Starting phenix.real_space_refine on Wed Mar 27 02:04:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/03_2024/6yl3_10835_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/03_2024/6yl3_10835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/03_2024/6yl3_10835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/03_2024/6yl3_10835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/03_2024/6yl3_10835_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/03_2024/6yl3_10835_trim_updated.pdb" } resolution = 1.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians Ni 24 6.56 5 S 420 5.16 5 C 45984 2.51 5 N 12984 2.21 5 O 17700 1.98 5 H 73044 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 7": "OE1" <-> "OE2" Residue "A ASP 18": "OD1" <-> "OD2" Residue "A ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 71": "OD1" <-> "OD2" Residue "A ASP 75": "OD1" <-> "OD2" Residue "B GLU 51": "OE1" <-> "OE2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 86": "OD1" <-> "OD2" Residue "B ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 243": "OE1" <-> "OE2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C GLU 279": "OE1" <-> "OE2" Residue "C GLU 350": "OE1" <-> "OE2" Residue "C TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 430": "OE1" <-> "OE2" Residue "C ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ASP 503": "OD1" <-> "OD2" Residue "C GLU 540": "OE1" <-> "OE2" Residue "C ASP 551": "OD1" <-> "OD2" Residue "C ASP 561": "OD1" <-> "OD2" Residue "D ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 7": "OE1" <-> "OE2" Residue "D ASP 18": "OD1" <-> "OD2" Residue "D ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 71": "OD1" <-> "OD2" Residue "D ASP 75": "OD1" <-> "OD2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ASP 86": "OD1" <-> "OD2" Residue "E ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ASP 147": "OD1" <-> "OD2" Residue "E GLU 157": "OE1" <-> "OE2" Residue "E ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 127": "OE1" <-> "OE2" Residue "F ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F GLU 243": "OE1" <-> "OE2" Residue "F GLU 269": "OE1" <-> "OE2" Residue "F GLU 279": "OE1" <-> "OE2" Residue "F GLU 350": "OE1" <-> "OE2" Residue "F TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F GLU 430": "OE1" <-> "OE2" Residue "F ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ASP 503": "OD1" <-> "OD2" Residue "F GLU 540": "OE1" <-> "OE2" Residue "F ASP 551": "OD1" <-> "OD2" Residue "F ASP 561": "OD1" <-> "OD2" Residue "G ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G GLU 7": "OE1" <-> "OE2" Residue "G ASP 18": "OD1" <-> "OD2" Residue "G ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "G ASP 71": "OD1" <-> "OD2" Residue "G ASP 75": "OD1" <-> "OD2" Residue "H GLU 51": "OE1" <-> "OE2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H ASP 86": "OD1" <-> "OD2" Residue "H ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "H ASP 147": "OD1" <-> "OD2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 127": "OE1" <-> "OE2" Residue "I ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I GLU 243": "OE1" <-> "OE2" Residue "I GLU 269": "OE1" <-> "OE2" Residue "I GLU 279": "OE1" <-> "OE2" Residue "I GLU 350": "OE1" <-> "OE2" Residue "I TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I GLU 430": "OE1" <-> "OE2" Residue "I ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "I ASP 503": "OD1" <-> "OD2" Residue "I GLU 540": "OE1" <-> "OE2" Residue "I ASP 551": "OD1" <-> "OD2" Residue "I ASP 561": "OD1" <-> "OD2" Residue "J ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J GLU 7": "OE1" <-> "OE2" Residue "J ASP 18": "OD1" <-> "OD2" Residue "J ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "J ASP 71": "OD1" <-> "OD2" Residue "J ASP 75": "OD1" <-> "OD2" Residue "K GLU 51": "OE1" <-> "OE2" Residue "K PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K ASP 86": "OD1" <-> "OD2" Residue "K ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ASP 147": "OD1" <-> "OD2" Residue "K GLU 157": "OE1" <-> "OE2" Residue "K ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 127": "OE1" <-> "OE2" Residue "L ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 243": "OE1" <-> "OE2" Residue "L GLU 269": "OE1" <-> "OE2" Residue "L GLU 279": "OE1" <-> "OE2" Residue "L GLU 350": "OE1" <-> "OE2" Residue "L TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L GLU 430": "OE1" <-> "OE2" Residue "L ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ASP 503": "OD1" <-> "OD2" Residue "L GLU 540": "OE1" <-> "OE2" Residue "L ASP 551": "OD1" <-> "OD2" Residue "L ASP 561": "OD1" <-> "OD2" Residue "M ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 7": "OE1" <-> "OE2" Residue "M ASP 18": "OD1" <-> "OD2" Residue "M ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ASP 71": "OD1" <-> "OD2" Residue "M ASP 75": "OD1" <-> "OD2" Residue "N GLU 51": "OE1" <-> "OE2" Residue "N PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N ASP 86": "OD1" <-> "OD2" Residue "N ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ASP 147": "OD1" <-> "OD2" Residue "N GLU 157": "OE1" <-> "OE2" Residue "N ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 127": "OE1" <-> "OE2" Residue "O ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O GLU 243": "OE1" <-> "OE2" Residue "O GLU 269": "OE1" <-> "OE2" Residue "O GLU 279": "OE1" <-> "OE2" Residue "O GLU 350": "OE1" <-> "OE2" Residue "O TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O GLU 430": "OE1" <-> "OE2" Residue "O ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ASP 503": "OD1" <-> "OD2" Residue "O GLU 540": "OE1" <-> "OE2" Residue "O ASP 551": "OD1" <-> "OD2" Residue "O ASP 561": "OD1" <-> "OD2" Residue "P ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 7": "OE1" <-> "OE2" Residue "P ASP 18": "OD1" <-> "OD2" Residue "P ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ASP 71": "OD1" <-> "OD2" Residue "P ASP 75": "OD1" <-> "OD2" Residue "Q GLU 51": "OE1" <-> "OE2" Residue "Q PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q ASP 86": "OD1" <-> "OD2" Residue "Q ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Q ASP 147": "OD1" <-> "OD2" Residue "Q GLU 157": "OE1" <-> "OE2" Residue "Q ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 127": "OE1" <-> "OE2" Residue "R ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 243": "OE1" <-> "OE2" Residue "R GLU 269": "OE1" <-> "OE2" Residue "R GLU 279": "OE1" <-> "OE2" Residue "R GLU 350": "OE1" <-> "OE2" Residue "R TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R GLU 430": "OE1" <-> "OE2" Residue "R ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ASP 503": "OD1" <-> "OD2" Residue "R GLU 540": "OE1" <-> "OE2" Residue "R ASP 551": "OD1" <-> "OD2" Residue "R ASP 561": "OD1" <-> "OD2" Residue "S ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 7": "OE1" <-> "OE2" Residue "S ASP 18": "OD1" <-> "OD2" Residue "S ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S ASP 71": "OD1" <-> "OD2" Residue "S ASP 75": "OD1" <-> "OD2" Residue "T GLU 51": "OE1" <-> "OE2" Residue "T PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ASP 86": "OD1" <-> "OD2" Residue "T ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ASP 147": "OD1" <-> "OD2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "T ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 127": "OE1" <-> "OE2" Residue "V ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 243": "OE1" <-> "OE2" Residue "V GLU 269": "OE1" <-> "OE2" Residue "V GLU 279": "OE1" <-> "OE2" Residue "V GLU 350": "OE1" <-> "OE2" Residue "V TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V GLU 430": "OE1" <-> "OE2" Residue "V ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ASP 503": "OD1" <-> "OD2" Residue "V GLU 540": "OE1" <-> "OE2" Residue "V ASP 551": "OD1" <-> "OD2" Residue "V ASP 561": "OD1" <-> "OD2" Residue "W ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W GLU 7": "OE1" <-> "OE2" Residue "W ASP 18": "OD1" <-> "OD2" Residue "W ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ASP 71": "OD1" <-> "OD2" Residue "W ASP 75": "OD1" <-> "OD2" Residue "X GLU 51": "OE1" <-> "OE2" Residue "X PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X ASP 86": "OD1" <-> "OD2" Residue "X ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ASP 147": "OD1" <-> "OD2" Residue "X GLU 157": "OE1" <-> "OE2" Residue "X ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 127": "OE1" <-> "OE2" Residue "Y ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y GLU 243": "OE1" <-> "OE2" Residue "Y GLU 269": "OE1" <-> "OE2" Residue "Y GLU 279": "OE1" <-> "OE2" Residue "Y GLU 350": "OE1" <-> "OE2" Residue "Y TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y GLU 430": "OE1" <-> "OE2" Residue "Y ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ASP 503": "OD1" <-> "OD2" Residue "Y GLU 540": "OE1" <-> "OE2" Residue "Y ASP 551": "OD1" <-> "OD2" Residue "Y ASP 561": "OD1" <-> "OD2" Residue "Z ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 7": "OE1" <-> "OE2" Residue "Z ASP 18": "OD1" <-> "OD2" Residue "Z ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ASP 71": "OD1" <-> "OD2" Residue "Z ASP 75": "OD1" <-> "OD2" Residue "0 GLU 51": "OE1" <-> "OE2" Residue "0 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 ASP 86": "OD1" <-> "OD2" Residue "0 ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "0 ASP 147": "OD1" <-> "OD2" Residue "0 GLU 157": "OE1" <-> "OE2" Residue "0 ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 GLU 127": "OE1" <-> "OE2" Residue "1 ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 GLU 243": "OE1" <-> "OE2" Residue "1 GLU 269": "OE1" <-> "OE2" Residue "1 GLU 279": "OE1" <-> "OE2" Residue "1 GLU 350": "OE1" <-> "OE2" Residue "1 TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 GLU 430": "OE1" <-> "OE2" Residue "1 ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "1 ASP 503": "OD1" <-> "OD2" Residue "1 GLU 540": "OE1" <-> "OE2" Residue "1 ASP 551": "OD1" <-> "OD2" Residue "1 ASP 561": "OD1" <-> "OD2" Residue "2 ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 GLU 7": "OE1" <-> "OE2" Residue "2 ASP 18": "OD1" <-> "OD2" Residue "2 ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "2 ASP 71": "OD1" <-> "OD2" Residue "2 ASP 75": "OD1" <-> "OD2" Residue "3 GLU 51": "OE1" <-> "OE2" Residue "3 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 ASP 86": "OD1" <-> "OD2" Residue "3 ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "3 ASP 147": "OD1" <-> "OD2" Residue "3 GLU 157": "OE1" <-> "OE2" Residue "3 ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 127": "OE1" <-> "OE2" Residue "4 ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 GLU 243": "OE1" <-> "OE2" Residue "4 GLU 269": "OE1" <-> "OE2" Residue "4 GLU 279": "OE1" <-> "OE2" Residue "4 GLU 350": "OE1" <-> "OE2" Residue "4 TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "4 GLU 430": "OE1" <-> "OE2" Residue "4 ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "4 ASP 503": "OD1" <-> "OD2" Residue "4 GLU 540": "OE1" <-> "OE2" Residue "4 ASP 551": "OD1" <-> "OD2" Residue "4 ASP 561": "OD1" <-> "OD2" Residue "5 ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 GLU 7": "OE1" <-> "OE2" Residue "5 ASP 18": "OD1" <-> "OD2" Residue "5 ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "5 ASP 71": "OD1" <-> "OD2" Residue "5 ASP 75": "OD1" <-> "OD2" Residue "6 GLU 51": "OE1" <-> "OE2" Residue "6 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 ASP 86": "OD1" <-> "OD2" Residue "6 ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "6 ASP 147": "OD1" <-> "OD2" Residue "6 GLU 157": "OE1" <-> "OE2" Residue "6 ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 127": "OE1" <-> "OE2" Residue "7 ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 GLU 243": "OE1" <-> "OE2" Residue "7 GLU 269": "OE1" <-> "OE2" Residue "7 GLU 279": "OE1" <-> "OE2" Residue "7 GLU 350": "OE1" <-> "OE2" Residue "7 TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "7 GLU 430": "OE1" <-> "OE2" Residue "7 ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "7 ASP 503": "OD1" <-> "OD2" Residue "7 GLU 540": "OE1" <-> "OE2" Residue "7 ASP 551": "OD1" <-> "OD2" Residue "7 ASP 561": "OD1" <-> "OD2" Residue "8 ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 GLU 7": "OE1" <-> "OE2" Residue "8 ASP 18": "OD1" <-> "OD2" Residue "8 ARG 23": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "8 ASP 71": "OD1" <-> "OD2" Residue "8 ASP 75": "OD1" <-> "OD2" Residue "9 GLU 51": "OE1" <-> "OE2" Residue "9 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 ASP 86": "OD1" <-> "OD2" Residue "9 ARG 104": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "9 ASP 147": "OD1" <-> "OD2" Residue "9 GLU 157": "OE1" <-> "OE2" Residue "9 ARG 158": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U TYR 45": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 127": "OE1" <-> "OE2" Residue "U ARG 183": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U GLU 243": "OE1" <-> "OE2" Residue "U GLU 269": "OE1" <-> "OE2" Residue "U GLU 279": "OE1" <-> "OE2" Residue "U GLU 350": "OE1" <-> "OE2" Residue "U TYR 408": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U GLU 430": "OE1" <-> "OE2" Residue "U ARG 479": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ASP 503": "OD1" <-> "OD2" Residue "U GLU 540": "OE1" <-> "OE2" Residue "U ASP 551": "OD1" <-> "OD2" Residue "U ASP 561": "OD1" <-> "OD2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 150156 Number of models: 1 Model: "" Number of chains: 84 Chain: "A" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "B" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "C" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "D" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "E" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "F" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "G" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "H" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "I" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "J" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "K" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "L" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "M" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "N" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "O" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "P" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "Q" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "R" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "S" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "T" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "V" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "W" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "X" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "Y" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "Z" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "0" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "1" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "2" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "3" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "4" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "5" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "6" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "7" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "8" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "9" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "U" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PCIS': 3, 'PTRANS': 25, 'TRANS': 535} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 8366 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 224 Classifications: {'water': 224} Link IDs: {None: 223} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 225 Classifications: {'water': 225} Link IDs: {None: 224} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "I" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "K" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "L" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "N" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "O" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 222 Classifications: {'water': 222} Link IDs: {None: 221} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "R" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 216 Classifications: {'water': 216} Link IDs: {None: 215} Chain: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "T" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "V" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "W" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "X" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Y" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 226 Classifications: {'water': 226} Link IDs: {None: 225} Chain: "Z" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "0" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "1" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 224 Classifications: {'water': 224} Link IDs: {None: 223} Chain: "2" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "3" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "4" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 216 Classifications: {'water': 216} Link IDs: {None: 215} Chain: "5" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "6" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "7" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 220 Classifications: {'water': 220} Link IDs: {None: 219} Chain: "8" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "9" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "U" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Classifications: {'water': 223} Link IDs: {None: 222} Residues with excluded nonbonded symmetry interactions: 132 residue: pdb=" N ALEU A 16 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU A 16 " occ=0.50 residue: pdb=" N ALYS A 29 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 29 " occ=0.50 residue: pdb=" N AMET A 57 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET A 57 " occ=0.50 residue: pdb=" N ALYS A 66 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 66 " occ=0.50 residue: pdb=" N AARG B 153 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 153 " occ=0.50 residue: pdb=" N ALYS C 20 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS C 20 " occ=0.50 residue: pdb=" N AMET C 55 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 55 " occ=0.50 residue: pdb=" N ALEU C 406 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU C 406 " occ=0.50 residue: pdb=" N AMET C 434 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 434 " occ=0.50 residue: pdb=" N AMET C 489 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 489 " occ=0.50 residue: pdb=" N ALEU D 16 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU D 16 " occ=0.50 residue: pdb=" N ALYS D 29 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS D 29 " occ=0.50 ... (remaining 120 not shown) Time building chain proxies: 89.30, per 1000 atoms: 0.59 Number of scatterers: 150156 At special positions: 0 Unit cell: (169.335, 176.364, 169.974, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ni 24 28.00 S 420 16.00 O 17700 8.00 N 12984 7.00 C 45984 6.00 H 73044 1.00 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: 110.17 Conformation dependent library (CDL) restraints added in 22.3 seconds 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17328 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 276 helices and 132 sheets defined 35.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 32.73 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET A 70 " --> pdb=" O ALYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'D' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 Processing helix chain 'D' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET D 70 " --> pdb=" O ALYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Proline residue: D 78 - end of helix Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR G 14 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G 27 " --> pdb=" O ARG G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 50 Processing helix chain 'G' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET G 70 " --> pdb=" O ALYS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Proline residue: G 78 - end of helix Processing helix chain 'J' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET J 12 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE J 13 " --> pdb=" O GLU J 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR J 14 " --> pdb=" O LYS J 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 50 Processing helix chain 'J' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS J 66 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP J 67 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL J 69 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET J 70 " --> pdb=" O ALYS J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU J 76 " --> pdb=" O GLY J 72 " (cutoff:3.500A) Proline residue: J 78 - end of helix Processing helix chain 'M' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU M 11 " --> pdb=" O GLU M 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE M 13 " --> pdb=" O GLU M 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR M 14 " --> pdb=" O LYS M 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY M 27 " --> pdb=" O ARG M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 50 Processing helix chain 'M' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS M 66 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP M 67 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL M 69 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET M 70 " --> pdb=" O ALYS M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU M 76 " --> pdb=" O GLY M 72 " (cutoff:3.500A) Proline residue: M 78 - end of helix Processing helix chain 'P' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU P 11 " --> pdb=" O GLU P 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET P 12 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY P 27 " --> pdb=" O ARG P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 50 Processing helix chain 'P' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP P 67 " --> pdb=" O VAL P 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP P 68 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL P 69 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET P 70 " --> pdb=" O ALYS P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Proline residue: P 78 - end of helix Processing helix chain 'S' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET S 12 " --> pdb=" O VAL S 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE S 13 " --> pdb=" O GLU S 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 50 Processing helix chain 'S' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL S 63 " --> pdb=" O GLU S 59 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU S 64 " --> pdb=" O ALA S 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS S 66 " --> pdb=" O LYS S 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP S 67 " --> pdb=" O VAL S 63 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP S 68 " --> pdb=" O LEU S 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL S 69 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET S 70 " --> pdb=" O ALYS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU S 76 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Proline residue: S 78 - end of helix Processing helix chain 'W' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU W 11 " --> pdb=" O GLU W 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET W 12 " --> pdb=" O VAL W 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE W 13 " --> pdb=" O GLU W 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR W 14 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY W 27 " --> pdb=" O ARG W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 50 Processing helix chain 'W' and resid 52 through 70 removed outlier: 3.612A pdb=" N VAL W 63 " --> pdb=" O GLU W 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU W 64 " --> pdb=" O ALA W 60 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS W 66 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP W 67 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP W 68 " --> pdb=" O LEU W 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL W 69 " --> pdb=" O THR W 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET W 70 " --> pdb=" O ALYS W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) Proline residue: W 78 - end of helix Processing helix chain 'Z' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 7 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET Z 12 " --> pdb=" O VAL Z 8 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE Z 13 " --> pdb=" O GLU Z 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR Z 14 " --> pdb=" O LYS Z 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY Z 27 " --> pdb=" O ARG Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 50 Processing helix chain 'Z' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL Z 63 " --> pdb=" O GLU Z 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU Z 64 " --> pdb=" O ALA Z 60 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS Z 66 " --> pdb=" O LYS Z 62 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP Z 67 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP Z 68 " --> pdb=" O LEU Z 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL Z 69 " --> pdb=" O THR Z 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET Z 70 " --> pdb=" O ALYS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU Z 76 " --> pdb=" O GLY Z 72 " (cutoff:3.500A) Proline residue: Z 78 - end of helix Processing helix chain '2' and resid 4 through 27 removed outlier: 3.767A pdb=" N LEU 2 11 " --> pdb=" O GLU 2 7 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET 2 12 " --> pdb=" O VAL 2 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE 2 13 " --> pdb=" O GLU 2 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY 2 27 " --> pdb=" O ARG 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 50 Processing helix chain '2' and resid 52 through 70 removed outlier: 3.612A pdb=" N VAL 2 63 " --> pdb=" O GLU 2 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU 2 64 " --> pdb=" O ALA 2 60 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR 2 65 " --> pdb=" O SER 2 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS 2 66 " --> pdb=" O LYS 2 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP 2 67 " --> pdb=" O VAL 2 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP 2 68 " --> pdb=" O LEU 2 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 2 69 " --> pdb=" O THR 2 65 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N MET 2 70 " --> pdb=" O ALYS 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU 2 76 " --> pdb=" O GLY 2 72 " (cutoff:3.500A) Proline residue: 2 78 - end of helix Processing helix chain '5' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU 5 11 " --> pdb=" O GLU 5 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET 5 12 " --> pdb=" O VAL 5 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE 5 13 " --> pdb=" O GLU 5 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR 5 14 " --> pdb=" O LYS 5 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY 5 27 " --> pdb=" O ARG 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 50 Processing helix chain '5' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL 5 63 " --> pdb=" O GLU 5 59 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU 5 64 " --> pdb=" O ALA 5 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR 5 65 " --> pdb=" O SER 5 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS 5 66 " --> pdb=" O LYS 5 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP 5 67 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP 5 68 " --> pdb=" O LEU 5 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 5 69 " --> pdb=" O THR 5 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET 5 70 " --> pdb=" O ALYS 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU 5 76 " --> pdb=" O GLY 5 72 " (cutoff:3.500A) Proline residue: 5 78 - end of helix Processing helix chain '8' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU 8 11 " --> pdb=" O GLU 8 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET 8 12 " --> pdb=" O VAL 8 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE 8 13 " --> pdb=" O GLU 8 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR 8 14 " --> pdb=" O LYS 8 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY 8 27 " --> pdb=" O ARG 8 23 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 50 Processing helix chain '8' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL 8 63 " --> pdb=" O GLU 8 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU 8 64 " --> pdb=" O ALA 8 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR 8 65 " --> pdb=" O SER 8 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS 8 66 " --> pdb=" O LYS 8 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP 8 67 " --> pdb=" O VAL 8 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP 8 68 " --> pdb=" O LEU 8 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 8 69 " --> pdb=" O THR 8 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET 8 70 " --> pdb=" O ALYS 8 66 " (cutoff:3.500A) Processing helix chain '8' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU 8 76 " --> pdb=" O GLY 8 72 " (cutoff:3.500A) Proline residue: 8 78 - end of helix Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 159 removed outlier: 3.717A pdb=" N LEU E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 91 removed outlier: 3.651A pdb=" N ALA H 90 " --> pdb=" O ASP H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU H 149 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA K 90 " --> pdb=" O ASP K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU K 149 " --> pdb=" O ARG K 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA N 90 " --> pdb=" O ASP N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU N 149 " --> pdb=" O ARG N 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 91 removed outlier: 3.649A pdb=" N ALA Q 90 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU Q 149 " --> pdb=" O ARG Q 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 91 removed outlier: 3.649A pdb=" N ALA T 90 " --> pdb=" O ASP T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU T 149 " --> pdb=" O ARG T 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA X 90 " --> pdb=" O ASP X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU X 149 " --> pdb=" O ARG X 145 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA 0 90 " --> pdb=" O ASP 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 0 149 " --> pdb=" O ARG 0 145 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA 3 90 " --> pdb=" O ASP 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 3 149 " --> pdb=" O ARG 3 145 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 91 removed outlier: 3.651A pdb=" N ALA 6 90 " --> pdb=" O ASP 6 86 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 6 149 " --> pdb=" O ARG 6 145 " (cutoff:3.500A) Processing helix chain '9' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA 9 90 " --> pdb=" O ASP 9 86 " (cutoff:3.500A) Processing helix chain '9' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 9 149 " --> pdb=" O ARG 9 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 150 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN C 213 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU C 269 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 295' Processing helix chain 'C' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN C 326 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER C 340 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG C 343 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 374 through 390 Processing helix chain 'C' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 412 " --> pdb=" O TYR C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY C 486 " --> pdb=" O PHE C 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 481 through 486' Processing helix chain 'C' and resid 487 through 493 Processing helix chain 'C' and resid 498 through 505 Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'F' and resid 5 through 13 Processing helix chain 'F' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR F 149 " --> pdb=" O PRO F 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN F 154 " --> pdb=" O HIS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) Proline residue: F 193 - end of helix Processing helix chain 'F' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 213 " --> pdb=" O PRO F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 245 Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU F 269 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER F 294 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN F 295 " --> pdb=" O ARG F 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 290 through 295' Processing helix chain 'F' and resid 312 through 326 removed outlier: 4.097A pdb=" N ASN F 326 " --> pdb=" O MET F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Proline residue: F 344 - end of helix Processing helix chain 'F' and resid 374 through 390 Processing helix chain 'F' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS F 411 " --> pdb=" O ARG F 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE F 412 " --> pdb=" O TYR F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY F 486 " --> pdb=" O PHE F 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 486' Processing helix chain 'F' and resid 487 through 493 Processing helix chain 'F' and resid 498 through 505 Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR I 149 " --> pdb=" O PRO I 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN I 154 " --> pdb=" O HIS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 173 Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) Proline residue: I 193 - end of helix Processing helix chain 'I' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU I 210 " --> pdb=" O GLY I 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 245 Processing helix chain 'I' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU I 269 " --> pdb=" O ILE I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 295 removed outlier: 4.905A pdb=" N SER I 294 " --> pdb=" O ILE I 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN I 295 " --> pdb=" O ARG I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 290 through 295' Processing helix chain 'I' and resid 312 through 326 removed outlier: 4.095A pdb=" N ASN I 326 " --> pdb=" O MET I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER I 340 " --> pdb=" O SER I 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG I 343 " --> pdb=" O GLU I 339 " (cutoff:3.500A) Proline residue: I 344 - end of helix Processing helix chain 'I' and resid 374 through 390 Processing helix chain 'I' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS I 411 " --> pdb=" O ARG I 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE I 412 " --> pdb=" O TYR I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 421 Processing helix chain 'I' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET I 485 " --> pdb=" O MET I 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY I 486 " --> pdb=" O PHE I 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 481 through 486' Processing helix chain 'I' and resid 487 through 493 Processing helix chain 'I' and resid 498 through 505 Processing helix chain 'I' and resid 506 through 511 Processing helix chain 'L' and resid 5 through 13 Processing helix chain 'L' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA L 148 " --> pdb=" O SER L 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR L 149 " --> pdb=" O PRO L 145 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS L 150 " --> pdb=" O GLN L 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN L 154 " --> pdb=" O HIS L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 173 Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY L 191 " --> pdb=" O ARG L 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) Proline residue: L 193 - end of helix Processing helix chain 'L' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU L 210 " --> pdb=" O GLY L 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN L 213 " --> pdb=" O PRO L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 245 Processing helix chain 'L' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU L 269 " --> pdb=" O ILE L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN L 295 " --> pdb=" O ARG L 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 290 through 295' Processing helix chain 'L' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN L 326 " --> pdb=" O MET L 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER L 340 " --> pdb=" O SER L 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG L 343 " --> pdb=" O GLU L 339 " (cutoff:3.500A) Proline residue: L 344 - end of helix Processing helix chain 'L' and resid 374 through 390 Processing helix chain 'L' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS L 411 " --> pdb=" O ARG L 407 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE L 412 " --> pdb=" O TYR L 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 421 Processing helix chain 'L' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET L 485 " --> pdb=" O MET L 481 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY L 486 " --> pdb=" O PHE L 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 481 through 486' Processing helix chain 'L' and resid 487 through 493 Processing helix chain 'L' and resid 498 through 505 Processing helix chain 'L' and resid 506 through 511 Processing helix chain 'O' and resid 5 through 13 Processing helix chain 'O' and resid 144 through 155 removed outlier: 4.988A pdb=" N ALA O 148 " --> pdb=" O SER O 144 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR O 149 " --> pdb=" O PRO O 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS O 150 " --> pdb=" O GLN O 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN O 154 " --> pdb=" O HIS O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 173 Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU O 190 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) Proline residue: O 193 - end of helix Processing helix chain 'O' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU O 210 " --> pdb=" O GLY O 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN O 213 " --> pdb=" O PRO O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 245 Processing helix chain 'O' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU O 269 " --> pdb=" O ILE O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER O 294 " --> pdb=" O ILE O 290 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 290 through 295' Processing helix chain 'O' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN O 326 " --> pdb=" O MET O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER O 340 " --> pdb=" O SER O 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG O 343 " --> pdb=" O GLU O 339 " (cutoff:3.500A) Proline residue: O 344 - end of helix Processing helix chain 'O' and resid 374 through 390 Processing helix chain 'O' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS O 411 " --> pdb=" O ARG O 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE O 412 " --> pdb=" O TYR O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 421 Processing helix chain 'O' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET O 485 " --> pdb=" O MET O 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY O 486 " --> pdb=" O PHE O 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 481 through 486' Processing helix chain 'O' and resid 487 through 493 Processing helix chain 'O' and resid 498 through 505 Processing helix chain 'O' and resid 506 through 511 Processing helix chain 'R' and resid 5 through 13 Processing helix chain 'R' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA R 148 " --> pdb=" O SER R 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR R 149 " --> pdb=" O PRO R 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS R 150 " --> pdb=" O GLN R 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN R 154 " --> pdb=" O HIS R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 173 Processing helix chain 'R' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY R 191 " --> pdb=" O ARG R 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU R 192 " --> pdb=" O SER R 188 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU R 210 " --> pdb=" O GLY R 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 245 Processing helix chain 'R' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU R 269 " --> pdb=" O ILE R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 290 through 295' Processing helix chain 'R' and resid 312 through 326 removed outlier: 4.095A pdb=" N ASN R 326 " --> pdb=" O MET R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER R 340 " --> pdb=" O SER R 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG R 343 " --> pdb=" O GLU R 339 " (cutoff:3.500A) Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 374 through 390 Processing helix chain 'R' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS R 411 " --> pdb=" O ARG R 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE R 412 " --> pdb=" O TYR R 408 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 421 Processing helix chain 'R' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET R 485 " --> pdb=" O MET R 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY R 486 " --> pdb=" O PHE R 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 481 through 486' Processing helix chain 'R' and resid 487 through 493 Processing helix chain 'R' and resid 498 through 505 Processing helix chain 'R' and resid 506 through 511 Processing helix chain 'V' and resid 5 through 13 Processing helix chain 'V' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA V 148 " --> pdb=" O SER V 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR V 149 " --> pdb=" O PRO V 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS V 150 " --> pdb=" O GLN V 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN V 154 " --> pdb=" O HIS V 150 " (cutoff:3.500A) Processing helix chain 'V' and resid 167 through 173 Processing helix chain 'V' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU V 190 " --> pdb=" O LEU V 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY V 191 " --> pdb=" O ARG V 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU V 192 " --> pdb=" O SER V 188 " (cutoff:3.500A) Proline residue: V 193 - end of helix Processing helix chain 'V' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU V 210 " --> pdb=" O GLY V 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN V 213 " --> pdb=" O PRO V 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 245 Processing helix chain 'V' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU V 269 " --> pdb=" O ILE V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER V 294 " --> pdb=" O ILE V 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN V 295 " --> pdb=" O ARG V 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 290 through 295' Processing helix chain 'V' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN V 326 " --> pdb=" O MET V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER V 340 " --> pdb=" O SER V 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG V 343 " --> pdb=" O GLU V 339 " (cutoff:3.500A) Proline residue: V 344 - end of helix Processing helix chain 'V' and resid 374 through 390 Processing helix chain 'V' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS V 411 " --> pdb=" O ARG V 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE V 412 " --> pdb=" O TYR V 408 " (cutoff:3.500A) Processing helix chain 'V' and resid 414 through 421 Processing helix chain 'V' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET V 485 " --> pdb=" O MET V 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY V 486 " --> pdb=" O PHE V 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 481 through 486' Processing helix chain 'V' and resid 487 through 493 Processing helix chain 'V' and resid 498 through 505 Processing helix chain 'V' and resid 506 through 511 Processing helix chain 'Y' and resid 5 through 13 Processing helix chain 'Y' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA Y 148 " --> pdb=" O SER Y 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR Y 149 " --> pdb=" O PRO Y 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS Y 150 " --> pdb=" O GLN Y 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN Y 154 " --> pdb=" O HIS Y 150 " (cutoff:3.500A) Processing helix chain 'Y' and resid 167 through 173 Processing helix chain 'Y' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU Y 190 " --> pdb=" O LEU Y 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY Y 191 " --> pdb=" O ARG Y 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU Y 192 " --> pdb=" O SER Y 188 " (cutoff:3.500A) Proline residue: Y 193 - end of helix Processing helix chain 'Y' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU Y 210 " --> pdb=" O GLY Y 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN Y 213 " --> pdb=" O PRO Y 209 " (cutoff:3.500A) Processing helix chain 'Y' and resid 230 through 245 Processing helix chain 'Y' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU Y 269 " --> pdb=" O ILE Y 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER Y 294 " --> pdb=" O ILE Y 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN Y 295 " --> pdb=" O ARG Y 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 290 through 295' Processing helix chain 'Y' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN Y 326 " --> pdb=" O MET Y 322 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER Y 340 " --> pdb=" O SER Y 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG Y 343 " --> pdb=" O GLU Y 339 " (cutoff:3.500A) Proline residue: Y 344 - end of helix Processing helix chain 'Y' and resid 374 through 390 Processing helix chain 'Y' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS Y 411 " --> pdb=" O ARG Y 407 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE Y 412 " --> pdb=" O TYR Y 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 414 through 421 Processing helix chain 'Y' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET Y 485 " --> pdb=" O MET Y 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY Y 486 " --> pdb=" O PHE Y 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 481 through 486' Processing helix chain 'Y' and resid 487 through 493 Processing helix chain 'Y' and resid 498 through 505 Processing helix chain 'Y' and resid 506 through 511 Processing helix chain '1' and resid 5 through 13 Processing helix chain '1' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA 1 148 " --> pdb=" O SER 1 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR 1 149 " --> pdb=" O PRO 1 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS 1 150 " --> pdb=" O GLN 1 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN 1 154 " --> pdb=" O HIS 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 167 through 173 Processing helix chain '1' and resid 178 through 193 removed outlier: 3.681A pdb=" N GLU 1 190 " --> pdb=" O LEU 1 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY 1 191 " --> pdb=" O ARG 1 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU 1 192 " --> pdb=" O SER 1 188 " (cutoff:3.500A) Proline residue: 1 193 - end of helix Processing helix chain '1' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU 1 210 " --> pdb=" O GLY 1 206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN 1 213 " --> pdb=" O PRO 1 209 " (cutoff:3.500A) Processing helix chain '1' and resid 230 through 245 Processing helix chain '1' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU 1 269 " --> pdb=" O ILE 1 265 " (cutoff:3.500A) Processing helix chain '1' and resid 290 through 295 removed outlier: 4.905A pdb=" N SER 1 294 " --> pdb=" O ILE 1 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN 1 295 " --> pdb=" O ARG 1 291 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 290 through 295' Processing helix chain '1' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN 1 326 " --> pdb=" O MET 1 322 " (cutoff:3.500A) Processing helix chain '1' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER 1 340 " --> pdb=" O SER 1 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG 1 343 " --> pdb=" O GLU 1 339 " (cutoff:3.500A) Proline residue: 1 344 - end of helix Processing helix chain '1' and resid 374 through 390 Processing helix chain '1' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS 1 411 " --> pdb=" O ARG 1 407 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE 1 412 " --> pdb=" O TYR 1 408 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 421 Processing helix chain '1' and resid 481 through 486 removed outlier: 3.661A pdb=" N MET 1 485 " --> pdb=" O MET 1 481 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY 1 486 " --> pdb=" O PHE 1 482 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 481 through 486' Processing helix chain '1' and resid 487 through 493 Processing helix chain '1' and resid 498 through 505 Processing helix chain '1' and resid 506 through 511 Processing helix chain '4' and resid 5 through 13 Processing helix chain '4' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR 4 149 " --> pdb=" O PRO 4 145 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS 4 150 " --> pdb=" O GLN 4 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN 4 154 " --> pdb=" O HIS 4 150 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 173 Processing helix chain '4' and resid 178 through 193 removed outlier: 3.681A pdb=" N GLU 4 190 " --> pdb=" O LEU 4 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY 4 191 " --> pdb=" O ARG 4 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU 4 192 " --> pdb=" O SER 4 188 " (cutoff:3.500A) Proline residue: 4 193 - end of helix Processing helix chain '4' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU 4 210 " --> pdb=" O GLY 4 206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN 4 213 " --> pdb=" O PRO 4 209 " (cutoff:3.500A) Processing helix chain '4' and resid 230 through 245 Processing helix chain '4' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU 4 269 " --> pdb=" O ILE 4 265 " (cutoff:3.500A) Processing helix chain '4' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER 4 294 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN 4 295 " --> pdb=" O ARG 4 291 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 290 through 295' Processing helix chain '4' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN 4 326 " --> pdb=" O MET 4 322 " (cutoff:3.500A) Processing helix chain '4' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER 4 340 " --> pdb=" O SER 4 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG 4 343 " --> pdb=" O GLU 4 339 " (cutoff:3.500A) Proline residue: 4 344 - end of helix Processing helix chain '4' and resid 374 through 390 Processing helix chain '4' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS 4 411 " --> pdb=" O ARG 4 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE 4 412 " --> pdb=" O TYR 4 408 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 421 Processing helix chain '4' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET 4 485 " --> pdb=" O MET 4 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY 4 486 " --> pdb=" O PHE 4 482 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 481 through 486' Processing helix chain '4' and resid 487 through 493 Processing helix chain '4' and resid 498 through 505 Processing helix chain '4' and resid 506 through 511 Processing helix chain '7' and resid 5 through 13 Processing helix chain '7' and resid 144 through 155 removed outlier: 4.988A pdb=" N ALA 7 148 " --> pdb=" O SER 7 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR 7 149 " --> pdb=" O PRO 7 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS 7 150 " --> pdb=" O GLN 7 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN 7 154 " --> pdb=" O HIS 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 167 through 173 Processing helix chain '7' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU 7 190 " --> pdb=" O LEU 7 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY 7 191 " --> pdb=" O ARG 7 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU 7 192 " --> pdb=" O SER 7 188 " (cutoff:3.500A) Proline residue: 7 193 - end of helix Processing helix chain '7' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU 7 210 " --> pdb=" O GLY 7 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN 7 213 " --> pdb=" O PRO 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 230 through 245 Processing helix chain '7' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU 7 269 " --> pdb=" O ILE 7 265 " (cutoff:3.500A) Processing helix chain '7' and resid 290 through 295 removed outlier: 4.905A pdb=" N SER 7 294 " --> pdb=" O ILE 7 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN 7 295 " --> pdb=" O ARG 7 291 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 290 through 295' Processing helix chain '7' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN 7 326 " --> pdb=" O MET 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER 7 340 " --> pdb=" O SER 7 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG 7 343 " --> pdb=" O GLU 7 339 " (cutoff:3.500A) Proline residue: 7 344 - end of helix Processing helix chain '7' and resid 374 through 390 Processing helix chain '7' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS 7 411 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE 7 412 " --> pdb=" O TYR 7 408 " (cutoff:3.500A) Processing helix chain '7' and resid 414 through 421 Processing helix chain '7' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET 7 485 " --> pdb=" O MET 7 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY 7 486 " --> pdb=" O PHE 7 482 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 481 through 486' Processing helix chain '7' and resid 487 through 493 Processing helix chain '7' and resid 498 through 505 Processing helix chain '7' and resid 506 through 511 Processing helix chain 'U' and resid 5 through 13 Processing helix chain 'U' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA U 148 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR U 149 " --> pdb=" O PRO U 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS U 150 " --> pdb=" O GLN U 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN U 154 " --> pdb=" O HIS U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 173 Processing helix chain 'U' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU U 190 " --> pdb=" O LEU U 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU U 192 " --> pdb=" O SER U 188 " (cutoff:3.500A) Proline residue: U 193 - end of helix Processing helix chain 'U' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU U 210 " --> pdb=" O GLY U 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN U 213 " --> pdb=" O PRO U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 245 Processing helix chain 'U' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU U 269 " --> pdb=" O ILE U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 290 through 295 removed outlier: 4.907A pdb=" N SER U 294 " --> pdb=" O ILE U 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN U 295 " --> pdb=" O ARG U 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 290 through 295' Processing helix chain 'U' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN U 326 " --> pdb=" O MET U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER U 340 " --> pdb=" O SER U 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG U 343 " --> pdb=" O GLU U 339 " (cutoff:3.500A) Proline residue: U 344 - end of helix Processing helix chain 'U' and resid 374 through 390 Processing helix chain 'U' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS U 411 " --> pdb=" O ARG U 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE U 412 " --> pdb=" O TYR U 408 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 421 Processing helix chain 'U' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET U 485 " --> pdb=" O MET U 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY U 486 " --> pdb=" O PHE U 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 481 through 486' Processing helix chain 'U' and resid 487 through 493 Processing helix chain 'U' and resid 498 through 505 Processing helix chain 'U' and resid 506 through 511 Processing sheet with id= 1, first strand: chain 'A' and resid 79 through 85 Processing sheet with id= 2, first strand: chain 'D' and resid 79 through 85 Processing sheet with id= 3, first strand: chain 'G' and resid 79 through 85 Processing sheet with id= 4, first strand: chain 'J' and resid 79 through 85 Processing sheet with id= 5, first strand: chain 'M' and resid 79 through 85 Processing sheet with id= 6, first strand: chain 'P' and resid 79 through 85 Processing sheet with id= 7, first strand: chain 'S' and resid 79 through 85 Processing sheet with id= 8, first strand: chain 'W' and resid 79 through 85 Processing sheet with id= 9, first strand: chain 'Z' and resid 79 through 85 Processing sheet with id= 10, first strand: chain '2' and resid 79 through 85 Processing sheet with id= 11, first strand: chain '5' and resid 79 through 85 Processing sheet with id= 12, first strand: chain '8' and resid 79 through 85 Processing sheet with id= 13, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP B 109 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR B 101 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP E 109 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR E 101 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP H 109 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 68 through 72 removed outlier: 7.525A pdb=" N THR H 101 " --> pdb=" O SER H 72 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP K 109 " --> pdb=" O ASN K 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 72 removed outlier: 7.527A pdb=" N THR K 101 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'N' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP N 109 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR N 101 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP Q 109 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR Q 101 " --> pdb=" O SER Q 72 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'T' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP T 109 " --> pdb=" O ASN T 62 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'T' and resid 68 through 72 removed outlier: 7.525A pdb=" N THR T 101 " --> pdb=" O SER T 72 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'X' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP X 109 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'X' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR X 101 " --> pdb=" O SER X 72 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '0' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP 0 109 " --> pdb=" O ASN 0 62 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '0' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR 0 101 " --> pdb=" O SER 0 72 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '3' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP 3 109 " --> pdb=" O ASN 3 62 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '3' and resid 68 through 72 removed outlier: 7.525A pdb=" N THR 3 101 " --> pdb=" O SER 3 72 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '6' and resid 55 through 62 removed outlier: 4.199A pdb=" N ASP 6 109 " --> pdb=" O ASN 6 62 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '6' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR 6 101 " --> pdb=" O SER 6 72 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '9' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP 9 109 " --> pdb=" O ASN 9 62 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '9' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR 9 101 " --> pdb=" O SER 9 72 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP C 19 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C 28 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY C 98 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 129 through 132 Processing sheet with id= 40, first strand: chain 'C' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY C 220 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS C 224 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 272 through 276 Processing sheet with id= 42, first strand: chain 'C' and resid 494 through 497 Processing sheet with id= 43, first strand: chain 'C' and resid 539 through 542 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'C' and resid 74 through 77 Processing sheet with id= 45, first strand: chain 'F' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP F 19 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU F 28 " --> pdb=" O LEU F 23 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY F 98 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'F' and resid 129 through 132 Processing sheet with id= 48, first strand: chain 'F' and resid 157 through 161 removed outlier: 4.148A pdb=" N GLY F 220 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS F 224 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'F' and resid 272 through 276 Processing sheet with id= 50, first strand: chain 'F' and resid 494 through 497 Processing sheet with id= 51, first strand: chain 'F' and resid 539 through 542 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'F' and resid 74 through 77 Processing sheet with id= 53, first strand: chain 'I' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP I 19 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU I 28 " --> pdb=" O LEU I 23 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'I' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY I 98 " --> pdb=" O GLY I 90 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'I' and resid 129 through 132 Processing sheet with id= 56, first strand: chain 'I' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY I 220 " --> pdb=" O ILE I 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS I 224 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'I' and resid 272 through 276 Processing sheet with id= 58, first strand: chain 'I' and resid 494 through 497 Processing sheet with id= 59, first strand: chain 'I' and resid 539 through 542 No H-bonds generated for sheet with id= 59 Processing sheet with id= 60, first strand: chain 'I' and resid 74 through 77 Processing sheet with id= 61, first strand: chain 'L' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP L 19 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU L 28 " --> pdb=" O LEU L 23 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'L' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY L 98 " --> pdb=" O GLY L 90 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'L' and resid 129 through 132 Processing sheet with id= 64, first strand: chain 'L' and resid 157 through 161 removed outlier: 4.148A pdb=" N GLY L 220 " --> pdb=" O ILE L 198 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N HIS L 224 " --> pdb=" O GLY L 202 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'L' and resid 272 through 276 Processing sheet with id= 66, first strand: chain 'L' and resid 494 through 497 Processing sheet with id= 67, first strand: chain 'L' and resid 539 through 542 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 69, first strand: chain 'O' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP O 19 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU O 28 " --> pdb=" O LEU O 23 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'O' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY O 98 " --> pdb=" O GLY O 90 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'O' and resid 129 through 132 Processing sheet with id= 72, first strand: chain 'O' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY O 220 " --> pdb=" O ILE O 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS O 224 " --> pdb=" O GLY O 202 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'O' and resid 272 through 276 Processing sheet with id= 74, first strand: chain 'O' and resid 494 through 497 Processing sheet with id= 75, first strand: chain 'O' and resid 539 through 542 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain 'O' and resid 74 through 77 Processing sheet with id= 77, first strand: chain 'R' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP R 19 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU R 28 " --> pdb=" O LEU R 23 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY R 98 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'R' and resid 129 through 132 Processing sheet with id= 80, first strand: chain 'R' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY R 220 " --> pdb=" O ILE R 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS R 224 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'R' and resid 272 through 276 Processing sheet with id= 82, first strand: chain 'R' and resid 494 through 497 Processing sheet with id= 83, first strand: chain 'R' and resid 539 through 542 No H-bonds generated for sheet with id= 83 Processing sheet with id= 84, first strand: chain 'R' and resid 74 through 77 Processing sheet with id= 85, first strand: chain 'V' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP V 19 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU V 28 " --> pdb=" O LEU V 23 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'V' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY V 98 " --> pdb=" O GLY V 90 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'V' and resid 129 through 132 Processing sheet with id= 88, first strand: chain 'V' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY V 220 " --> pdb=" O ILE V 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS V 224 " --> pdb=" O GLY V 202 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'V' and resid 272 through 276 Processing sheet with id= 90, first strand: chain 'V' and resid 494 through 497 Processing sheet with id= 91, first strand: chain 'V' and resid 539 through 542 No H-bonds generated for sheet with id= 91 Processing sheet with id= 92, first strand: chain 'V' and resid 74 through 77 Processing sheet with id= 93, first strand: chain 'Y' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP Y 19 " --> pdb=" O ILE Y 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU Y 28 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'Y' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY Y 98 " --> pdb=" O GLY Y 90 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id= 96, first strand: chain 'Y' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY Y 220 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N HIS Y 224 " --> pdb=" O GLY Y 202 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'Y' and resid 272 through 276 Processing sheet with id= 98, first strand: chain 'Y' and resid 494 through 497 Processing sheet with id= 99, first strand: chain 'Y' and resid 539 through 542 No H-bonds generated for sheet with id= 99 Processing sheet with id=100, first strand: chain 'Y' and resid 74 through 77 Processing sheet with id=101, first strand: chain '1' and resid 19 through 23 removed outlier: 4.903A pdb=" N ASP 1 19 " --> pdb=" O ILE 1 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU 1 28 " --> pdb=" O LEU 1 23 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '1' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY 1 98 " --> pdb=" O GLY 1 90 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain '1' and resid 129 through 132 Processing sheet with id=104, first strand: chain '1' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY 1 220 " --> pdb=" O ILE 1 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS 1 224 " --> pdb=" O GLY 1 202 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain '1' and resid 272 through 276 Processing sheet with id=106, first strand: chain '1' and resid 494 through 497 Processing sheet with id=107, first strand: chain '1' and resid 539 through 542 No H-bonds generated for sheet with id=107 Processing sheet with id=108, first strand: chain '1' and resid 74 through 77 Processing sheet with id=109, first strand: chain '4' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP 4 19 " --> pdb=" O ILE 4 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU 4 28 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain '4' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY 4 98 " --> pdb=" O GLY 4 90 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain '4' and resid 129 through 132 Processing sheet with id=112, first strand: chain '4' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY 4 220 " --> pdb=" O ILE 4 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS 4 224 " --> pdb=" O GLY 4 202 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain '4' and resid 272 through 276 Processing sheet with id=114, first strand: chain '4' and resid 494 through 497 Processing sheet with id=115, first strand: chain '4' and resid 539 through 542 No H-bonds generated for sheet with id=115 Processing sheet with id=116, first strand: chain '4' and resid 74 through 77 Processing sheet with id=117, first strand: chain '7' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP 7 19 " --> pdb=" O ILE 7 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU 7 28 " --> pdb=" O LEU 7 23 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain '7' and resid 97 through 100 removed outlier: 3.766A pdb=" N GLY 7 98 " --> pdb=" O GLY 7 90 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain '7' and resid 129 through 132 Processing sheet with id=120, first strand: chain '7' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY 7 220 " --> pdb=" O ILE 7 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS 7 224 " --> pdb=" O GLY 7 202 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain '7' and resid 272 through 276 Processing sheet with id=122, first strand: chain '7' and resid 494 through 497 Processing sheet with id=123, first strand: chain '7' and resid 539 through 542 No H-bonds generated for sheet with id=123 Processing sheet with id=124, first strand: chain '7' and resid 74 through 77 Processing sheet with id=125, first strand: chain 'U' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP U 19 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU U 28 " --> pdb=" O LEU U 23 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'U' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY U 98 " --> pdb=" O GLY U 90 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'U' and resid 129 through 132 Processing sheet with id=128, first strand: chain 'U' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY U 220 " --> pdb=" O ILE U 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS U 224 " --> pdb=" O GLY U 202 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'U' and resid 272 through 276 Processing sheet with id=130, first strand: chain 'U' and resid 494 through 497 Processing sheet with id=131, first strand: chain 'U' and resid 539 through 542 No H-bonds generated for sheet with id=131 Processing sheet with id=132, first strand: chain 'U' and resid 74 through 77 2676 hydrogen bonds defined for protein. 7944 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: 73.37 Time building geometry restraints manager: 115.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.54 - 0.81: 14585 0.81 - 1.08: 58542 1.08 - 1.35: 30737 1.35 - 1.62: 43136 1.62 - 1.89: 936 Bond restraints: 147936 Sorted by residual: bond pdb=" N ALA O 435 " pdb=" H AALA O 435 " ideal model delta sigma weight residual 0.860 1.322 -0.462 2.00e-02 2.50e+03 5.33e+02 bond pdb=" N ALA L 435 " pdb=" H AALA L 435 " ideal model delta sigma weight residual 0.860 1.322 -0.462 2.00e-02 2.50e+03 5.33e+02 bond pdb=" N ALA 7 435 " pdb=" H AALA 7 435 " ideal model delta sigma weight residual 0.860 1.322 -0.462 2.00e-02 2.50e+03 5.33e+02 bond pdb=" N ALA V 435 " pdb=" H AALA V 435 " ideal model delta sigma weight residual 0.860 1.321 -0.461 2.00e-02 2.50e+03 5.32e+02 bond pdb=" N ALA C 435 " pdb=" H AALA C 435 " ideal model delta sigma weight residual 0.860 1.321 -0.461 2.00e-02 2.50e+03 5.32e+02 ... (remaining 147931 not shown) Histogram of bond angle deviations from ideal: 51.47 - 76.98: 168 76.98 - 102.49: 25160 102.49 - 128.00: 237116 128.00 - 153.51: 5432 153.51 - 179.01: 24 Bond angle restraints: 267900 Sorted by residual: angle pdb=" C AARG N 153 " pdb=" N ARG N 154 " pdb=" H AARG N 154 " ideal model delta sigma weight residual 124.93 57.56 67.37 3.00e+00 1.11e-01 5.04e+02 angle pdb=" C AARG X 153 " pdb=" N ARG X 154 " pdb=" H AARG X 154 " ideal model delta sigma weight residual 124.93 57.59 67.34 3.00e+00 1.11e-01 5.04e+02 angle pdb=" C AARG H 153 " pdb=" N ARG H 154 " pdb=" H AARG H 154 " ideal model delta sigma weight residual 124.93 57.61 67.32 3.00e+00 1.11e-01 5.04e+02 angle pdb=" C AARG B 153 " pdb=" N ARG B 154 " pdb=" H AARG B 154 " ideal model delta sigma weight residual 124.93 57.63 67.30 3.00e+00 1.11e-01 5.03e+02 angle pdb=" C AARG Q 153 " pdb=" N ARG Q 154 " pdb=" H AARG Q 154 " ideal model delta sigma weight residual 124.93 57.63 67.30 3.00e+00 1.11e-01 5.03e+02 ... (remaining 267895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 57703 17.94 - 35.88: 7432 35.88 - 53.82: 3266 53.82 - 71.76: 992 71.76 - 89.70: 159 Dihedral angle restraints: 69552 sinusoidal: 38724 harmonic: 30828 Sorted by residual: dihedral pdb=" CA PRO Y 287 " pdb=" C PRO Y 287 " pdb=" N ASP Y 288 " pdb=" CA ASP Y 288 " ideal model delta harmonic sigma weight residual -180.00 -149.08 -30.92 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA PRO R 287 " pdb=" C PRO R 287 " pdb=" N ASP R 288 " pdb=" CA ASP R 288 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA PRO F 287 " pdb=" C PRO F 287 " pdb=" N ASP F 288 " pdb=" CA ASP F 288 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 69549 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.322: 8404 0.322 - 0.644: 2108 0.644 - 0.966: 696 0.966 - 1.288: 192 1.288 - 1.610: 36 Chirality restraints: 11436 Sorted by residual: chirality pdb=" CG LEU F 299 " pdb=" CB LEU F 299 " pdb=" CD1 LEU F 299 " pdb=" CD2 LEU F 299 " both_signs ideal model delta sigma weight residual False -2.59 -0.98 -1.61 2.00e-01 2.50e+01 6.48e+01 chirality pdb=" CG LEU 4 299 " pdb=" CB LEU 4 299 " pdb=" CD1 LEU 4 299 " pdb=" CD2 LEU 4 299 " both_signs ideal model delta sigma weight residual False -2.59 -0.98 -1.61 2.00e-01 2.50e+01 6.47e+01 chirality pdb=" CG LEU U 299 " pdb=" CB LEU U 299 " pdb=" CD1 LEU U 299 " pdb=" CD2 LEU U 299 " both_signs ideal model delta sigma weight residual False -2.59 -0.98 -1.61 2.00e-01 2.50e+01 6.46e+01 ... (remaining 11433 not shown) Planarity restraints: 22704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 304 " -0.259 2.00e-02 2.50e+03 3.33e-01 1.66e+03 pdb=" CG ASN F 304 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN F 304 " 0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN F 304 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN F 304 " -0.528 2.00e-02 2.50e+03 pdb="HD22 ASN F 304 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 304 " 0.259 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CG ASN R 304 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN R 304 " -0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN R 304 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN R 304 " 0.528 2.00e-02 2.50e+03 pdb="HD22 ASN R 304 " -0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 4 304 " 0.258 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CG ASN 4 304 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN 4 304 " -0.242 2.00e-02 2.50e+03 pdb=" ND2 ASN 4 304 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN 4 304 " 0.528 2.00e-02 2.50e+03 pdb="HD22 ASN 4 304 " -0.507 2.00e-02 2.50e+03 ... (remaining 22701 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.76: 2828 1.76 - 2.47: 110546 2.47 - 3.18: 488965 3.18 - 3.89: 699775 3.89 - 4.60: 1110811 Nonbonded interactions: 2412925 Sorted by model distance: nonbonded pdb=" HG1 THR L 167 " pdb=" OD2 ASP V 122 " model vdw 1.050 1.850 nonbonded pdb=" OD2 ASP F 122 " pdb=" HG1 THR Y 167 " model vdw 1.165 1.850 nonbonded pdb=" HG1 THR I 167 " pdb=" OD2 ASP U 122 " model vdw 1.244 1.850 nonbonded pdb=" OD2 ASP R 122 " pdb=" HG1 THR V 167 " model vdw 1.271 1.850 nonbonded pdb=" OD2 ASP 1 122 " pdb=" HG1 THR 7 167 " model vdw 1.308 1.850 ... (remaining 2412920 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 '0' and (resid 31 through 152 or resid 155 through 162)) selection = (chain '3' and (resid 31 through 152 or resid 155 through 162)) selection = (chain '6' and (resid 31 through 152 or resid 155 through 162)) selection = (chain '9' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'B' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'E' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'H' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'K' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'N' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'Q' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'T' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'X' and (resid 31 through 152 or resid 155 through 162)) } ncs_group { reference = (chain '1' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain '4' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain '7' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'C' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'F' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'I' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'L' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'O' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'R' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'U' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'V' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'Y' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) } ncs_group { reference = (chain '2' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain '5' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain '8' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'A' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'D' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'G' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'J' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'M' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'P' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'S' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'W' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'Z' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) } 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=0.50 max=1.00 mean=0.98 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: 10.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 2.470 Extract box with map and model: 31.670 Check model and map are aligned: 1.620 Set scattering table: 1.090 Process input model: 489.920 Find NCS groups from input model: 7.080 Set up NCS constraints: 0.650 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: 0.030 Load rotamer database and sin/cos tables:11.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 556.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 0.067 0.515 74892 Z= 4.444 Angle : 3.597 20.148 101616 Z= 2.117 Chirality : 0.358 1.610 11436 Planarity : 0.018 0.069 13488 Dihedral : 16.306 89.703 27804 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.25 % Favored : 94.36 % Rotamer: Outliers : 2.74 % Allowed : 7.46 % Favored : 89.80 % Cbeta Deviations : 2.84 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.07), residues: 9780 helix: -2.65 (0.06), residues: 3060 sheet: 0.73 (0.15), residues: 1032 loop : -1.50 (0.07), residues: 5688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.019 TRP V 180 HIS 0.046 0.011 HIS F 251 PHE 0.074 0.013 PHE R 362 TYR 0.058 0.019 TYR V 9 ARG 0.059 0.008 ARG V 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1164 time to evaluate : 8.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 240 MET cc_start: 0.8422 (tpp) cc_final: 0.8180 (tpp) REVERT: E 110 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: F 485 MET cc_start: 0.7951 (mmp) cc_final: 0.7657 (mmt) REVERT: I 3 GLN cc_start: 0.8284 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: I 4 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8307 (tt) REVERT: I 203 ASN cc_start: 0.8007 (OUTLIER) cc_final: 0.7766 (m110) REVERT: K 53 LYS cc_start: 0.7878 (mttp) cc_final: 0.7529 (mtmt) REVERT: K 110 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: O 386 MET cc_start: 0.8357 (mmp) cc_final: 0.7973 (mmp) REVERT: V 4 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8323 (tt) REVERT: V 386 MET cc_start: 0.8081 (mmp) cc_final: 0.7819 (mmp) REVERT: Y 3 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.7822 (tt0) REVERT: 0 53 LYS cc_start: 0.7928 (mttp) cc_final: 0.7678 (mttt) REVERT: 1 565 MET cc_start: 0.8381 (mmm) cc_final: 0.8138 (mmm) REVERT: 7 380 MET cc_start: 0.7681 (mmp) cc_final: 0.7403 (mmm) REVERT: 9 110 GLU cc_start: 0.6940 (OUTLIER) cc_final: 0.6685 (tm-30) outliers start: 132 outliers final: 46 residues processed: 1250 average time/residue: 4.0268 time to fit residues: 6608.4997 Evaluate side-chains 1039 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 985 time to evaluate : 8.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain D residue 75 ASP Chi-restraints excluded: chain E residue 110 GLU Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 379 VAL Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain J residue 75 ASP Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain P residue 75 ASP Chi-restraints excluded: chain R residue 4 ILE Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 339 GLU Chi-restraints excluded: chain R residue 379 VAL Chi-restraints excluded: chain S residue 75 ASP Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 203 ASN Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 75 ASP Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain Y residue 203 ASN Chi-restraints excluded: chain Y residue 454 LYS Chi-restraints excluded: chain 1 residue 4 ILE Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 203 ASN Chi-restraints excluded: chain 1 residue 339 GLU Chi-restraints excluded: chain 1 residue 379 VAL Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 5 residue 75 ASP Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 379 VAL Chi-restraints excluded: chain 9 residue 110 GLU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 37 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 5.9990 chunk 718 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 484 optimal weight: 6.9990 chunk 383 optimal weight: 5.9990 chunk 743 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 451 optimal weight: 5.9990 chunk 553 optimal weight: 5.9990 chunk 860 optimal weight: 0.9980 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN B 52 ASN C 184 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS E 52 ASN F 184 GLN F 521 ASN F 528 HIS G 2 GLN H 52 ASN I 184 GLN ** I 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN O 184 GLN O 528 HIS P 2 GLN Q 52 ASN R 184 GLN R 521 ASN T 52 ASN V 184 GLN W 2 GLN X 52 ASN Y 184 GLN 0 52 ASN 1 184 GLN 3 52 ASN 4 528 HIS 4 538 ASN 6 52 ASN 7 184 GLN ** 9 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 ASN U 184 GLN U 521 ASN U 538 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 74892 Z= 0.372 Angle : 0.870 8.545 101616 Z= 0.474 Chirality : 0.053 0.256 11436 Planarity : 0.007 0.060 13488 Dihedral : 7.157 56.157 10650 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.07 % Favored : 95.81 % Rotamer: Outliers : 2.46 % Allowed : 8.17 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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 (0.08), residues: 9780 helix: -1.00 (0.08), residues: 3144 sheet: 0.80 (0.14), residues: 1140 loop : -0.68 (0.08), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP L 440 HIS 0.009 0.002 HIS 4 354 PHE 0.023 0.003 PHE 4 268 TYR 0.025 0.004 TYR 4 478 ARG 0.009 0.001 ARG U 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1105 time to evaluate : 8.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 386 MET cc_start: 0.8284 (mmp) cc_final: 0.8078 (mmp) REVERT: G 59 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6992 (tp30) REVERT: I 239 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7313 (mtp85) REVERT: K 53 LYS cc_start: 0.8063 (mttp) cc_final: 0.7788 (mttt) REVERT: O 8 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.7050 (tp30) REVERT: V 386 MET cc_start: 0.8291 (mmp) cc_final: 0.8085 (mmp) REVERT: V 549 LYS cc_start: 0.8136 (mttp) cc_final: 0.7871 (mtmm) REVERT: Y 3 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: Y 240 MET cc_start: 0.8401 (tpp) cc_final: 0.8140 (tpp) REVERT: 1 239 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7158 (mtp85) REVERT: 6 110 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6614 (mt-10) REVERT: 7 239 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7295 (mtp85) REVERT: 7 380 MET cc_start: 0.7569 (mmp) cc_final: 0.7308 (mmm) REVERT: 9 53 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7859 (mttt) REVERT: U 380 MET cc_start: 0.7411 (mmp) cc_final: 0.7175 (mmm) outliers start: 122 outliers final: 39 residues processed: 1168 average time/residue: 3.8918 time to fit residues: 5917.5754 Evaluate side-chains 1116 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1069 time to evaluate : 8.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 379 VAL Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain F residue 319 ASP Chi-restraints excluded: chain F residue 454 LYS Chi-restraints excluded: chain G residue 59 GLU Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 203 ASN Chi-restraints excluded: chain I residue 239 ARG Chi-restraints excluded: chain I residue 319 ASP Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 203 ASN Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain Y residue 3 GLN Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain Y residue 203 ASN Chi-restraints excluded: chain 0 residue 162 SER Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 203 ASN Chi-restraints excluded: chain 1 residue 239 ARG Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 2 residue 59 GLU Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 7 residue 4 ILE Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 239 ARG Chi-restraints excluded: chain 7 residue 322 MET Chi-restraints excluded: chain 9 residue 53 LYS Chi-restraints excluded: chain 9 residue 112 GLU Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 8.9990 chunk 267 optimal weight: 3.9990 chunk 716 optimal weight: 0.9980 chunk 586 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 862 optimal weight: 4.9990 chunk 931 optimal weight: 4.9990 chunk 768 optimal weight: 5.9990 chunk 855 optimal weight: 3.9990 chunk 294 optimal weight: 10.0000 chunk 691 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN B 52 ASN C 521 ASN F 528 HIS H 52 ASN J 2 GLN L 184 GLN M 2 GLN N 34 ASN O 203 ASN O 521 ASN O 528 HIS R 203 ASN R 528 HIS V 351 ASN V 528 HIS V 538 ASN Z 2 GLN 0 52 ASN 1 528 HIS 3 34 ASN 4 528 HIS 7 528 HIS 9 34 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 74892 Z= 0.297 Angle : 0.751 7.896 101616 Z= 0.406 Chirality : 0.049 0.225 11436 Planarity : 0.005 0.046 13488 Dihedral : 6.495 57.880 10594 Min Nonbonded Distance : 1.711 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.89 % Favored : 95.99 % Rotamer: Outliers : 2.19 % Allowed : 8.26 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.51 (0.08), residues: 9780 helix: -0.41 (0.08), residues: 3156 sheet: 0.93 (0.14), residues: 1164 loop : -0.50 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP U 440 HIS 0.008 0.002 HIS 4 354 PHE 0.022 0.002 PHE U 482 TYR 0.021 0.003 TYR 4 478 ARG 0.007 0.001 ARG U 523 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1086 time to evaluate : 8.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LYS cc_start: 0.8218 (mttp) cc_final: 0.7915 (mttt) REVERT: O 8 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7042 (tp30) REVERT: O 185 MET cc_start: 0.8504 (mmm) cc_final: 0.8219 (mmm) REVERT: Y 240 MET cc_start: 0.8407 (tpp) cc_final: 0.8091 (tpp) REVERT: 1 319 ASP cc_start: 0.7470 (OUTLIER) cc_final: 0.7201 (t0) REVERT: 4 550 VAL cc_start: 0.8536 (p) cc_final: 0.8249 (t) REVERT: 5 1 MET cc_start: 0.7729 (ptp) cc_final: 0.7483 (ptp) REVERT: 7 380 MET cc_start: 0.7551 (mmp) cc_final: 0.7294 (mmm) REVERT: 9 53 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7892 (mttt) REVERT: U 380 MET cc_start: 0.7427 (mmp) cc_final: 0.7195 (mmm) outliers start: 101 outliers final: 38 residues processed: 1123 average time/residue: 3.9376 time to fit residues: 5752.9497 Evaluate side-chains 1099 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1058 time to evaluate : 8.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 203 ASN Chi-restraints excluded: chain H residue 59 LYS Chi-restraints excluded: chain I residue 4 ILE Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain O residue 8 GLU Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 430 GLU Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 215 ILE Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 0 residue 162 SER Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 319 ASP Chi-restraints excluded: chain 1 residue 430 GLU Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 203 ASN Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain 7 residue 322 MET Chi-restraints excluded: chain 9 residue 53 LYS Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 4.9990 chunk 648 optimal weight: 6.9990 chunk 447 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 411 optimal weight: 4.9990 chunk 579 optimal weight: 5.9990 chunk 865 optimal weight: 0.9990 chunk 916 optimal weight: 5.9990 chunk 452 optimal weight: 5.9990 chunk 820 optimal weight: 5.9990 chunk 246 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN B 52 ASN C 521 ASN C 538 ASN F 312 ASN F 528 HIS H 52 ASN I 203 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN Y 203 ASN 0 52 ASN 1 521 ASN 1 528 HIS 2 2 GLN 7 528 HIS 7 538 ASN 9 34 ASN U 203 ASN U 528 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 74892 Z= 0.251 Angle : 0.698 7.657 101616 Z= 0.375 Chirality : 0.048 0.203 11436 Planarity : 0.005 0.064 13488 Dihedral : 6.196 52.565 10574 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % Rotamer: Outliers : 2.00 % Allowed : 8.63 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.25 (0.08), residues: 9780 helix: -0.08 (0.08), residues: 3168 sheet: 1.03 (0.14), residues: 1164 loop : -0.42 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP 7 440 HIS 0.006 0.001 HIS 4 354 PHE 0.024 0.002 PHE U 318 TYR 0.019 0.003 TYR 4 478 ARG 0.006 0.001 ARG 1 341 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1176 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1090 time to evaluate : 8.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LYS cc_start: 0.8212 (mttp) cc_final: 0.7908 (mttt) REVERT: L 6 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7588 (ttt-90) REVERT: O 185 MET cc_start: 0.8501 (mmm) cc_final: 0.8221 (mmm) REVERT: Y 240 MET cc_start: 0.8411 (tpp) cc_final: 0.8100 (tpp) REVERT: 4 185 MET cc_start: 0.8447 (mmm) cc_final: 0.8154 (mmm) REVERT: 4 550 VAL cc_start: 0.8552 (p) cc_final: 0.8253 (t) REVERT: 7 380 MET cc_start: 0.7526 (mmp) cc_final: 0.7310 (mmm) REVERT: U 550 VAL cc_start: 0.8507 (p) cc_final: 0.8283 (t) outliers start: 86 outliers final: 35 residues processed: 1133 average time/residue: 3.9704 time to fit residues: 5889.1340 Evaluate side-chains 1105 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1069 time to evaluate : 8.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 243 GLU Chi-restraints excluded: chain N residue 59 LYS Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 319 ASP Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 0 residue 162 SER Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 82 LEU Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 3 residue 59 LYS Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 5.9990 chunk 520 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 682 optimal weight: 6.9990 chunk 378 optimal weight: 4.9990 chunk 781 optimal weight: 4.9990 chunk 633 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 467 optimal weight: 5.9990 chunk 822 optimal weight: 6.9990 chunk 231 optimal weight: 4.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN B 52 ASN C 521 ASN C 538 ASN F 312 ASN F 528 HIS I 203 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN R 203 ASN R 528 HIS T 34 ASN V 538 ASN Y 203 ASN 0 34 ASN 1 528 HIS 3 34 ASN 7 528 HIS 9 34 ASN U 203 ASN U 538 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 74892 Z= 0.364 Angle : 0.785 7.734 101616 Z= 0.426 Chirality : 0.051 0.239 11436 Planarity : 0.006 0.056 13488 Dihedral : 6.394 54.790 10568 Min Nonbonded Distance : 1.651 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 1.94 % Allowed : 8.74 % Favored : 89.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.42 (0.08), residues: 9780 helix: -0.28 (0.08), residues: 3144 sheet: 0.97 (0.14), residues: 1164 loop : -0.48 (0.08), residues: 5472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 7 440 HIS 0.008 0.002 HIS L 354 PHE 0.025 0.003 PHE U 482 TYR 0.022 0.003 TYR 4 478 ARG 0.012 0.001 ARG U 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1069 time to evaluate : 8.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 12 MET cc_start: 0.7452 (mtm) cc_final: 0.7235 (ttp) REVERT: K 53 LYS cc_start: 0.8220 (mttp) cc_final: 0.7916 (mttt) REVERT: Y 240 MET cc_start: 0.8443 (tpp) cc_final: 0.8099 (tpp) REVERT: 1 319 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7283 (t0) REVERT: 4 550 VAL cc_start: 0.8568 (p) cc_final: 0.8251 (t) REVERT: 6 144 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.6648 (mt-10) REVERT: 7 380 MET cc_start: 0.7574 (mmp) cc_final: 0.7301 (mmm) outliers start: 81 outliers final: 44 residues processed: 1112 average time/residue: 3.8892 time to fit residues: 5626.0195 Evaluate side-chains 1112 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1066 time to evaluate : 8.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 243 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain N residue 110 GLU Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain O residue 430 GLU Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain T residue 48 THR Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 430 GLU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 0 residue 162 SER Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 319 ASP Chi-restraints excluded: chain 1 residue 430 GLU Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 3 residue 59 LYS Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 6 residue 144 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 82 LEU Chi-restraints excluded: chain 7 residue 203 ASN Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 3.9990 chunk 825 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 538 optimal weight: 3.9990 chunk 226 optimal weight: 5.9990 chunk 917 optimal weight: 5.9990 chunk 761 optimal weight: 7.9990 chunk 424 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 303 optimal weight: 4.9990 chunk 481 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN F 528 HIS F 538 ASN I 203 ASN I 521 ASN I 538 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 74892 Z= 0.339 Angle : 0.762 7.795 101616 Z= 0.413 Chirality : 0.050 0.233 11436 Planarity : 0.006 0.051 13488 Dihedral : 6.355 56.208 10568 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.94 % Favored : 95.93 % Rotamer: Outliers : 1.97 % Allowed : 8.66 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.38 (0.08), residues: 9780 helix: -0.25 (0.08), residues: 3144 sheet: 0.98 (0.14), residues: 1164 loop : -0.46 (0.08), residues: 5472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP F 440 HIS 0.007 0.002 HIS V 128 PHE 0.024 0.003 PHE U 482 TYR 0.022 0.003 TYR 5 14 ARG 0.010 0.001 ARG U 523 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1164 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 1081 time to evaluate : 8.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 53 LYS cc_start: 0.8222 (mttp) cc_final: 0.7880 (mttt) REVERT: O 185 MET cc_start: 0.8513 (mmm) cc_final: 0.8214 (mmm) REVERT: Y 240 MET cc_start: 0.8437 (tpp) cc_final: 0.8093 (tpp) REVERT: 1 319 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7288 (t0) REVERT: 2 59 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: 4 185 MET cc_start: 0.8435 (mmm) cc_final: 0.8145 (mmm) REVERT: 4 550 VAL cc_start: 0.8581 (p) cc_final: 0.8249 (t) REVERT: 6 144 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.6683 (mt-10) REVERT: 7 380 MET cc_start: 0.7579 (mmp) cc_final: 0.7303 (mmm) outliers start: 83 outliers final: 45 residues processed: 1125 average time/residue: 4.1007 time to fit residues: 6115.5554 Evaluate side-chains 1129 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1081 time to evaluate : 8.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 430 GLU Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 243 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain O residue 430 GLU Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 430 GLU Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 430 GLU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain Y residue 8 GLU Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 0 residue 162 SER Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 319 ASP Chi-restraints excluded: chain 1 residue 430 GLU Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 2 residue 59 GLU Chi-restraints excluded: chain 3 residue 59 LYS Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 6 residue 144 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 82 LEU Chi-restraints excluded: chain 7 residue 203 ASN Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 522 optimal weight: 6.9990 chunk 669 optimal weight: 4.9990 chunk 518 optimal weight: 5.9990 chunk 772 optimal weight: 3.9990 chunk 512 optimal weight: 3.9990 chunk 913 optimal weight: 6.9990 chunk 571 optimal weight: 3.9990 chunk 557 optimal weight: 7.9990 chunk 421 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN E 34 ASN F 528 HIS I 203 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 521 ASN R 528 HIS T 34 ASN V 538 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 521 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 74892 Z= 0.303 Angle : 0.736 7.546 101616 Z= 0.398 Chirality : 0.049 0.222 11436 Planarity : 0.006 0.046 13488 Dihedral : 6.304 57.083 10568 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.91 % Favored : 95.97 % Rotamer: Outliers : 1.83 % Allowed : 9.01 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.30 (0.08), residues: 9780 helix: -0.16 (0.08), residues: 3156 sheet: 1.01 (0.14), residues: 1164 loop : -0.42 (0.08), residues: 5460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP 7 440 HIS 0.006 0.002 HIS Y 277 PHE 0.023 0.002 PHE U 482 TYR 0.021 0.003 TYR Z 14 ARG 0.008 0.001 ARG U 523 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1162 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1090 time to evaluate : 8.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 339 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5434 (pm20) REVERT: K 53 LYS cc_start: 0.8221 (mttp) cc_final: 0.7881 (mttt) REVERT: O 185 MET cc_start: 0.8510 (mmm) cc_final: 0.8230 (mmm) REVERT: Y 240 MET cc_start: 0.8427 (tpp) cc_final: 0.8077 (tpp) REVERT: 2 59 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6772 (tm-30) REVERT: 4 185 MET cc_start: 0.8485 (mmm) cc_final: 0.8169 (mmm) REVERT: 4 339 GLU cc_start: 0.6276 (OUTLIER) cc_final: 0.5315 (pm20) REVERT: 6 144 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.6665 (mt-10) REVERT: 7 380 MET cc_start: 0.7566 (mmp) cc_final: 0.7286 (mmm) REVERT: U 339 GLU cc_start: 0.6320 (OUTLIER) cc_final: 0.5314 (pm20) outliers start: 72 outliers final: 42 residues processed: 1128 average time/residue: 3.8617 time to fit residues: 5672.5118 Evaluate side-chains 1119 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1072 time to evaluate : 8.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 339 GLU Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 4 ILE Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 243 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 319 ASP Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 430 GLU Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 0 residue 162 SER Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 82 LEU Chi-restraints excluded: chain 1 residue 430 GLU Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 2 residue 59 GLU Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 339 GLU Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 6 residue 144 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 203 ASN Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Chi-restraints excluded: chain U residue 339 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 5.9990 chunk 364 optimal weight: 4.9990 chunk 545 optimal weight: 1.9990 chunk 275 optimal weight: 3.9990 chunk 179 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 580 optimal weight: 7.9990 chunk 622 optimal weight: 0.3980 chunk 451 optimal weight: 0.9990 chunk 85 optimal weight: 7.9990 chunk 718 optimal weight: 8.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN E 34 ASN F 528 HIS H 34 ASN I 203 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 521 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 74892 Z= 0.211 Angle : 0.662 7.465 101616 Z= 0.354 Chirality : 0.047 0.191 11436 Planarity : 0.005 0.042 13488 Dihedral : 6.097 57.400 10568 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.29 % Favored : 96.58 % Rotamer: Outliers : 1.69 % Allowed : 9.32 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.08 (0.08), residues: 9780 helix: 0.12 (0.08), residues: 3168 sheet: 1.08 (0.14), residues: 1164 loop : -0.34 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 440 HIS 0.005 0.001 HIS U 236 PHE 0.021 0.002 PHE U 318 TYR 0.017 0.002 TYR U 478 ARG 0.007 0.001 ARG M 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1110 time to evaluate : 8.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 54 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: K 53 LYS cc_start: 0.8213 (mttp) cc_final: 0.7868 (mttt) REVERT: L 6 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7657 (ttt-90) REVERT: O 185 MET cc_start: 0.8492 (mmm) cc_final: 0.8263 (mmm) REVERT: Y 240 MET cc_start: 0.8360 (tpp) cc_final: 0.8028 (tpp) REVERT: 2 59 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6785 (tm-30) REVERT: 4 185 MET cc_start: 0.8434 (mmm) cc_final: 0.8089 (mmm) REVERT: 4 550 VAL cc_start: 0.8551 (p) cc_final: 0.8232 (t) REVERT: 7 380 MET cc_start: 0.7526 (mmp) cc_final: 0.7300 (mmm) outliers start: 61 outliers final: 39 residues processed: 1150 average time/residue: 4.0067 time to fit residues: 6037.4387 Evaluate side-chains 1131 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 1089 time to evaluate : 8.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 243 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 2 residue 59 GLU Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 5 residue 41 VAL Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 82 LEU Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 3.9990 chunk 875 optimal weight: 0.7980 chunk 798 optimal weight: 8.9990 chunk 851 optimal weight: 4.9990 chunk 512 optimal weight: 4.9990 chunk 370 optimal weight: 10.0000 chunk 668 optimal weight: 3.9990 chunk 261 optimal weight: 0.7980 chunk 769 optimal weight: 9.9990 chunk 805 optimal weight: 5.9990 chunk 848 optimal weight: 7.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN E 34 ASN F 528 HIS H 34 ASN I 203 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 521 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 521 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 74892 Z= 0.244 Angle : 0.686 7.838 101616 Z= 0.368 Chirality : 0.047 0.197 11436 Planarity : 0.005 0.041 13488 Dihedral : 6.124 58.041 10568 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.78 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 9.47 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.08 (0.08), residues: 9780 helix: 0.12 (0.08), residues: 3168 sheet: 1.05 (0.14), residues: 1164 loop : -0.33 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP 7 440 HIS 0.005 0.001 HIS Y 277 PHE 0.020 0.002 PHE U 482 TYR 0.017 0.002 TYR 4 478 ARG 0.006 0.001 ARG M 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1085 time to evaluate : 8.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 54 GLU cc_start: 0.6830 (OUTLIER) cc_final: 0.6557 (mp0) REVERT: I 339 GLU cc_start: 0.6303 (OUTLIER) cc_final: 0.5373 (pm20) REVERT: K 53 LYS cc_start: 0.8215 (mttp) cc_final: 0.7870 (mttt) REVERT: L 6 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7621 (ttt-90) REVERT: O 185 MET cc_start: 0.8502 (mmm) cc_final: 0.8239 (mmm) REVERT: Y 240 MET cc_start: 0.8397 (tpp) cc_final: 0.8049 (tpp) REVERT: 2 59 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6814 (tm-30) REVERT: 3 109 ASP cc_start: 0.6520 (OUTLIER) cc_final: 0.6265 (t0) REVERT: 4 185 MET cc_start: 0.8455 (mmm) cc_final: 0.8114 (mmm) REVERT: 4 550 VAL cc_start: 0.8534 (p) cc_final: 0.8206 (t) REVERT: 7 380 MET cc_start: 0.7527 (mmp) cc_final: 0.7296 (mmm) outliers start: 61 outliers final: 41 residues processed: 1126 average time/residue: 3.8305 time to fit residues: 5651.3783 Evaluate side-chains 1127 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1081 time to evaluate : 8.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 203 ASN Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 339 GLU Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 6 ARG Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 243 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain R residue 203 ASN Chi-restraints excluded: chain R residue 319 ASP Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 430 GLU Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 2 residue 59 GLU Chi-restraints excluded: chain 3 residue 109 ASP Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 5 residue 41 VAL Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 6.9990 chunk 900 optimal weight: 8.9990 chunk 549 optimal weight: 0.8980 chunk 427 optimal weight: 0.0970 chunk 625 optimal weight: 3.9990 chunk 944 optimal weight: 0.9980 chunk 869 optimal weight: 5.9990 chunk 752 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 580 optimal weight: 7.9990 chunk 461 optimal weight: 4.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN E 34 ASN F 528 HIS H 34 ASN I 203 ASN I 312 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 312 ASN 7 521 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 74892 Z= 0.188 Angle : 0.633 7.369 101616 Z= 0.336 Chirality : 0.046 0.173 11436 Planarity : 0.004 0.042 13488 Dihedral : 5.953 58.462 10568 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.21 % Favored : 96.67 % Rotamer: Outliers : 1.57 % Allowed : 9.59 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: 0.12 (0.08), residues: 9780 helix: 0.36 (0.09), residues: 3168 sheet: 1.12 (0.14), residues: 1164 loop : -0.25 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 440 HIS 0.005 0.001 HIS L 236 PHE 0.026 0.001 PHE 1 318 TYR 0.015 0.002 TYR I 478 ARG 0.005 0.000 ARG M 26 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 1100 time to evaluate : 9.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 380 MET cc_start: 0.7486 (mmp) cc_final: 0.7208 (mmm) REVERT: G 54 GLU cc_start: 0.6786 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: I 339 GLU cc_start: 0.6233 (OUTLIER) cc_final: 0.5367 (pm20) REVERT: K 53 LYS cc_start: 0.8209 (mttp) cc_final: 0.7861 (mttt) REVERT: L 339 GLU cc_start: 0.6096 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: O 34 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7563 (ttpt) REVERT: O 550 VAL cc_start: 0.8435 (p) cc_final: 0.8225 (t) REVERT: W 12 MET cc_start: 0.7545 (mtp) cc_final: 0.7277 (ttp) REVERT: Y 240 MET cc_start: 0.8342 (tpp) cc_final: 0.8015 (tpp) REVERT: 2 59 GLU cc_start: 0.7152 (OUTLIER) cc_final: 0.6801 (tm-30) REVERT: 4 185 MET cc_start: 0.8405 (mmm) cc_final: 0.8092 (mmm) REVERT: 4 339 GLU cc_start: 0.6188 (OUTLIER) cc_final: 0.5118 (pm20) REVERT: 4 550 VAL cc_start: 0.8532 (p) cc_final: 0.8209 (t) REVERT: 7 380 MET cc_start: 0.7493 (mmp) cc_final: 0.7264 (mmm) outliers start: 52 outliers final: 38 residues processed: 1134 average time/residue: 3.8272 time to fit residues: 5672.3490 Evaluate side-chains 1138 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1094 time to evaluate : 8.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 37 ARG Chi-restraints excluded: chain C residue 454 LYS Chi-restraints excluded: chain F residue 37 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 41 VAL Chi-restraints excluded: chain G residue 54 GLU Chi-restraints excluded: chain I residue 37 ARG Chi-restraints excluded: chain I residue 339 GLU Chi-restraints excluded: chain I residue 454 LYS Chi-restraints excluded: chain K residue 48 THR Chi-restraints excluded: chain L residue 37 ARG Chi-restraints excluded: chain L residue 243 GLU Chi-restraints excluded: chain L residue 319 ASP Chi-restraints excluded: chain L residue 339 GLU Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain N residue 79 VAL Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 319 ASP Chi-restraints excluded: chain P residue 41 VAL Chi-restraints excluded: chain Q residue 79 VAL Chi-restraints excluded: chain Q residue 110 GLU Chi-restraints excluded: chain R residue 37 ARG Chi-restraints excluded: chain R residue 43 SER Chi-restraints excluded: chain R residue 82 LEU Chi-restraints excluded: chain V residue 37 ARG Chi-restraints excluded: chain V residue 319 ASP Chi-restraints excluded: chain V residue 454 LYS Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain Y residue 37 ARG Chi-restraints excluded: chain 1 residue 37 ARG Chi-restraints excluded: chain 1 residue 454 LYS Chi-restraints excluded: chain 2 residue 59 GLU Chi-restraints excluded: chain 4 residue 37 ARG Chi-restraints excluded: chain 4 residue 339 GLU Chi-restraints excluded: chain 4 residue 454 LYS Chi-restraints excluded: chain 5 residue 41 VAL Chi-restraints excluded: chain 6 residue 79 VAL Chi-restraints excluded: chain 6 residue 110 GLU Chi-restraints excluded: chain 7 residue 37 ARG Chi-restraints excluded: chain 7 residue 319 ASP Chi-restraints excluded: chain 8 residue 41 VAL Chi-restraints excluded: chain U residue 37 ARG Chi-restraints excluded: chain U residue 319 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 6.9990 chunk 801 optimal weight: 6.9990 chunk 230 optimal weight: 3.9990 chunk 693 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 208 optimal weight: 8.9990 chunk 753 optimal weight: 0.8980 chunk 315 optimal weight: 5.9990 chunk 773 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN E 34 ASN F 528 HIS H 34 ASN I 203 ASN I 312 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 521 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 312 ASN 7 521 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.150799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.131004 restraints weight = 429154.974| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.52 r_work: 0.3196 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3079 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 74892 Z= 0.263 Angle : 0.696 8.092 101616 Z= 0.373 Chirality : 0.048 0.196 11436 Planarity : 0.005 0.040 13488 Dihedral : 6.094 59.238 10568 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Rotamer: Outliers : 1.60 % Allowed : 9.60 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % 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: -0.04 (0.08), residues: 9780 helix: 0.16 (0.08), residues: 3168 sheet: 1.07 (0.14), residues: 1164 loop : -0.31 (0.08), residues: 5448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 7 440 HIS 0.005 0.002 HIS 1 354 PHE 0.025 0.002 PHE I 318 TYR 0.018 0.003 TYR 5 14 ARG 0.008 0.001 ARG A 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 73616.49 seconds wall clock time: 1258 minutes 14.58 seconds (75494.58 seconds total)