Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 19:19:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/04_2023/8fnv_29327.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/04_2023/8fnv_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_29327/04_2023/8fnv_29327.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/04_2023/8fnv_29327.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/04_2023/8fnv_29327.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fnv_29327/04_2023/8fnv_29327.pdb" } resolution = 2.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 28.91, per 1000 atoms: 0.39 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: 25.59 Conformation dependent library (CDL) restraints added in 8.7 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: 3.40 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: 31.25 Time building geometry restraints manager: 27.85 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: 5.800 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: 0.080 Extract box with map and model: 26.620 Check model and map are aligned: 0.870 Set scattering table: 0.540 Process input model: 155.920 Find NCS groups from input model: 4.700 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 207.040 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 7.007 Fit side-chains outliers start: 312 outliers final: 67 residues processed: 1146 average time/residue: 2.0230 time to fit residues: 2910.0600 Evaluate side-chains 965 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 898 time to evaluate : 6.983 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 59 residues processed: 9 average time/residue: 2.2588 time to fit residues: 34.4917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 779 optimal weight: 3.9990 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: 0.0970 chunk 279 optimal weight: 0.8980 chunk 439 optimal weight: 0.5980 chunk 538 optimal weight: 10.0000 chunk 838 optimal weight: 1.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 ASN ** A 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 149 HIS ** 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 149 HIS ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 HIS ** 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 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 HIS ** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 76775 Z= 0.171 Angle : 0.570 11.910 104029 Z= 0.286 Chirality : 0.039 0.138 11349 Planarity : 0.004 0.060 13302 Dihedral : 4.418 27.495 10100 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.79 % Allowed : 5.06 % Favored : 94.16 % Rotamer Outliers : 2.47 % 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: 0.98 (0.09), residues: 9139 helix: 1.90 (0.07), residues: 5364 sheet: -2.21 (0.21), residues: 564 loop : -0.97 (0.11), residues: 3211 *********************** 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 1201 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1000 time to evaluate : 7.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 201 outliers final: 79 residues processed: 1143 average time/residue: 2.0252 time to fit residues: 2907.0657 Evaluate side-chains 948 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 869 time to evaluate : 6.961 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 73 residues processed: 6 average time/residue: 0.8035 time to fit residues: 17.4579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 465 optimal weight: 0.9980 chunk 260 optimal weight: 7.9990 chunk 697 optimal weight: 0.9990 chunk 570 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 839 optimal weight: 0.0870 chunk 907 optimal weight: 3.9990 chunk 747 optimal weight: 0.2980 chunk 832 optimal weight: 10.0000 chunk 286 optimal weight: 0.0370 chunk 673 optimal weight: 9.9990 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN ** A 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 236 ASN ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 ASN B 589 HIS B 664 ASN ** B 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 62 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 236 ASN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 403 ASN C 589 HIS ** C 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN ** D 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 403 ASN D 664 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** E 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 124 GLN ** F 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN F 403 ASN F 589 HIS F 664 ASN G 62 GLN ** G 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 403 ASN ** J 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN ** K 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 76775 Z= 0.144 Angle : 0.524 9.184 104029 Z= 0.262 Chirality : 0.038 0.142 11349 Planarity : 0.004 0.047 13302 Dihedral : 4.214 28.529 10100 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.67 % Allowed : 4.98 % Favored : 94.35 % Rotamer Outliers : 2.24 % 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: 1.22 (0.09), residues: 9139 helix: 2.04 (0.07), residues: 5412 sheet: -2.11 (0.21), residues: 574 loop : -0.81 (0.11), residues: 3153 *********************** 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 1109 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 927 time to evaluate : 7.108 Fit side-chains revert: symmetry clash outliers start: 182 outliers final: 86 residues processed: 1056 average time/residue: 2.0480 time to fit residues: 2728.8856 Evaluate side-chains 942 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 856 time to evaluate : 7.091 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 81 residues processed: 6 average time/residue: 1.1227 time to fit residues: 19.5645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 829 optimal weight: 9.9990 chunk 631 optimal weight: 5.9990 chunk 435 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 400 optimal weight: 5.9990 chunk 563 optimal weight: 0.6980 chunk 842 optimal weight: 10.0000 chunk 892 optimal weight: 4.9990 chunk 440 optimal weight: 1.9990 chunk 798 optimal weight: 2.9990 chunk 240 optimal weight: 2.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 124 GLN ** 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 589 HIS B 664 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 664 ASN C 718 ASN C 763 HIS D 83 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** D 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 763 HIS ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 391 HIS ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 763 HIS F 83 ASN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 ASN 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 62 GLN H 83 ASN H 124 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS H 664 ASN ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 763 HIS ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 83 ASN I 124 GLN ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS I 664 ASN I 763 HIS J 83 ASN J 236 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 589 HIS J 664 ASN J 763 HIS ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS K 664 ASN ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 763 HIS ** L 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 124 GLN L 236 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 367 GLN L 664 ASN ** L 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 76775 Z= 0.296 Angle : 0.661 11.810 104029 Z= 0.340 Chirality : 0.045 0.175 11349 Planarity : 0.006 0.070 13302 Dihedral : 4.873 32.403 10100 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.07 % Favored : 93.27 % Rotamer Outliers : 2.51 % 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: 1.09 (0.09), residues: 9139 helix: 1.85 (0.07), residues: 5435 sheet: -2.21 (0.20), residues: 564 loop : -0.69 (0.11), residues: 3140 *********************** 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 1144 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 940 time to evaluate : 7.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 121 residues processed: 1081 average time/residue: 2.0555 time to fit residues: 2817.8811 Evaluate side-chains 1002 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 881 time to evaluate : 7.156 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 95 residues processed: 28 average time/residue: 1.2181 time to fit residues: 58.6329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 12 optimal weight: 0.4980 chunk 664 optimal weight: 0.7980 chunk 368 optimal weight: 4.9990 chunk 761 optimal weight: 1.9990 chunk 616 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 455 optimal weight: 8.9990 chunk 800 optimal weight: 9.9990 chunk 225 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 763 HIS ** B 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS B 664 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 664 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 664 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 471 ASN ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 718 ASN ** 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** ** I 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS I 664 ASN J 124 GLN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 ASN J 718 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS K 664 ASN ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 236 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 664 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 76775 Z= 0.228 Angle : 0.603 11.272 104029 Z= 0.311 Chirality : 0.042 0.149 11349 Planarity : 0.005 0.058 13302 Dihedral : 4.816 32.759 10100 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.55 % Allowed : 5.42 % Favored : 94.04 % Rotamer Outliers : 2.39 % 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: 1.14 (0.09), residues: 9139 helix: 1.89 (0.07), residues: 5425 sheet: -2.09 (0.20), residues: 564 loop : -0.68 (0.11), residues: 3150 *********************** 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 1095 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 901 time to evaluate : 7.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 194 outliers final: 119 residues processed: 1045 average time/residue: 2.0227 time to fit residues: 2675.8263 Evaluate side-chains 1002 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 883 time to evaluate : 7.055 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 103 residues processed: 18 average time/residue: 1.0357 time to fit residues: 38.3619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.1980 chunk 176 optimal weight: 0.8980 chunk 523 optimal weight: 1.9990 chunk 220 optimal weight: 6.9990 chunk 893 optimal weight: 0.1980 chunk 741 optimal weight: 1.9990 chunk 413 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 468 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 589 HIS 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 664 ASN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 664 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN D 718 ASN E 124 GLN E 236 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 718 ASN ** 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** ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS I 664 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS K 664 ASN ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 664 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2469 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= 0.175 Angle : 0.548 10.472 104029 Z= 0.282 Chirality : 0.039 0.140 11349 Planarity : 0.004 0.051 13302 Dihedral : 4.595 31.052 10100 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.61 % Favored : 93.86 % Rotamer Outliers : 2.31 % 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: 1.29 (0.09), residues: 9139 helix: 2.03 (0.07), residues: 5425 sheet: -1.91 (0.22), residues: 542 loop : -0.68 (0.11), residues: 3172 *********************** 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 1090 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 902 time to evaluate : 7.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 188 outliers final: 125 residues processed: 1044 average time/residue: 2.0532 time to fit residues: 2719.9082 Evaluate side-chains 993 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 868 time to evaluate : 7.128 Switching outliers to nearest non-outliers outliers start: 125 outliers final: 105 residues processed: 23 average time/residue: 1.1070 time to fit residues: 47.5138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.3980 chunk 508 optimal weight: 8.9990 chunk 652 optimal weight: 0.8980 chunk 505 optimal weight: 0.8980 chunk 751 optimal weight: 0.9990 chunk 498 optimal weight: 3.9990 chunk 889 optimal weight: 6.9990 chunk 556 optimal weight: 0.9980 chunk 542 optimal weight: 3.9990 chunk 410 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS B 664 ASN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 664 ASN C 718 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 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 124 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 664 ASN ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 664 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 ASN K 236 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 664 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 76775 Z= 0.163 Angle : 0.536 11.550 104029 Z= 0.274 Chirality : 0.039 0.139 11349 Planarity : 0.004 0.054 13302 Dihedral : 4.474 30.219 10100 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.20 % Favored : 94.28 % Rotamer Outliers : 2.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.37 (0.09), residues: 9139 helix: 2.08 (0.07), residues: 5424 sheet: -1.81 (0.22), residues: 540 loop : -0.65 (0.11), residues: 3175 *********************** 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 1062 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 899 time to evaluate : 7.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 106 residues processed: 1023 average time/residue: 2.0771 time to fit residues: 2681.6956 Evaluate side-chains 978 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 872 time to evaluate : 7.057 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 96 residues processed: 12 average time/residue: 1.1934 time to fit residues: 30.3133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 550 optimal weight: 0.2980 chunk 355 optimal weight: 10.0000 chunk 531 optimal weight: 0.7980 chunk 267 optimal weight: 6.9990 chunk 174 optimal weight: 0.6980 chunk 172 optimal weight: 8.9990 chunk 565 optimal weight: 0.9990 chunk 606 optimal weight: 0.9980 chunk 439 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 699 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS B 664 ASN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 664 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 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 664 ASN ** H 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 763 HIS ** I 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 589 HIS I 664 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 ASN ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS K 664 ASN ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 589 HIS L 664 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 76775 Z= 0.155 Angle : 0.526 11.076 104029 Z= 0.268 Chirality : 0.038 0.138 11349 Planarity : 0.004 0.054 13302 Dihedral : 4.364 29.510 10100 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.30 % Favored : 94.18 % Rotamer Outliers : 1.75 % 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: 1.42 (0.09), residues: 9139 helix: 2.12 (0.07), residues: 5424 sheet: -1.77 (0.22), residues: 540 loop : -0.64 (0.11), residues: 3175 *********************** 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 1050 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 908 time to evaluate : 7.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 142 outliers final: 108 residues processed: 1019 average time/residue: 2.0542 time to fit residues: 2650.1994 Evaluate side-chains 971 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 863 time to evaluate : 7.102 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 98 residues processed: 12 average time/residue: 1.2066 time to fit residues: 30.9118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 809 optimal weight: 5.9990 chunk 852 optimal weight: 1.9990 chunk 777 optimal weight: 4.9990 chunk 829 optimal weight: 9.9990 chunk 498 optimal weight: 2.9990 chunk 361 optimal weight: 2.9990 chunk 650 optimal weight: 0.9990 chunk 254 optimal weight: 0.5980 chunk 749 optimal weight: 5.9990 chunk 784 optimal weight: 10.0000 chunk 826 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 GLN ** A 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 763 HIS ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 HIS B 664 ASN B 763 HIS ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 589 HIS C 664 ASN ** D 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 HIS D 664 ASN D 718 ASN ** E 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 589 HIS ** E 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 235 GLN ** 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 367 GLN G 763 HIS H 124 GLN ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS H 664 ASN ** 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 I 664 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 ASN ** K 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 589 HIS K 664 ASN ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 664 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 76775 Z= 0.224 Angle : 0.598 11.165 104029 Z= 0.309 Chirality : 0.041 0.153 11349 Planarity : 0.005 0.064 13302 Dihedral : 4.686 31.679 10100 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.47 % Favored : 94.00 % Rotamer Outliers : 1.72 % 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: 1.29 (0.09), residues: 9139 helix: 2.00 (0.07), residues: 5425 sheet: -1.93 (0.21), residues: 564 loop : -0.61 (0.11), residues: 3150 *********************** 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 1024 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 884 time to evaluate : 7.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 109 residues processed: 998 average time/residue: 2.1090 time to fit residues: 2674.1688 Evaluate side-chains 963 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 854 time to evaluate : 7.145 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 100 residues processed: 9 average time/residue: 1.6582 time to fit residues: 29.4168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 544 optimal weight: 2.9990 chunk 876 optimal weight: 6.9990 chunk 535 optimal weight: 0.9980 chunk 415 optimal weight: 20.0000 chunk 609 optimal weight: 6.9990 chunk 919 optimal weight: 7.9990 chunk 846 optimal weight: 10.0000 chunk 732 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 565 optimal weight: 4.9990 chunk 448 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 664 ASN ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 ASN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 ASN ** 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 F 235 GLN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS G 83 ASN G 186 GLN ** G 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 589 HIS H 664 ASN ** 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** I 589 HIS I 664 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 ASN ** K 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 664 ASN ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 664 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 76775 Z= 0.268 Angle : 0.640 11.193 104029 Z= 0.332 Chirality : 0.043 0.168 11349 Planarity : 0.005 0.069 13302 Dihedral : 4.886 32.117 10100 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.61 % Favored : 93.86 % Rotamer Outliers : 1.44 % 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: 1.18 (0.09), residues: 9139 helix: 1.87 (0.07), residues: 5436 sheet: -1.91 (0.21), residues: 564 loop : -0.60 (0.11), residues: 3139 ********************** 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 1000 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 883 time to evaluate : 7.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 108 residues processed: 987 average time/residue: 2.0522 time to fit residues: 2565.8950 Evaluate side-chains 949 residues out of total 8133 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 841 time to evaluate : 7.082 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 102 residues processed: 7 average time/residue: 1.4288 time to fit residues: 23.5091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 923 random chunks: chunk 581 optimal weight: 0.8980 chunk 780 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 675 optimal weight: 8.9990 chunk 108 optimal weight: 8.9990 chunk 203 optimal weight: 0.0670 chunk 733 optimal weight: 0.5980 chunk 306 optimal weight: 0.6980 chunk 753 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 135 optimal weight: 7.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- 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** ** B 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 664 ASN ** C 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 664 ASN ** 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 F 235 GLN ** F 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 664 ASN F 763 HIS G 186 GLN ** G 247 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 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 664 ASN ** J 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 664 ASN ** K 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 715 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 247 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 664 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.161253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125343 restraints weight = 67634.880| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 1.30 r_work: 0.3331 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 76775 Z= 0.195 Angle : 0.577 10.809 104029 Z= 0.297 Chirality : 0.040 0.142 11349 Planarity : 0.004 0.068 13302 Dihedral : 4.676 31.068 10100 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.53 % Allowed : 5.24 % Favored : 94.23 % Rotamer Outliers : 1.49 % 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: 1.28 (0.09), residues: 9139 helix: 1.97 (0.07), residues: 5437 sheet: -1.77 (0.22), residues: 540 loop : -0.63 (0.11), residues: 3162 =============================================================================== Job complete usr+sys time: 36077.70 seconds wall clock time: 624 minutes 27.86 seconds (37467.86 seconds total)