110) REVERT: G 186 GLN cc_start: 0.7182 (tp40) cc_final: 0.6913 (tp-100) REVERT: G 309 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7211 (mtm180) REVERT: G 387 MET cc_start: 0.7278 (ptm) cc_final: 0.7057 (ptm) REVERT: H 186 GLN cc_start: 0.7073 (tp40) cc_final: 0.6503 (tp-100) REVERT: H 405 GLU cc_start: 0.7614 (mt-10) cc_final: 0.7358 (tt0) REVERT: H 450 MET cc_start: 0.8378 (mtm) cc_final: 0.8093 (mtm) REVERT: H 595 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6193 (tt0) REVERT: H 664 ASN cc_start: 0.7448 (t0) cc_final: 0.7158 (t0) REVERT: I 25 LEU cc_start: 0.7596 (mt) cc_final: 0.7388 (mp) REVERT: I 186 GLN cc_start: 0.6968 (tp40) cc_final: 0.6685 (tp-100) REVERT: I 187 GLU cc_start: 0.6245 (tm-30) cc_final: 0.5697 (tp30) REVERT: I 235 GLN cc_start: 0.6985 (mm110) cc_final: 0.6344 (mm-40) REVERT: I 366 MET cc_start: 0.8844 (tpt) cc_final: 0.8567 (tpt) REVERT: I 387 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6893 (ptm) REVERT: I 489 LYS cc_start: 0.8019 (mttp) cc_final: 0.7716 (mppt) REVERT: I 568 ARG cc_start: 0.8105 (OUTLIER) cc_final: 0.7568 (mtm180) REVERT: I 664 ASN cc_start: 0.7482 (t0) cc_final: 0.7145 (t0) REVERT: J 186 GLN cc_start: 0.7132 (tp40) cc_final: 0.6870 (tp40) REVERT: J 187 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5663 (tp30) REVERT: J 325 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6674 (mm-30) REVERT: J 473 MET cc_start: 0.7394 (mtt) cc_final: 0.6936 (mtt) REVERT: J 664 ASN cc_start: 0.7511 (t0) cc_final: 0.7190 (t0) REVERT: K 186 GLN cc_start: 0.7094 (tp40) cc_final: 0.6687 (tp-100) REVERT: K 267 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: K 452 MET cc_start: 0.8035 (mtp) cc_final: 0.7775 (mtp) REVERT: K 489 LYS cc_start: 0.8160 (mmmt) cc_final: 0.7892 (mppt) REVERT: K 664 ASN cc_start: 0.7368 (t0) cc_final: 0.7129 (t0) REVERT: L 173 GLU cc_start: 0.7057 (pm20) cc_final: 0.6530 (tp30) REVERT: L 235 GLN cc_start: 0.6940 (mm110) cc_final: 0.6273 (mm-40) REVERT: L 267 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: L 387 MET cc_start: 0.7197 (ptm) cc_final: 0.6751 (ptm) REVERT: L 489 LYS cc_start: 0.8104 (mttp) cc_final: 0.7805 (mppt) REVERT: L 664 ASN cc_start: 0.7371 (t0) cc_final: 0.7149 (t0) outliers start: 147 outliers final: 76 residues processed: 983 average time/residue: 2.0309 time to fit residues: 2512.2279 Evaluate side-chains 959 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 863 time to evaluate : 6.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 718 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 235 GLN Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 601 THR Chi-restraints excluded: chain F residue 602 THR Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 639 ARG Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 594 LEU Chi-restraints excluded: chain G residue 602 THR Chi-restraints excluded: chain G residue 641 ARG Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 595 GLU Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 568 ARG Chi-restraints excluded: chain I residue 644 VAL Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 187 GLU Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 601 THR Chi-restraints excluded: chain J residue 602 THR Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 235 GLN Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 308 GLN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 568 ARG Chi-restraints excluded: chain K residue 644 VAL Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 602 THR Chi-restraints excluded: chain L residue 780 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 550 optimal weight: 9.9990 chunk 355 optimal weight: 10.0000 chunk 531 optimal weight: 2.9990 chunk 267 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 172 optimal weight: 5.9990 chunk 565 optimal weight: 0.9990 chunk 606 optimal weight: 9.9990 chunk 439 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 699 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 763 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 HIS E 664 ASN E 763 HIS ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS G 223 GLN ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 367 GLN G 763 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 124 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 763 HIS ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 76775 Z= 0.227 Angle : 0.594 10.696 104029 Z= 0.307 Chirality : 0.041 0.149 11349 Planarity : 0.005 0.060 13302 Dihedral : 4.761 32.112 10100 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.62 % Favored : 93.85 % Rotamer: Outliers : 1.77 % Allowed : 19.93 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.22 (0.09), residues: 9139 helix: 1.92 (0.07), residues: 5446 sheet: -1.94 (0.21), residues: 564 loop : -0.60 (0.11), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 659 HIS 0.009 0.001 HIS K 149 PHE 0.017 0.002 PHE K 725 TYR 0.015 0.002 TYR G 142 ARG 0.012 0.001 ARG I 586 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 896 time to evaluate : 6.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7080 (pm20) cc_final: 0.6640 (tp30) REVERT: A 308 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: A 332 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7359 (mmmt) REVERT: A 387 MET cc_start: 0.7319 (ptm) cc_final: 0.6943 (ptm) REVERT: A 489 LYS cc_start: 0.8006 (mttp) cc_final: 0.7756 (mppt) REVERT: A 594 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8178 (mp) REVERT: A 639 ARG cc_start: 0.7820 (ttm110) cc_final: 0.7618 (ttp-110) REVERT: B 28 ARG cc_start: 0.7264 (mmm160) cc_final: 0.6813 (mtm180) REVERT: B 325 GLU cc_start: 0.7093 (mp0) cc_final: 0.6849 (mm-30) REVERT: B 489 LYS cc_start: 0.7933 (mttp) cc_final: 0.7674 (mppt) REVERT: B 641 ARG cc_start: 0.6545 (OUTLIER) cc_final: 0.5643 (mtt90) REVERT: B 664 ASN cc_start: 0.7512 (t0) cc_final: 0.7213 (t0) REVERT: C 309 ARG cc_start: 0.7365 (OUTLIER) cc_final: 0.7128 (mtm180) REVERT: C 375 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.8023 (ttt180) REVERT: C 664 ASN cc_start: 0.7443 (t0) cc_final: 0.7068 (t160) REVERT: C 718 ASN cc_start: 0.8133 (OUTLIER) cc_final: 0.7910 (p0) REVERT: D 28 ARG cc_start: 0.7250 (mmm160) cc_final: 0.6701 (mtm180) REVERT: D 186 GLN cc_start: 0.7126 (tp40) cc_final: 0.6805 (tp40) REVERT: D 187 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5572 (tm-30) REVERT: D 330 THR cc_start: 0.7732 (p) cc_final: 0.7380 (t) REVERT: D 370 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8712 (mp) REVERT: D 590 LYS cc_start: 0.7962 (mtmt) cc_final: 0.7688 (mppt) REVERT: D 639 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7210 (ttp-110) REVERT: D 718 ASN cc_start: 0.8066 (OUTLIER) cc_final: 0.7833 (p0) REVERT: E 177 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7456 (ttp80) REVERT: E 186 GLN cc_start: 0.7046 (tp40) cc_final: 0.6593 (tp-100) REVERT: E 309 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7020 (mtm-85) REVERT: E 387 MET cc_start: 0.7300 (ptm) cc_final: 0.6770 (ptm) REVERT: E 405 GLU cc_start: 0.7679 (mt-10) cc_final: 0.7368 (tt0) REVERT: E 489 LYS cc_start: 0.8011 (mttp) cc_final: 0.7722 (mppt) REVERT: E 590 LYS cc_start: 0.7832 (mmtm) cc_final: 0.7462 (mttt) REVERT: F 308 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: F 489 LYS cc_start: 0.7975 (mttp) cc_final: 0.7685 (mppt) REVERT: F 551 MET cc_start: 0.9168 (ptp) cc_final: 0.8782 (ptp) REVERT: F 639 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.6058 (ttp-110) REVERT: G 173 GLU cc_start: 0.7001 (pm20) cc_final: 0.6646 (tp30) REVERT: G 186 GLN cc_start: 0.7199 (tp40) cc_final: 0.6940 (tp-100) REVERT: G 309 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7223 (mtm180) REVERT: G 387 MET cc_start: 0.7271 (ptm) cc_final: 0.7050 (ptm) REVERT: H 186 GLN cc_start: 0.7110 (tp40) cc_final: 0.6549 (tp-100) REVERT: H 405 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7349 (tt0) REVERT: H 639 ARG cc_start: 0.7683 (OUTLIER) cc_final: 0.6901 (ttp-110) REVERT: H 664 ASN cc_start: 0.7474 (t0) cc_final: 0.7183 (t0) REVERT: I 91 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7292 (t0) REVERT: I 186 GLN cc_start: 0.6958 (tp40) cc_final: 0.6667 (tp-100) REVERT: I 187 GLU cc_start: 0.6226 (tm-30) cc_final: 0.5703 (tp30) REVERT: I 235 GLN cc_start: 0.6986 (mm110) cc_final: 0.6343 (mm-40) REVERT: I 387 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.6877 (ptm) REVERT: I 489 LYS cc_start: 0.8041 (mttp) cc_final: 0.7738 (mppt) REVERT: I 664 ASN cc_start: 0.7503 (t0) cc_final: 0.7159 (t0) REVERT: J 173 GLU cc_start: 0.6494 (tp30) cc_final: 0.6238 (tp30) REVERT: J 186 GLN cc_start: 0.7158 (tp40) cc_final: 0.6881 (tp40) REVERT: J 664 ASN cc_start: 0.7499 (t0) cc_final: 0.7174 (t0) REVERT: K 186 GLN cc_start: 0.7110 (tp40) cc_final: 0.6664 (tp-100) REVERT: K 267 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6969 (mp0) REVERT: K 452 MET cc_start: 0.8066 (mtp) cc_final: 0.7796 (mtp) REVERT: K 489 LYS cc_start: 0.8145 (mmmt) cc_final: 0.7916 (mppt) REVERT: K 664 ASN cc_start: 0.7366 (t0) cc_final: 0.7132 (t0) REVERT: L 173 GLU cc_start: 0.7103 (pm20) cc_final: 0.6565 (tp30) REVERT: L 235 GLN cc_start: 0.6894 (mm110) cc_final: 0.6251 (mm-40) REVERT: L 267 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: L 387 MET cc_start: 0.7211 (ptm) cc_final: 0.6759 (ptm) REVERT: L 489 LYS cc_start: 0.8108 (mttp) cc_final: 0.7797 (mppt) REVERT: L 586 ARG cc_start: 0.7868 (ttm110) cc_final: 0.7659 (ttp-110) REVERT: L 664 ASN cc_start: 0.7384 (t0) cc_final: 0.7162 (t0) outliers start: 144 outliers final: 87 residues processed: 979 average time/residue: 1.9927 time to fit residues: 2449.7777 Evaluate side-chains 977 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 869 time to evaluate : 6.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain C residue 235 GLN Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 483 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 718 ASN Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 187 GLU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 609 MET Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 235 GLN Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 601 THR Chi-restraints excluded: chain F residue 602 THR Chi-restraints excluded: chain F residue 615 GLU Chi-restraints excluded: chain F residue 639 ARG Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 594 LEU Chi-restraints excluded: chain G residue 602 THR Chi-restraints excluded: chain G residue 641 ARG Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 639 ARG Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain I residue 91 ASP Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 644 VAL Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 601 THR Chi-restraints excluded: chain J residue 602 THR Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 235 GLN Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 308 GLN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 568 ARG Chi-restraints excluded: chain K residue 601 THR Chi-restraints excluded: chain K residue 602 THR Chi-restraints excluded: chain K residue 644 VAL Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 602 THR Chi-restraints excluded: chain L residue 615 GLU Chi-restraints excluded: chain L residue 644 VAL Chi-restraints excluded: chain L residue 741 MET Chi-restraints excluded: chain L residue 780 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 809 optimal weight: 7.9990 chunk 852 optimal weight: 3.9990 chunk 777 optimal weight: 3.9990 chunk 829 optimal weight: 0.6980 chunk 498 optimal weight: 3.9990 chunk 361 optimal weight: 2.9990 chunk 650 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 749 optimal weight: 1.9990 chunk 784 optimal weight: 10.0000 chunk 826 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 HIS E 664 ASN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 236 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 76775 Z= 0.207 Angle : 0.577 10.371 104029 Z= 0.298 Chirality : 0.040 0.141 11349 Planarity : 0.004 0.064 13302 Dihedral : 4.720 31.896 10100 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.23 % Favored : 94.24 % Rotamer: Outliers : 1.70 % Allowed : 20.07 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.09), residues: 9139 helix: 1.94 (0.07), residues: 5447 sheet: -1.80 (0.22), residues: 542 loop : -0.64 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 659 HIS 0.008 0.001 HIS K 149 PHE 0.016 0.002 PHE K 725 TYR 0.014 0.002 TYR G 142 ARG 0.012 0.000 ARG D 586 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 875 time to evaluate : 6.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7072 (pm20) cc_final: 0.6744 (tp30) REVERT: A 308 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: A 332 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7346 (mmmt) REVERT: A 387 MET cc_start: 0.7339 (ptm) cc_final: 0.7001 (ptm) REVERT: A 489 LYS cc_start: 0.7998 (mttp) cc_final: 0.7736 (mppt) REVERT: A 590 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7508 (mppt) REVERT: A 595 GLU cc_start: 0.6481 (tp30) cc_final: 0.6019 (tt0) REVERT: A 639 ARG cc_start: 0.7803 (ttm110) cc_final: 0.7578 (ttp-110) REVERT: B 28 ARG cc_start: 0.7261 (mmm160) cc_final: 0.6812 (mtm180) REVERT: B 325 GLU cc_start: 0.7140 (mp0) cc_final: 0.6846 (mm-30) REVERT: B 489 LYS cc_start: 0.7928 (mttp) cc_final: 0.7671 (mppt) REVERT: B 641 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.5610 (mtt90) REVERT: B 664 ASN cc_start: 0.7557 (t0) cc_final: 0.7261 (t0) REVERT: C 309 ARG cc_start: 0.7347 (OUTLIER) cc_final: 0.7109 (mtm180) REVERT: C 375 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8007 (ttt180) REVERT: C 664 ASN cc_start: 0.7444 (t0) cc_final: 0.7063 (t160) REVERT: D 28 ARG cc_start: 0.7246 (mmm160) cc_final: 0.6699 (mtm180) REVERT: D 186 GLN cc_start: 0.7138 (tp40) cc_final: 0.6775 (tp40) REVERT: D 330 THR cc_start: 0.7695 (p) cc_final: 0.7339 (t) REVERT: D 370 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8730 (mp) REVERT: D 590 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7646 (mppt) REVERT: D 639 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7127 (ttp-110) REVERT: D 718 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7809 (p0) REVERT: E 177 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7486 (ttp80) REVERT: E 186 GLN cc_start: 0.7155 (tp40) cc_final: 0.6579 (tp-100) REVERT: E 309 ARG cc_start: 0.7419 (OUTLIER) cc_final: 0.7006 (mtm-85) REVERT: E 387 MET cc_start: 0.7324 (ptm) cc_final: 0.6789 (ptm) REVERT: E 405 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7352 (tt0) REVERT: E 489 LYS cc_start: 0.8014 (mttp) cc_final: 0.7727 (mppt) REVERT: E 575 ARG cc_start: 0.7563 (ttp-110) cc_final: 0.7351 (tpp-160) REVERT: E 590 LYS cc_start: 0.7776 (mmtm) cc_final: 0.7403 (mttt) REVERT: F 308 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7641 (mt0) REVERT: F 452 MET cc_start: 0.7679 (mtp) cc_final: 0.7222 (ttp) REVERT: F 489 LYS cc_start: 0.8006 (mttp) cc_final: 0.7721 (mppt) REVERT: F 551 MET cc_start: 0.9157 (ptp) cc_final: 0.8847 (ptp) REVERT: F 639 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.6063 (ttp-110) REVERT: G 173 GLU cc_start: 0.7006 (pm20) cc_final: 0.6689 (tp30) REVERT: G 186 GLN cc_start: 0.7200 (tp40) cc_final: 0.6949 (tp-100) REVERT: G 309 ARG cc_start: 0.7466 (OUTLIER) cc_final: 0.7184 (mtm180) REVERT: G 387 MET cc_start: 0.7240 (ptm) cc_final: 0.7016 (ptm) REVERT: G 785 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7609 (tp30) REVERT: H 186 GLN cc_start: 0.7130 (tp40) cc_final: 0.6519 (tp-100) REVERT: H 235 GLN cc_start: 0.6641 (mm110) cc_final: 0.6020 (mm-40) REVERT: H 323 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.5327 (tmt) REVERT: H 405 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7341 (tt0) REVERT: H 639 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.6878 (ttp-110) REVERT: H 664 ASN cc_start: 0.7471 (t0) cc_final: 0.7188 (t0) REVERT: I 186 GLN cc_start: 0.6947 (tp40) cc_final: 0.6662 (tp-100) REVERT: I 187 GLU cc_start: 0.6295 (tm-30) cc_final: 0.5724 (tp30) REVERT: I 235 GLN cc_start: 0.6938 (mm110) cc_final: 0.6305 (mm-40) REVERT: I 387 MET cc_start: 0.7335 (ptm) cc_final: 0.6886 (ptm) REVERT: I 489 LYS cc_start: 0.8014 (mttp) cc_final: 0.7693 (mppt) REVERT: I 568 ARG cc_start: 0.8146 (OUTLIER) cc_final: 0.7542 (mtm180) REVERT: I 664 ASN cc_start: 0.7498 (t0) cc_final: 0.7160 (t0) REVERT: J 186 GLN cc_start: 0.7128 (tp40) cc_final: 0.6854 (tp40) REVERT: J 664 ASN cc_start: 0.7525 (t0) cc_final: 0.7205 (t0) REVERT: K 186 GLN cc_start: 0.7125 (tp40) cc_final: 0.6672 (tp-100) REVERT: K 267 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: K 452 MET cc_start: 0.8037 (mtp) cc_final: 0.7779 (mtp) REVERT: K 489 LYS cc_start: 0.8154 (mmmt) cc_final: 0.7909 (mppt) REVERT: K 664 ASN cc_start: 0.7379 (t0) cc_final: 0.7139 (t0) REVERT: L 173 GLU cc_start: 0.7061 (pm20) cc_final: 0.6536 (tp30) REVERT: L 177 ARG cc_start: 0.7658 (OUTLIER) cc_final: 0.7331 (ttm110) REVERT: L 235 GLN cc_start: 0.6909 (mm110) cc_final: 0.6269 (mm-40) REVERT: L 267 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.6813 (mp0) REVERT: L 387 MET cc_start: 0.7242 (ptm) cc_final: 0.6809 (ptm) REVERT: L 489 LYS cc_start: 0.8121 (mttp) cc_final: 0.7806 (mppt) REVERT: L 568 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7038 (mtm180) REVERT: L 586 ARG cc_start: 0.7850 (ttm110) cc_final: 0.7629 (ttp-110) REVERT: L 664 ASN cc_start: 0.7383 (t0) cc_final: 0.7162 (t0) outliers start: 138 outliers final: 83 residues processed: 962 average time/residue: 2.0478 time to fit residues: 2468.7434 Evaluate side-chains 962 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 858 time to evaluate : 6.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 91 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 718 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 609 MET Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain E residue 177 ARG Chi-restraints excluded: chain E residue 235 GLN Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 601 THR Chi-restraints excluded: chain F residue 602 THR Chi-restraints excluded: chain F residue 639 ARG Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 235 GLN Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 594 LEU Chi-restraints excluded: chain G residue 602 THR Chi-restraints excluded: chain G residue 641 ARG Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 639 ARG Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain I residue 483 LEU Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 568 ARG Chi-restraints excluded: chain I residue 644 VAL Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 601 THR Chi-restraints excluded: chain J residue 602 THR Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 235 GLN Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 308 GLN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 568 ARG Chi-restraints excluded: chain K residue 601 THR Chi-restraints excluded: chain K residue 602 THR Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 177 ARG Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 568 ARG Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 602 THR Chi-restraints excluded: chain L residue 615 GLU Chi-restraints excluded: chain L residue 756 ASP Chi-restraints excluded: chain L residue 780 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 544 optimal weight: 1.9990 chunk 876 optimal weight: 7.9990 chunk 535 optimal weight: 1.9990 chunk 415 optimal weight: 20.0000 chunk 609 optimal weight: 4.9990 chunk 919 optimal weight: 7.9990 chunk 846 optimal weight: 10.0000 chunk 732 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 565 optimal weight: 4.9990 chunk 448 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 GLN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 664 ASN A 763 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 474 HIS D 589 HIS D 664 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 HIS E 589 HIS E 664 ASN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS G 83 ASN ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 763 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 76775 Z= 0.328 Angle : 0.683 10.813 104029 Z= 0.356 Chirality : 0.046 0.179 11349 Planarity : 0.006 0.065 13302 Dihedral : 5.052 33.479 10100 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.65 % Favored : 93.83 % Rotamer: Outliers : 1.70 % Allowed : 20.13 % Favored : 78.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: 1.04 (0.09), residues: 9139 helix: 1.73 (0.07), residues: 5456 sheet: -1.81 (0.22), residues: 542 loop : -0.66 (0.11), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP L 462 HIS 0.012 0.002 HIS K 149 PHE 0.021 0.003 PHE K 725 TYR 0.021 0.003 TYR K 497 ARG 0.013 0.001 ARG I 586 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18278 Ramachandran restraints generated. 9139 Oldfield, 0 Emsley, 9139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 903 time to evaluate : 6.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 173 GLU cc_start: 0.7077 (pm20) cc_final: 0.6553 (tp30) REVERT: A 221 VAL cc_start: 0.8155 (p) cc_final: 0.7910 (m) REVERT: A 308 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: A 387 MET cc_start: 0.7300 (ptm) cc_final: 0.6857 (ptm) REVERT: A 489 LYS cc_start: 0.8061 (mttp) cc_final: 0.7800 (mppt) REVERT: A 590 LYS cc_start: 0.7968 (mtmt) cc_final: 0.7556 (mppt) REVERT: A 639 ARG cc_start: 0.7880 (ttm110) cc_final: 0.7673 (ttp-110) REVERT: B 28 ARG cc_start: 0.7256 (mmm160) cc_final: 0.6784 (mtm180) REVERT: B 186 GLN cc_start: 0.7061 (tp-100) cc_final: 0.6800 (tp40) REVERT: B 325 GLU cc_start: 0.7143 (mp0) cc_final: 0.6849 (mm-30) REVERT: B 489 LYS cc_start: 0.7951 (mttp) cc_final: 0.7670 (mppt) REVERT: B 641 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.5781 (mtt90) REVERT: B 664 ASN cc_start: 0.7527 (t0) cc_final: 0.7235 (t0) REVERT: C 309 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.7164 (mtm180) REVERT: C 375 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.8053 (tpt170) REVERT: C 664 ASN cc_start: 0.7458 (t0) cc_final: 0.7083 (t160) REVERT: D 28 ARG cc_start: 0.7289 (mmm160) cc_final: 0.6724 (mtm180) REVERT: D 186 GLN cc_start: 0.7208 (tp40) cc_final: 0.6856 (tp40) REVERT: D 370 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8723 (mp) REVERT: D 590 LYS cc_start: 0.8017 (mtmt) cc_final: 0.7716 (mppt) REVERT: D 639 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7274 (ttp-110) REVERT: D 718 ASN cc_start: 0.8114 (OUTLIER) cc_final: 0.7860 (p0) REVERT: E 186 GLN cc_start: 0.7169 (tp40) cc_final: 0.6649 (tp-100) REVERT: E 309 ARG cc_start: 0.7465 (OUTLIER) cc_final: 0.7065 (mtm-85) REVERT: E 387 MET cc_start: 0.7244 (ptm) cc_final: 0.6716 (ptm) REVERT: E 405 GLU cc_start: 0.7669 (mt-10) cc_final: 0.7383 (tt0) REVERT: E 489 LYS cc_start: 0.8001 (mttp) cc_final: 0.7645 (mppt) REVERT: E 572 GLU cc_start: 0.7449 (mp0) cc_final: 0.7212 (mp0) REVERT: E 595 GLU cc_start: 0.6767 (tp30) cc_final: 0.6489 (mm-30) REVERT: F 308 GLN cc_start: 0.7970 (OUTLIER) cc_final: 0.7751 (mt0) REVERT: F 489 LYS cc_start: 0.7999 (mttp) cc_final: 0.7690 (mppt) REVERT: F 551 MET cc_start: 0.9179 (ptp) cc_final: 0.8799 (ptp) REVERT: F 639 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.6147 (ttp-110) REVERT: G 173 GLU cc_start: 0.7037 (pm20) cc_final: 0.6617 (tp30) REVERT: G 186 GLN cc_start: 0.7192 (tp40) cc_final: 0.6948 (tp-100) REVERT: G 309 ARG cc_start: 0.7508 (OUTLIER) cc_final: 0.7228 (mtm180) REVERT: G 387 MET cc_start: 0.7183 (ptm) cc_final: 0.6947 (ptm) REVERT: G 502 ASP cc_start: 0.7585 (p0) cc_final: 0.7337 (p0) REVERT: G 785 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: H 186 GLN cc_start: 0.7167 (tp40) cc_final: 0.6557 (tp-100) REVERT: H 323 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5446 (tmt) REVERT: H 664 ASN cc_start: 0.7482 (t0) cc_final: 0.7191 (t0) REVERT: I 186 GLN cc_start: 0.6965 (tp40) cc_final: 0.6677 (tp-100) REVERT: I 235 GLN cc_start: 0.6978 (mm110) cc_final: 0.6337 (mm-40) REVERT: I 387 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6822 (ptm) REVERT: I 489 LYS cc_start: 0.8070 (mttp) cc_final: 0.7754 (mppt) REVERT: I 664 ASN cc_start: 0.7528 (t0) cc_final: 0.7190 (t0) REVERT: J 186 GLN cc_start: 0.7154 (tp40) cc_final: 0.6872 (tp40) REVERT: J 664 ASN cc_start: 0.7528 (t0) cc_final: 0.7182 (t0) REVERT: K 186 GLN cc_start: 0.7126 (tp40) cc_final: 0.6689 (tp-100) REVERT: K 267 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: K 452 MET cc_start: 0.8073 (mtp) cc_final: 0.7824 (mtp) REVERT: L 173 GLU cc_start: 0.7122 (pm20) cc_final: 0.6422 (tp30) REVERT: L 235 GLN cc_start: 0.6937 (mm110) cc_final: 0.6278 (mm-40) REVERT: L 267 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: L 387 MET cc_start: 0.7161 (ptm) cc_final: 0.6774 (ptm) REVERT: L 405 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7382 (tt0) REVERT: L 489 LYS cc_start: 0.8136 (mttp) cc_final: 0.7807 (mppt) REVERT: L 568 ARG cc_start: 0.8270 (OUTLIER) cc_final: 0.7511 (mtm180) outliers start: 138 outliers final: 96 residues processed: 995 average time/residue: 1.9714 time to fit residues: 2463.4131 Evaluate side-chains 991 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 878 time to evaluate : 6.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 GLN Chi-restraints excluded: chain A residue 309 ARG Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 641 ARG Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 780 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 324 THR Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 550 SER Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 641 ARG Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 654 LYS Chi-restraints excluded: chain B residue 718 ASN Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain C residue 309 ARG Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 375 ARG Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 644 VAL Chi-restraints excluded: chain C residue 653 LEU Chi-restraints excluded: chain C residue 780 LEU Chi-restraints excluded: chain D residue 25 LEU Chi-restraints excluded: chain D residue 113 CYS Chi-restraints excluded: chain D residue 271 CYS Chi-restraints excluded: chain D residue 272 TRP Chi-restraints excluded: chain D residue 370 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 594 LEU Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 602 THR Chi-restraints excluded: chain D residue 609 MET Chi-restraints excluded: chain D residue 639 ARG Chi-restraints excluded: chain D residue 718 ASN Chi-restraints excluded: chain D residue 756 ASP Chi-restraints excluded: chain E residue 235 GLN Chi-restraints excluded: chain E residue 309 ARG Chi-restraints excluded: chain E residue 490 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 568 ARG Chi-restraints excluded: chain E residue 644 VAL Chi-restraints excluded: chain E residue 780 LEU Chi-restraints excluded: chain F residue 200 THR Chi-restraints excluded: chain F residue 308 GLN Chi-restraints excluded: chain F residue 499 VAL Chi-restraints excluded: chain F residue 547 LEU Chi-restraints excluded: chain F residue 594 LEU Chi-restraints excluded: chain F residue 601 THR Chi-restraints excluded: chain F residue 602 THR Chi-restraints excluded: chain F residue 639 ARG Chi-restraints excluded: chain F residue 756 ASP Chi-restraints excluded: chain G residue 156 ASN Chi-restraints excluded: chain G residue 308 GLN Chi-restraints excluded: chain G residue 309 ARG Chi-restraints excluded: chain G residue 324 THR Chi-restraints excluded: chain G residue 375 ARG Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 568 ARG Chi-restraints excluded: chain G residue 594 LEU Chi-restraints excluded: chain G residue 602 THR Chi-restraints excluded: chain G residue 641 ARG Chi-restraints excluded: chain G residue 653 LEU Chi-restraints excluded: chain G residue 780 LEU Chi-restraints excluded: chain G residue 785 GLU Chi-restraints excluded: chain H residue 271 CYS Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 547 LEU Chi-restraints excluded: chain H residue 718 ASN Chi-restraints excluded: chain H residue 780 LEU Chi-restraints excluded: chain I residue 324 THR Chi-restraints excluded: chain I residue 387 MET Chi-restraints excluded: chain I residue 499 VAL Chi-restraints excluded: chain I residue 547 LEU Chi-restraints excluded: chain I residue 568 ARG Chi-restraints excluded: chain I residue 644 VAL Chi-restraints excluded: chain I residue 718 ASN Chi-restraints excluded: chain J residue 499 VAL Chi-restraints excluded: chain J residue 550 SER Chi-restraints excluded: chain J residue 601 THR Chi-restraints excluded: chain J residue 602 THR Chi-restraints excluded: chain J residue 780 LEU Chi-restraints excluded: chain K residue 156 ASN Chi-restraints excluded: chain K residue 235 GLN Chi-restraints excluded: chain K residue 267 GLU Chi-restraints excluded: chain K residue 308 GLN Chi-restraints excluded: chain K residue 324 THR Chi-restraints excluded: chain K residue 499 VAL Chi-restraints excluded: chain K residue 568 ARG Chi-restraints excluded: chain K residue 601 THR Chi-restraints excluded: chain K residue 602 THR Chi-restraints excluded: chain K residue 644 VAL Chi-restraints excluded: chain K residue 780 LEU Chi-restraints excluded: chain L residue 177 ARG Chi-restraints excluded: chain L residue 267 GLU Chi-restraints excluded: chain L residue 499 VAL Chi-restraints excluded: chain L residue 547 LEU Chi-restraints excluded: chain L residue 568 ARG Chi-restraints excluded: chain L residue 594 LEU Chi-restraints excluded: chain L residue 602 THR Chi-restraints excluded: chain L residue 615 GLU Chi-restraints excluded: chain L residue 644 VAL Chi-restraints excluded: chain L residue 756 ASP Chi-restraints excluded: chain L residue 780 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 581 optimal weight: 0.7980 chunk 780 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 675 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 203 optimal weight: 0.0010 chunk 733 optimal weight: 0.7980 chunk 306 optimal weight: 1.9990 chunk 753 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 763 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 718 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN E 124 GLN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 664 ASN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 589 HIS G 763 HIS ** H 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.124834 restraints weight = 67465.327| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.30 r_work: 0.3326 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 76775 Z= 0.198 Angle : 0.577 10.226 104029 Z= 0.299 Chirality : 0.040 0.157 11349 Planarity : 0.004 0.064 13302 Dihedral : 4.776 31.679 10100 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.19 % Favored : 94.29 % Rotamer: Outliers : 1.44 % Allowed : 20.50 % Favored : 78.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.09), residues: 9139 helix: 1.93 (0.07), residues: 5436 sheet: -1.75 (0.22), residues: 542 loop : -0.67 (0.11), residues: 3161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 659 HIS 0.008 0.001 HIS K 149 PHE 0.016 0.002 PHE C 725 TYR 0.016 0.002 TYR A 637 ARG 0.014 0.000 ARG E 586 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34649.57 seconds wall clock time: 600 minutes 18.93 seconds (36018.93 seconds total)