Starting phenix.real_space_refine on Sat Dec 9 01:02:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/12_2023/3j6f_5896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/12_2023/3j6f_5896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/12_2023/3j6f_5896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/12_2023/3j6f_5896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/12_2023/3j6f_5896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/12_2023/3j6f_5896_updated.pdb" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.528 sd= 1.926 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 P 45 5.49 5 Mg 9 5.21 5 S 414 5.16 5 C 38214 2.51 5 N 10395 2.21 5 O 11826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 396": "OD1" <-> "OD2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 433": "OE1" <-> "OE2" Residue "B ASP 31": "OD1" <-> "OD2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 414": "OD1" <-> "OD2" Residue "B TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 199": "OD1" <-> "OD2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 396": "OD1" <-> "OD2" Residue "C PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 433": "OE1" <-> "OE2" Residue "D ASP 31": "OD1" <-> "OD2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "D TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 414": "OD1" <-> "OD2" Residue "D TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 199": "OD1" <-> "OD2" Residue "E ASP 211": "OD1" <-> "OD2" Residue "E TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 396": "OD1" <-> "OD2" Residue "E PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 433": "OE1" <-> "OE2" Residue "F ASP 31": "OD1" <-> "OD2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 110": "OE1" <-> "OE2" Residue "F TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 414": "OD1" <-> "OD2" Residue "F TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 199": "OD1" <-> "OD2" Residue "G ASP 211": "OD1" <-> "OD2" Residue "G TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 396": "OD1" <-> "OD2" Residue "G PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 433": "OE1" <-> "OE2" Residue "H ASP 31": "OD1" <-> "OD2" Residue "H TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "H TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 414": "OD1" <-> "OD2" Residue "H TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I ASP 211": "OD1" <-> "OD2" Residue "I TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 396": "OD1" <-> "OD2" Residue "I PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 433": "OE1" <-> "OE2" Residue "J ASP 31": "OD1" <-> "OD2" Residue "J TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 110": "OE1" <-> "OE2" Residue "J TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 414": "OD1" <-> "OD2" Residue "J TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 199": "OD1" <-> "OD2" Residue "K ASP 211": "OD1" <-> "OD2" Residue "K TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 396": "OD1" <-> "OD2" Residue "K PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 433": "OE1" <-> "OE2" Residue "L ASP 31": "OD1" <-> "OD2" Residue "L TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 110": "OE1" <-> "OE2" Residue "L TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 414": "OD1" <-> "OD2" Residue "L TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 199": "OD1" <-> "OD2" Residue "M ASP 211": "OD1" <-> "OD2" Residue "M TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 396": "OD1" <-> "OD2" Residue "M PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 433": "OE1" <-> "OE2" Residue "N ASP 31": "OD1" <-> "OD2" Residue "N TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 110": "OE1" <-> "OE2" Residue "N TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 414": "OD1" <-> "OD2" Residue "N TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 199": "OD1" <-> "OD2" Residue "O ASP 211": "OD1" <-> "OD2" Residue "O TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 396": "OD1" <-> "OD2" Residue "O PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 433": "OE1" <-> "OE2" Residue "P ASP 31": "OD1" <-> "OD2" Residue "P TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 110": "OE1" <-> "OE2" Residue "P TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 414": "OD1" <-> "OD2" Residue "P TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 199": "OD1" <-> "OD2" Residue "Q ASP 211": "OD1" <-> "OD2" Residue "Q TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 396": "OD1" <-> "OD2" Residue "Q PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 433": "OE1" <-> "OE2" Residue "R ASP 31": "OD1" <-> "OD2" Residue "R TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 110": "OE1" <-> "OE2" Residue "R TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 395": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 414": "OD1" <-> "OD2" Residue "R TYR 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 60903 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "B" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "C" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "D" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "E" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "F" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "G" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "H" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "I" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "J" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "K" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "L" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "M" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "N" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "O" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "P" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "Q" Number of atoms: 3350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3350 Classifications: {'peptide': 428} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 407} Chain breaks: 1 Chain: "R" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3352 Classifications: {'peptide': 426} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 405} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "M" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 23.55, per 1000 atoms: 0.39 Number of scatterers: 60903 At special positions: 0 Unit cell: (170.52, 88.74, 290.58, 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) S 414 16.00 P 45 15.00 Mg 9 11.99 O 11826 8.00 N 10395 7.00 C 38214 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS B 241 " - pdb=" SG CYS B 356 " distance=2.02 Simple disulfide: pdb=" SG CYS D 241 " - pdb=" SG CYS D 356 " distance=2.02 Simple disulfide: pdb=" SG CYS F 241 " - pdb=" SG CYS F 356 " distance=2.02 Simple disulfide: pdb=" SG CYS H 241 " - pdb=" SG CYS H 356 " distance=2.02 Simple disulfide: pdb=" SG CYS J 241 " - pdb=" SG CYS J 356 " distance=2.02 Simple disulfide: pdb=" SG CYS L 241 " - pdb=" SG CYS L 356 " distance=2.02 Simple disulfide: pdb=" SG CYS N 241 " - pdb=" SG CYS N 356 " distance=2.02 Simple disulfide: pdb=" SG CYS P 241 " - pdb=" SG CYS P 356 " distance=2.02 Simple disulfide: pdb=" SG CYS R 241 " - pdb=" SG CYS R 356 " distance=2.02 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: 19.59 Conformation dependent library (CDL) restraints added in 8.7 seconds 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14202 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 324 helices and 54 sheets defined 46.3% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.04 Creating SS restraints... Processing helix chain 'A' and resid 10 through 28 Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 103 through 106 No H-bonds generated for 'chain 'A' and resid 103 through 106' Processing helix chain 'A' and resid 111 through 128 removed outlier: 5.007A pdb=" N ASP A 116 " --> pdb=" O LYS A 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.538A pdb=" N ARG A 156 " --> pdb=" O LEU A 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 224 through 238 removed outlier: 4.190A pdb=" N ARG A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 259 Processing helix chain 'A' and resid 278 through 281 No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 288 through 296 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 325 through 337 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.590A pdb=" N PHE A 395 " --> pdb=" O ASP A 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 397 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 400 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL A 409 " --> pdb=" O HIS A 406 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY A 410 " --> pdb=" O TRP A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 Processing helix chain 'B' and resid 10 through 28 removed outlier: 3.595A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 47 Processing helix chain 'B' and resid 49 through 51 No H-bonds generated for 'chain 'B' and resid 49 through 51' Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 106 No H-bonds generated for 'chain 'B' and resid 103 through 106' Processing helix chain 'B' and resid 110 through 128 removed outlier: 3.802A pdb=" N LEU B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP B 116 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 160 Processing helix chain 'B' and resid 183 through 197 removed outlier: 5.104A pdb=" N GLU B 196 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN B 197 " --> pdb=" O GLN B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 215 removed outlier: 3.614A pdb=" N PHE B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 243 removed outlier: 4.037A pdb=" N CYS B 241 " --> pdb=" O GLY B 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU B 242 " --> pdb=" O VAL B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 259 Processing helix chain 'B' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN B 282 " --> pdb=" O ARG B 278 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 278 through 283' Processing helix chain 'B' and resid 288 through 296 Processing helix chain 'B' and resid 298 through 300 No H-bonds generated for 'chain 'B' and resid 298 through 300' Processing helix chain 'B' and resid 325 through 338 Processing helix chain 'B' and resid 383 through 401 removed outlier: 3.708A pdb=" N GLU B 393 " --> pdb=" O ARG B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 Processing helix chain 'B' and resid 415 through 436 Processing helix chain 'C' and resid 10 through 28 Processing helix chain 'C' and resid 72 through 79 Processing helix chain 'C' and resid 82 through 84 No H-bonds generated for 'chain 'C' and resid 82 through 84' Processing helix chain 'C' and resid 103 through 106 No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 111 through 128 removed outlier: 5.007A pdb=" N ASP C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N LEU C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 160 removed outlier: 3.537A pdb=" N ARG C 156 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL C 159 " --> pdb=" O GLU C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 194 Processing helix chain 'C' and resid 206 through 215 Processing helix chain 'C' and resid 224 through 238 removed outlier: 4.190A pdb=" N ARG C 229 " --> pdb=" O THR C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 278 through 281 No H-bonds generated for 'chain 'C' and resid 278 through 281' Processing helix chain 'C' and resid 288 through 296 Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 325 through 337 Processing helix chain 'C' and resid 382 through 401 removed outlier: 3.590A pdb=" N PHE C 395 " --> pdb=" O ASP C 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 397 " --> pdb=" O LYS C 394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA C 400 " --> pdb=" O LEU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL C 409 " --> pdb=" O HIS C 406 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLY C 410 " --> pdb=" O TRP C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 436 Processing helix chain 'D' and resid 10 through 28 removed outlier: 3.595A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 22 " --> pdb=" O ALA D 18 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 47 Processing helix chain 'D' and resid 49 through 51 No H-bonds generated for 'chain 'D' and resid 49 through 51' Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 89 through 91 No H-bonds generated for 'chain 'D' and resid 89 through 91' Processing helix chain 'D' and resid 103 through 106 No H-bonds generated for 'chain 'D' and resid 103 through 106' Processing helix chain 'D' and resid 110 through 128 removed outlier: 3.801A pdb=" N LEU D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP D 116 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 160 Processing helix chain 'D' and resid 183 through 197 removed outlier: 5.104A pdb=" N GLU D 196 " --> pdb=" O HIS D 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN D 197 " --> pdb=" O GLN D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 215 removed outlier: 3.614A pdb=" N PHE D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 243 removed outlier: 4.037A pdb=" N CYS D 241 " --> pdb=" O GLY D 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU D 242 " --> pdb=" O VAL D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 259 Processing helix chain 'D' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR D 283 " --> pdb=" O GLY D 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 278 through 283' Processing helix chain 'D' and resid 288 through 296 Processing helix chain 'D' and resid 298 through 300 No H-bonds generated for 'chain 'D' and resid 298 through 300' Processing helix chain 'D' and resid 325 through 338 Processing helix chain 'D' and resid 383 through 401 removed outlier: 3.707A pdb=" N GLU D 393 " --> pdb=" O ARG D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 410 Processing helix chain 'D' and resid 415 through 436 Processing helix chain 'E' and resid 10 through 28 Processing helix chain 'E' and resid 72 through 79 Processing helix chain 'E' and resid 82 through 84 No H-bonds generated for 'chain 'E' and resid 82 through 84' Processing helix chain 'E' and resid 103 through 106 No H-bonds generated for 'chain 'E' and resid 103 through 106' Processing helix chain 'E' and resid 111 through 128 removed outlier: 5.007A pdb=" N ASP E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.538A pdb=" N ARG E 156 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 194 Processing helix chain 'E' and resid 206 through 215 Processing helix chain 'E' and resid 224 through 238 removed outlier: 4.190A pdb=" N ARG E 229 " --> pdb=" O THR E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 259 Processing helix chain 'E' and resid 278 through 281 No H-bonds generated for 'chain 'E' and resid 278 through 281' Processing helix chain 'E' and resid 288 through 296 Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 325 through 337 Processing helix chain 'E' and resid 382 through 401 removed outlier: 3.590A pdb=" N PHE E 395 " --> pdb=" O ASP E 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU E 397 " --> pdb=" O LYS E 394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA E 400 " --> pdb=" O LEU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL E 409 " --> pdb=" O HIS E 406 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N GLY E 410 " --> pdb=" O TRP E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 436 Processing helix chain 'F' and resid 10 through 28 removed outlier: 3.596A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU F 22 " --> pdb=" O ALA F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 47 Processing helix chain 'F' and resid 49 through 51 No H-bonds generated for 'chain 'F' and resid 49 through 51' Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 106 No H-bonds generated for 'chain 'F' and resid 103 through 106' Processing helix chain 'F' and resid 110 through 128 removed outlier: 3.801A pdb=" N LEU F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP F 116 " --> pdb=" O ALA F 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 160 Processing helix chain 'F' and resid 183 through 197 removed outlier: 5.105A pdb=" N GLU F 196 " --> pdb=" O HIS F 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN F 197 " --> pdb=" O GLN F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 215 removed outlier: 3.615A pdb=" N PHE F 214 " --> pdb=" O TYR F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 243 removed outlier: 4.037A pdb=" N CYS F 241 " --> pdb=" O GLY F 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU F 242 " --> pdb=" O VAL F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 252 through 259 Processing helix chain 'F' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN F 282 " --> pdb=" O ARG F 278 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 283' Processing helix chain 'F' and resid 288 through 296 Processing helix chain 'F' and resid 298 through 300 No H-bonds generated for 'chain 'F' and resid 298 through 300' Processing helix chain 'F' and resid 325 through 338 Processing helix chain 'F' and resid 383 through 401 removed outlier: 3.708A pdb=" N GLU F 393 " --> pdb=" O ARG F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 410 Processing helix chain 'F' and resid 415 through 436 Processing helix chain 'G' and resid 10 through 28 Processing helix chain 'G' and resid 72 through 79 Processing helix chain 'G' and resid 82 through 84 No H-bonds generated for 'chain 'G' and resid 82 through 84' Processing helix chain 'G' and resid 103 through 106 No H-bonds generated for 'chain 'G' and resid 103 through 106' Processing helix chain 'G' and resid 111 through 128 removed outlier: 5.006A pdb=" N ASP G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 160 removed outlier: 3.538A pdb=" N ARG G 156 " --> pdb=" O LEU G 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL G 159 " --> pdb=" O GLU G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 194 Processing helix chain 'G' and resid 206 through 215 Processing helix chain 'G' and resid 224 through 238 removed outlier: 4.190A pdb=" N ARG G 229 " --> pdb=" O THR G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 252 through 259 Processing helix chain 'G' and resid 278 through 281 No H-bonds generated for 'chain 'G' and resid 278 through 281' Processing helix chain 'G' and resid 288 through 296 Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 325 through 337 Processing helix chain 'G' and resid 382 through 401 removed outlier: 3.590A pdb=" N PHE G 395 " --> pdb=" O ASP G 392 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU G 397 " --> pdb=" O LYS G 394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA G 400 " --> pdb=" O LEU G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL G 409 " --> pdb=" O HIS G 406 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY G 410 " --> pdb=" O TRP G 407 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 436 Processing helix chain 'H' and resid 10 through 28 removed outlier: 3.596A pdb=" N LYS H 19 " --> pdb=" O GLN H 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 22 " --> pdb=" O ALA H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 47 Processing helix chain 'H' and resid 49 through 51 No H-bonds generated for 'chain 'H' and resid 49 through 51' Processing helix chain 'H' and resid 72 through 80 Processing helix chain 'H' and resid 89 through 91 No H-bonds generated for 'chain 'H' and resid 89 through 91' Processing helix chain 'H' and resid 103 through 106 No H-bonds generated for 'chain 'H' and resid 103 through 106' Processing helix chain 'H' and resid 110 through 128 removed outlier: 3.802A pdb=" N LEU H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER H 117 " --> pdb=" O GLU H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 160 Processing helix chain 'H' and resid 183 through 197 removed outlier: 5.104A pdb=" N GLU H 196 " --> pdb=" O HIS H 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN H 197 " --> pdb=" O GLN H 193 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 215 removed outlier: 3.614A pdb=" N PHE H 214 " --> pdb=" O TYR H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 243 removed outlier: 4.038A pdb=" N CYS H 241 " --> pdb=" O GLY H 237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU H 242 " --> pdb=" O VAL H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 252 through 259 Processing helix chain 'H' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN H 282 " --> pdb=" O ARG H 278 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR H 283 " --> pdb=" O GLY H 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 278 through 283' Processing helix chain 'H' and resid 288 through 296 Processing helix chain 'H' and resid 298 through 300 No H-bonds generated for 'chain 'H' and resid 298 through 300' Processing helix chain 'H' and resid 325 through 338 Processing helix chain 'H' and resid 383 through 401 removed outlier: 3.708A pdb=" N GLU H 393 " --> pdb=" O ARG H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 405 through 410 Processing helix chain 'H' and resid 415 through 436 Processing helix chain 'I' and resid 10 through 28 Processing helix chain 'I' and resid 72 through 79 Processing helix chain 'I' and resid 82 through 84 No H-bonds generated for 'chain 'I' and resid 82 through 84' Processing helix chain 'I' and resid 103 through 106 No H-bonds generated for 'chain 'I' and resid 103 through 106' Processing helix chain 'I' and resid 111 through 128 removed outlier: 5.006A pdb=" N ASP I 116 " --> pdb=" O LYS I 112 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU I 117 " --> pdb=" O GLU I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 160 removed outlier: 3.538A pdb=" N ARG I 156 " --> pdb=" O LEU I 152 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL I 159 " --> pdb=" O GLU I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 194 Processing helix chain 'I' and resid 206 through 215 Processing helix chain 'I' and resid 224 through 238 removed outlier: 4.190A pdb=" N ARG I 229 " --> pdb=" O THR I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 252 through 259 Processing helix chain 'I' and resid 278 through 281 No H-bonds generated for 'chain 'I' and resid 278 through 281' Processing helix chain 'I' and resid 288 through 296 Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 325 through 337 Processing helix chain 'I' and resid 382 through 401 removed outlier: 3.590A pdb=" N PHE I 395 " --> pdb=" O ASP I 392 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU I 397 " --> pdb=" O LYS I 394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA I 400 " --> pdb=" O LEU I 397 " (cutoff:3.500A) Processing helix chain 'I' and resid 405 through 411 removed outlier: 3.684A pdb=" N VAL I 409 " --> pdb=" O HIS I 406 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY I 410 " --> pdb=" O TRP I 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 415 through 436 Processing helix chain 'J' and resid 10 through 28 removed outlier: 3.596A pdb=" N LYS J 19 " --> pdb=" O GLN J 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU J 22 " --> pdb=" O ALA J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 47 Processing helix chain 'J' and resid 49 through 51 No H-bonds generated for 'chain 'J' and resid 49 through 51' Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 89 through 91 No H-bonds generated for 'chain 'J' and resid 89 through 91' Processing helix chain 'J' and resid 103 through 106 No H-bonds generated for 'chain 'J' and resid 103 through 106' Processing helix chain 'J' and resid 110 through 128 removed outlier: 3.802A pdb=" N LEU J 114 " --> pdb=" O GLU J 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP J 116 " --> pdb=" O ALA J 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER J 117 " --> pdb=" O GLU J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 148 through 160 Processing helix chain 'J' and resid 183 through 197 removed outlier: 5.104A pdb=" N GLU J 196 " --> pdb=" O HIS J 192 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN J 197 " --> pdb=" O GLN J 193 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 215 removed outlier: 3.615A pdb=" N PHE J 214 " --> pdb=" O TYR J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 224 through 243 removed outlier: 4.037A pdb=" N CYS J 241 " --> pdb=" O GLY J 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU J 242 " --> pdb=" O VAL J 238 " (cutoff:3.500A) Processing helix chain 'J' and resid 252 through 259 Processing helix chain 'J' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN J 282 " --> pdb=" O ARG J 278 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR J 283 " --> pdb=" O GLY J 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 278 through 283' Processing helix chain 'J' and resid 288 through 296 Processing helix chain 'J' and resid 298 through 300 No H-bonds generated for 'chain 'J' and resid 298 through 300' Processing helix chain 'J' and resid 325 through 338 Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.708A pdb=" N GLU J 393 " --> pdb=" O ARG J 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 405 through 410 Processing helix chain 'J' and resid 415 through 436 Processing helix chain 'K' and resid 10 through 28 Processing helix chain 'K' and resid 72 through 79 Processing helix chain 'K' and resid 82 through 84 No H-bonds generated for 'chain 'K' and resid 82 through 84' Processing helix chain 'K' and resid 103 through 106 No H-bonds generated for 'chain 'K' and resid 103 through 106' Processing helix chain 'K' and resid 111 through 128 removed outlier: 5.006A pdb=" N ASP K 116 " --> pdb=" O LYS K 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 160 removed outlier: 3.538A pdb=" N ARG K 156 " --> pdb=" O LEU K 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL K 159 " --> pdb=" O GLU K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 194 Processing helix chain 'K' and resid 206 through 215 Processing helix chain 'K' and resid 224 through 238 removed outlier: 4.191A pdb=" N ARG K 229 " --> pdb=" O THR K 225 " (cutoff:3.500A) Processing helix chain 'K' and resid 252 through 259 Processing helix chain 'K' and resid 278 through 281 No H-bonds generated for 'chain 'K' and resid 278 through 281' Processing helix chain 'K' and resid 288 through 296 Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 325 through 337 Processing helix chain 'K' and resid 382 through 401 removed outlier: 3.590A pdb=" N PHE K 395 " --> pdb=" O ASP K 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 397 " --> pdb=" O LYS K 394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA K 400 " --> pdb=" O LEU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL K 409 " --> pdb=" O HIS K 406 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY K 410 " --> pdb=" O TRP K 407 " (cutoff:3.500A) Processing helix chain 'K' and resid 415 through 436 Processing helix chain 'L' and resid 10 through 28 removed outlier: 3.595A pdb=" N LYS L 19 " --> pdb=" O GLN L 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU L 22 " --> pdb=" O ALA L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 41 through 47 Processing helix chain 'L' and resid 49 through 51 No H-bonds generated for 'chain 'L' and resid 49 through 51' Processing helix chain 'L' and resid 72 through 80 Processing helix chain 'L' and resid 89 through 91 No H-bonds generated for 'chain 'L' and resid 89 through 91' Processing helix chain 'L' and resid 103 through 106 No H-bonds generated for 'chain 'L' and resid 103 through 106' Processing helix chain 'L' and resid 110 through 128 removed outlier: 3.803A pdb=" N LEU L 114 " --> pdb=" O GLU L 110 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP L 116 " --> pdb=" O ALA L 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER L 117 " --> pdb=" O GLU L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 148 through 160 Processing helix chain 'L' and resid 183 through 197 removed outlier: 5.104A pdb=" N GLU L 196 " --> pdb=" O HIS L 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN L 197 " --> pdb=" O GLN L 193 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 215 removed outlier: 3.615A pdb=" N PHE L 214 " --> pdb=" O TYR L 210 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 243 removed outlier: 4.038A pdb=" N CYS L 241 " --> pdb=" O GLY L 237 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LEU L 242 " --> pdb=" O VAL L 238 " (cutoff:3.500A) Processing helix chain 'L' and resid 252 through 259 Processing helix chain 'L' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN L 282 " --> pdb=" O ARG L 278 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR L 283 " --> pdb=" O GLY L 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 278 through 283' Processing helix chain 'L' and resid 288 through 296 Processing helix chain 'L' and resid 298 through 300 No H-bonds generated for 'chain 'L' and resid 298 through 300' Processing helix chain 'L' and resid 325 through 338 Processing helix chain 'L' and resid 383 through 401 removed outlier: 3.708A pdb=" N GLU L 393 " --> pdb=" O ARG L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 410 Processing helix chain 'L' and resid 415 through 436 Processing helix chain 'M' and resid 10 through 28 Processing helix chain 'M' and resid 72 through 79 Processing helix chain 'M' and resid 82 through 84 No H-bonds generated for 'chain 'M' and resid 82 through 84' Processing helix chain 'M' and resid 103 through 106 No H-bonds generated for 'chain 'M' and resid 103 through 106' Processing helix chain 'M' and resid 111 through 128 removed outlier: 5.007A pdb=" N ASP M 116 " --> pdb=" O LYS M 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU M 117 " --> pdb=" O GLU M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 148 through 160 removed outlier: 3.538A pdb=" N ARG M 156 " --> pdb=" O LEU M 152 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL M 159 " --> pdb=" O GLU M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 194 Processing helix chain 'M' and resid 206 through 215 Processing helix chain 'M' and resid 224 through 238 removed outlier: 4.191A pdb=" N ARG M 229 " --> pdb=" O THR M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 259 Processing helix chain 'M' and resid 278 through 281 No H-bonds generated for 'chain 'M' and resid 278 through 281' Processing helix chain 'M' and resid 288 through 296 Processing helix chain 'M' and resid 298 through 300 No H-bonds generated for 'chain 'M' and resid 298 through 300' Processing helix chain 'M' and resid 325 through 337 Processing helix chain 'M' and resid 382 through 401 removed outlier: 3.590A pdb=" N PHE M 395 " --> pdb=" O ASP M 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU M 397 " --> pdb=" O LYS M 394 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA M 400 " --> pdb=" O LEU M 397 " (cutoff:3.500A) Processing helix chain 'M' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL M 409 " --> pdb=" O HIS M 406 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY M 410 " --> pdb=" O TRP M 407 " (cutoff:3.500A) Processing helix chain 'M' and resid 415 through 436 Processing helix chain 'N' and resid 10 through 28 removed outlier: 3.595A pdb=" N LYS N 19 " --> pdb=" O GLN N 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU N 22 " --> pdb=" O ALA N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 41 through 47 Processing helix chain 'N' and resid 49 through 51 No H-bonds generated for 'chain 'N' and resid 49 through 51' Processing helix chain 'N' and resid 72 through 80 Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'N' and resid 103 through 106 No H-bonds generated for 'chain 'N' and resid 103 through 106' Processing helix chain 'N' and resid 110 through 128 removed outlier: 3.802A pdb=" N LEU N 114 " --> pdb=" O GLU N 110 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP N 116 " --> pdb=" O ALA N 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER N 117 " --> pdb=" O GLU N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 160 Processing helix chain 'N' and resid 183 through 197 removed outlier: 5.105A pdb=" N GLU N 196 " --> pdb=" O HIS N 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN N 197 " --> pdb=" O GLN N 193 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 215 removed outlier: 3.615A pdb=" N PHE N 214 " --> pdb=" O TYR N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 224 through 243 removed outlier: 4.037A pdb=" N CYS N 241 " --> pdb=" O GLY N 237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU N 242 " --> pdb=" O VAL N 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 252 through 259 Processing helix chain 'N' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN N 282 " --> pdb=" O ARG N 278 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR N 283 " --> pdb=" O GLY N 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 278 through 283' Processing helix chain 'N' and resid 288 through 296 Processing helix chain 'N' and resid 298 through 300 No H-bonds generated for 'chain 'N' and resid 298 through 300' Processing helix chain 'N' and resid 325 through 338 Processing helix chain 'N' and resid 383 through 401 removed outlier: 3.707A pdb=" N GLU N 393 " --> pdb=" O ARG N 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 405 through 410 Processing helix chain 'N' and resid 415 through 436 Processing helix chain 'O' and resid 10 through 28 Processing helix chain 'O' and resid 72 through 79 Processing helix chain 'O' and resid 82 through 84 No H-bonds generated for 'chain 'O' and resid 82 through 84' Processing helix chain 'O' and resid 103 through 106 No H-bonds generated for 'chain 'O' and resid 103 through 106' Processing helix chain 'O' and resid 111 through 128 removed outlier: 5.006A pdb=" N ASP O 116 " --> pdb=" O LYS O 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU O 117 " --> pdb=" O GLU O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 160 removed outlier: 3.537A pdb=" N ARG O 156 " --> pdb=" O LEU O 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL O 159 " --> pdb=" O GLU O 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 194 Processing helix chain 'O' and resid 206 through 215 Processing helix chain 'O' and resid 224 through 238 removed outlier: 4.191A pdb=" N ARG O 229 " --> pdb=" O THR O 225 " (cutoff:3.500A) Processing helix chain 'O' and resid 252 through 259 Processing helix chain 'O' and resid 278 through 281 No H-bonds generated for 'chain 'O' and resid 278 through 281' Processing helix chain 'O' and resid 288 through 296 Processing helix chain 'O' and resid 298 through 300 No H-bonds generated for 'chain 'O' and resid 298 through 300' Processing helix chain 'O' and resid 325 through 337 Processing helix chain 'O' and resid 382 through 401 removed outlier: 3.589A pdb=" N PHE O 395 " --> pdb=" O ASP O 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU O 397 " --> pdb=" O LYS O 394 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA O 400 " --> pdb=" O LEU O 397 " (cutoff:3.500A) Processing helix chain 'O' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL O 409 " --> pdb=" O HIS O 406 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY O 410 " --> pdb=" O TRP O 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 415 through 436 Processing helix chain 'P' and resid 10 through 28 removed outlier: 3.595A pdb=" N LYS P 19 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU P 22 " --> pdb=" O ALA P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 41 through 47 Processing helix chain 'P' and resid 49 through 51 No H-bonds generated for 'chain 'P' and resid 49 through 51' Processing helix chain 'P' and resid 72 through 80 Processing helix chain 'P' and resid 89 through 91 No H-bonds generated for 'chain 'P' and resid 89 through 91' Processing helix chain 'P' and resid 103 through 106 No H-bonds generated for 'chain 'P' and resid 103 through 106' Processing helix chain 'P' and resid 110 through 128 removed outlier: 3.803A pdb=" N LEU P 114 " --> pdb=" O GLU P 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP P 116 " --> pdb=" O ALA P 112 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 148 through 160 Processing helix chain 'P' and resid 183 through 197 removed outlier: 5.104A pdb=" N GLU P 196 " --> pdb=" O HIS P 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN P 197 " --> pdb=" O GLN P 193 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 215 removed outlier: 3.615A pdb=" N PHE P 214 " --> pdb=" O TYR P 210 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 243 removed outlier: 4.038A pdb=" N CYS P 241 " --> pdb=" O GLY P 237 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LEU P 242 " --> pdb=" O VAL P 238 " (cutoff:3.500A) Processing helix chain 'P' and resid 252 through 259 Processing helix chain 'P' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN P 282 " --> pdb=" O ARG P 278 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR P 283 " --> pdb=" O GLY P 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 278 through 283' Processing helix chain 'P' and resid 288 through 296 Processing helix chain 'P' and resid 298 through 300 No H-bonds generated for 'chain 'P' and resid 298 through 300' Processing helix chain 'P' and resid 325 through 338 Processing helix chain 'P' and resid 383 through 401 removed outlier: 3.708A pdb=" N GLU P 393 " --> pdb=" O ARG P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 405 through 410 Processing helix chain 'P' and resid 415 through 436 Processing helix chain 'Q' and resid 10 through 28 Processing helix chain 'Q' and resid 72 through 79 Processing helix chain 'Q' and resid 82 through 84 No H-bonds generated for 'chain 'Q' and resid 82 through 84' Processing helix chain 'Q' and resid 103 through 106 No H-bonds generated for 'chain 'Q' and resid 103 through 106' Processing helix chain 'Q' and resid 111 through 128 removed outlier: 5.006A pdb=" N ASP Q 116 " --> pdb=" O LYS Q 112 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N LEU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 148 through 160 removed outlier: 3.538A pdb=" N ARG Q 156 " --> pdb=" O LEU Q 152 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL Q 159 " --> pdb=" O GLU Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 194 Processing helix chain 'Q' and resid 206 through 215 Processing helix chain 'Q' and resid 224 through 238 removed outlier: 4.190A pdb=" N ARG Q 229 " --> pdb=" O THR Q 225 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 259 Processing helix chain 'Q' and resid 278 through 281 No H-bonds generated for 'chain 'Q' and resid 278 through 281' Processing helix chain 'Q' and resid 288 through 296 Processing helix chain 'Q' and resid 298 through 300 No H-bonds generated for 'chain 'Q' and resid 298 through 300' Processing helix chain 'Q' and resid 325 through 337 Processing helix chain 'Q' and resid 382 through 401 removed outlier: 3.589A pdb=" N PHE Q 395 " --> pdb=" O ASP Q 392 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Q 397 " --> pdb=" O LYS Q 394 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA Q 400 " --> pdb=" O LEU Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 405 through 411 removed outlier: 3.683A pdb=" N VAL Q 409 " --> pdb=" O HIS Q 406 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N GLY Q 410 " --> pdb=" O TRP Q 407 " (cutoff:3.500A) Processing helix chain 'Q' and resid 415 through 436 Processing helix chain 'R' and resid 10 through 28 removed outlier: 3.596A pdb=" N LYS R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU R 22 " --> pdb=" O ALA R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 47 Processing helix chain 'R' and resid 49 through 51 No H-bonds generated for 'chain 'R' and resid 49 through 51' Processing helix chain 'R' and resid 72 through 80 Processing helix chain 'R' and resid 89 through 91 No H-bonds generated for 'chain 'R' and resid 89 through 91' Processing helix chain 'R' and resid 103 through 106 No H-bonds generated for 'chain 'R' and resid 103 through 106' Processing helix chain 'R' and resid 110 through 128 removed outlier: 3.802A pdb=" N LEU R 114 " --> pdb=" O GLU R 110 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP R 116 " --> pdb=" O ALA R 112 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER R 117 " --> pdb=" O GLU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 160 Processing helix chain 'R' and resid 183 through 197 removed outlier: 5.105A pdb=" N GLU R 196 " --> pdb=" O HIS R 192 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN R 197 " --> pdb=" O GLN R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 215 removed outlier: 3.615A pdb=" N PHE R 214 " --> pdb=" O TYR R 210 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 243 removed outlier: 4.037A pdb=" N CYS R 241 " --> pdb=" O GLY R 237 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU R 242 " --> pdb=" O VAL R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 259 Processing helix chain 'R' and resid 278 through 283 removed outlier: 3.837A pdb=" N GLN R 282 " --> pdb=" O ARG R 278 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TYR R 283 " --> pdb=" O GLY R 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 278 through 283' Processing helix chain 'R' and resid 288 through 296 Processing helix chain 'R' and resid 298 through 300 No H-bonds generated for 'chain 'R' and resid 298 through 300' Processing helix chain 'R' and resid 325 through 338 Processing helix chain 'R' and resid 383 through 401 removed outlier: 3.708A pdb=" N GLU R 393 " --> pdb=" O ARG R 390 " (cutoff:3.500A) Processing helix chain 'R' and resid 405 through 410 Processing helix chain 'R' and resid 415 through 436 Processing sheet with id= A, first strand: chain 'A' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE A 93 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE A 67 " --> pdb=" O ILE A 93 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL A 66 " --> pdb=" O CYS A 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 6 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL A 68 " --> pdb=" O SER A 6 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS A 8 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE A 5 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A 135 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A 7 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 137 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL A 9 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N HIS A 139 " --> pdb=" O VAL A 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER A 165 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL A 137 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU A 167 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS A 139 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE A 169 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS A 200 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER A 170 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE A 202 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR A 172 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL A 204 " --> pdb=" O TYR A 172 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 53 through 55 Processing sheet with id= C, first strand: chain 'A' and resid 269 through 273 removed outlier: 5.878A pdb=" N LYS A 352 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR A 319 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY A 354 " --> pdb=" O TYR A 319 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY A 321 " --> pdb=" O GLY A 354 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL B 93 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU B 67 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE B 66 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS B 6 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL B 68 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN B 8 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL B 5 " --> pdb=" O GLN B 133 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE B 135 " --> pdb=" O VAL B 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE B 7 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU B 137 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA B 9 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS B 139 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE B 165 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU B 137 " --> pdb=" O ILE B 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN B 167 " --> pdb=" O LEU B 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS B 139 " --> pdb=" O ASN B 167 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE B 169 " --> pdb=" O HIS B 139 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU B 200 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER B 170 " --> pdb=" O GLU B 200 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR B 202 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 53 through 56 Processing sheet with id= F, first strand: chain 'B' and resid 269 through 273 Processing sheet with id= G, first strand: chain 'C' and resid 92 through 94 removed outlier: 7.865A pdb=" N ILE C 93 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE C 67 " --> pdb=" O ILE C 93 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL C 66 " --> pdb=" O CYS C 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER C 6 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL C 68 " --> pdb=" O SER C 6 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS C 8 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE C 5 " --> pdb=" O GLN C 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE C 135 " --> pdb=" O ILE C 5 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 7 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL C 137 " --> pdb=" O ILE C 7 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL C 9 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N HIS C 139 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER C 165 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL C 137 " --> pdb=" O SER C 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU C 167 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS C 139 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE C 169 " --> pdb=" O HIS C 139 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS C 200 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER C 170 " --> pdb=" O CYS C 200 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE C 202 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR C 172 " --> pdb=" O PHE C 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL C 204 " --> pdb=" O TYR C 172 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 53 through 55 Processing sheet with id= I, first strand: chain 'C' and resid 269 through 273 removed outlier: 5.878A pdb=" N LYS C 352 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR C 319 " --> pdb=" O LYS C 352 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY C 354 " --> pdb=" O TYR C 319 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY C 321 " --> pdb=" O GLY C 354 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL D 93 " --> pdb=" O ALA D 65 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU D 67 " --> pdb=" O VAL D 93 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N ILE D 66 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS D 6 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL D 68 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN D 8 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL D 5 " --> pdb=" O GLN D 133 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE D 135 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE D 7 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU D 137 " --> pdb=" O ILE D 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA D 9 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS D 139 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE D 165 " --> pdb=" O PHE D 135 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU D 137 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN D 167 " --> pdb=" O LEU D 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS D 139 " --> pdb=" O ASN D 167 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE D 169 " --> pdb=" O HIS D 139 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU D 200 " --> pdb=" O THR D 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER D 170 " --> pdb=" O GLU D 200 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR D 202 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 53 through 56 Processing sheet with id= L, first strand: chain 'D' and resid 269 through 273 Processing sheet with id= M, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE E 93 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE E 67 " --> pdb=" O ILE E 93 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE E 5 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N PHE E 135 " --> pdb=" O ILE E 5 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE E 7 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL E 137 " --> pdb=" O ILE E 7 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL E 9 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS E 139 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER E 165 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL E 137 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU E 167 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N HIS E 139 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE E 169 " --> pdb=" O HIS E 139 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS E 200 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER E 170 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE E 202 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR E 172 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL E 204 " --> pdb=" O TYR E 172 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 53 through 55 Processing sheet with id= O, first strand: chain 'E' and resid 269 through 273 removed outlier: 5.877A pdb=" N LYS E 352 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR E 319 " --> pdb=" O LYS E 352 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY E 354 " --> pdb=" O TYR E 319 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY E 321 " --> pdb=" O GLY E 354 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL F 93 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU F 67 " --> pdb=" O VAL F 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE F 66 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS F 6 " --> pdb=" O ILE F 66 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL F 68 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN F 8 " --> pdb=" O VAL F 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL F 5 " --> pdb=" O GLN F 133 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE F 135 " --> pdb=" O VAL F 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE F 7 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU F 137 " --> pdb=" O ILE F 7 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N ALA F 9 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS F 139 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE F 165 " --> pdb=" O PHE F 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU F 137 " --> pdb=" O ILE F 165 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN F 167 " --> pdb=" O LEU F 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS F 139 " --> pdb=" O ASN F 167 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE F 169 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU F 200 " --> pdb=" O THR F 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER F 170 " --> pdb=" O GLU F 200 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR F 202 " --> pdb=" O SER F 170 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 53 through 56 Processing sheet with id= R, first strand: chain 'F' and resid 269 through 273 Processing sheet with id= S, first strand: chain 'G' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE G 93 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE G 67 " --> pdb=" O ILE G 93 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL G 66 " --> pdb=" O CYS G 4 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER G 6 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL G 68 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS G 8 " --> pdb=" O VAL G 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE G 5 " --> pdb=" O GLN G 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE G 135 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE G 7 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL G 137 " --> pdb=" O ILE G 7 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL G 9 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N HIS G 139 " --> pdb=" O VAL G 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER G 165 " --> pdb=" O PHE G 135 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL G 137 " --> pdb=" O SER G 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU G 167 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N HIS G 139 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE G 169 " --> pdb=" O HIS G 139 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS G 200 " --> pdb=" O GLU G 168 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER G 170 " --> pdb=" O CYS G 200 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE G 202 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR G 172 " --> pdb=" O PHE G 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL G 204 " --> pdb=" O TYR G 172 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 53 through 55 Processing sheet with id= U, first strand: chain 'G' and resid 269 through 273 removed outlier: 5.878A pdb=" N LYS G 352 " --> pdb=" O LEU G 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR G 319 " --> pdb=" O LYS G 352 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY G 354 " --> pdb=" O TYR G 319 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY G 321 " --> pdb=" O GLY G 354 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL H 93 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU H 67 " --> pdb=" O VAL H 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE H 66 " --> pdb=" O ILE H 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS H 6 " --> pdb=" O ILE H 66 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL H 68 " --> pdb=" O HIS H 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN H 8 " --> pdb=" O VAL H 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL H 5 " --> pdb=" O GLN H 133 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE H 135 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE H 7 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU H 137 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA H 9 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS H 139 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE H 165 " --> pdb=" O PHE H 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU H 137 " --> pdb=" O ILE H 165 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASN H 167 " --> pdb=" O LEU H 137 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N HIS H 139 " --> pdb=" O ASN H 167 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE H 169 " --> pdb=" O HIS H 139 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU H 200 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER H 170 " --> pdb=" O GLU H 200 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR H 202 " --> pdb=" O SER H 170 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 53 through 56 Processing sheet with id= X, first strand: chain 'H' and resid 269 through 273 Processing sheet with id= Y, first strand: chain 'I' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE I 93 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE I 67 " --> pdb=" O ILE I 93 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL I 66 " --> pdb=" O CYS I 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER I 6 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL I 68 " --> pdb=" O SER I 6 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS I 8 " --> pdb=" O VAL I 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE I 5 " --> pdb=" O GLN I 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE I 135 " --> pdb=" O ILE I 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE I 7 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL I 137 " --> pdb=" O ILE I 7 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL I 9 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N HIS I 139 " --> pdb=" O VAL I 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER I 165 " --> pdb=" O PHE I 135 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL I 137 " --> pdb=" O SER I 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU I 167 " --> pdb=" O VAL I 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS I 139 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE I 169 " --> pdb=" O HIS I 139 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS I 200 " --> pdb=" O GLU I 168 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N SER I 170 " --> pdb=" O CYS I 200 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE I 202 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR I 172 " --> pdb=" O PHE I 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL I 204 " --> pdb=" O TYR I 172 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 53 through 55 Processing sheet with id= AA, first strand: chain 'I' and resid 269 through 273 removed outlier: 5.877A pdb=" N LYS I 352 " --> pdb=" O LEU I 317 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR I 319 " --> pdb=" O LYS I 352 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY I 354 " --> pdb=" O TYR I 319 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY I 321 " --> pdb=" O GLY I 354 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL J 93 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N LEU J 67 " --> pdb=" O VAL J 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE J 66 " --> pdb=" O ILE J 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS J 6 " --> pdb=" O ILE J 66 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL J 68 " --> pdb=" O HIS J 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN J 8 " --> pdb=" O VAL J 68 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL J 5 " --> pdb=" O GLN J 133 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE J 135 " --> pdb=" O VAL J 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE J 7 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU J 137 " --> pdb=" O ILE J 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA J 9 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS J 139 " --> pdb=" O ALA J 9 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ILE J 165 " --> pdb=" O PHE J 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU J 137 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN J 167 " --> pdb=" O LEU J 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS J 139 " --> pdb=" O ASN J 167 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE J 169 " --> pdb=" O HIS J 139 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU J 200 " --> pdb=" O THR J 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER J 170 " --> pdb=" O GLU J 200 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR J 202 " --> pdb=" O SER J 170 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'J' and resid 53 through 56 Processing sheet with id= AD, first strand: chain 'J' and resid 269 through 273 Processing sheet with id= AE, first strand: chain 'K' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE K 93 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE K 67 " --> pdb=" O ILE K 93 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL K 66 " --> pdb=" O CYS K 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER K 6 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL K 68 " --> pdb=" O SER K 6 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS K 8 " --> pdb=" O VAL K 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE K 5 " --> pdb=" O GLN K 133 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE K 135 " --> pdb=" O ILE K 5 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE K 7 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL K 137 " --> pdb=" O ILE K 7 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL K 9 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N HIS K 139 " --> pdb=" O VAL K 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER K 165 " --> pdb=" O PHE K 135 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL K 137 " --> pdb=" O SER K 165 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU K 167 " --> pdb=" O VAL K 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS K 139 " --> pdb=" O LEU K 167 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE K 169 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS K 200 " --> pdb=" O GLU K 168 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER K 170 " --> pdb=" O CYS K 200 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N PHE K 202 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYR K 172 " --> pdb=" O PHE K 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL K 204 " --> pdb=" O TYR K 172 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'K' and resid 53 through 55 Processing sheet with id= AG, first strand: chain 'K' and resid 269 through 273 removed outlier: 5.878A pdb=" N LYS K 352 " --> pdb=" O LEU K 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR K 319 " --> pdb=" O LYS K 352 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY K 354 " --> pdb=" O TYR K 319 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY K 321 " --> pdb=" O GLY K 354 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 92 through 94 removed outlier: 7.870A pdb=" N VAL L 93 " --> pdb=" O ALA L 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU L 67 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE L 66 " --> pdb=" O ILE L 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS L 6 " --> pdb=" O ILE L 66 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL L 68 " --> pdb=" O HIS L 6 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN L 8 " --> pdb=" O VAL L 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL L 5 " --> pdb=" O GLN L 133 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE L 135 " --> pdb=" O VAL L 5 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE L 7 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU L 137 " --> pdb=" O ILE L 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA L 9 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS L 139 " --> pdb=" O ALA L 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE L 165 " --> pdb=" O PHE L 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU L 137 " --> pdb=" O ILE L 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN L 167 " --> pdb=" O LEU L 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS L 139 " --> pdb=" O ASN L 167 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N PHE L 169 " --> pdb=" O HIS L 139 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU L 200 " --> pdb=" O THR L 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER L 170 " --> pdb=" O GLU L 200 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR L 202 " --> pdb=" O SER L 170 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 53 through 56 Processing sheet with id= AJ, first strand: chain 'L' and resid 269 through 273 Processing sheet with id= AK, first strand: chain 'M' and resid 92 through 94 removed outlier: 7.865A pdb=" N ILE M 93 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE M 67 " --> pdb=" O ILE M 93 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL M 66 " --> pdb=" O CYS M 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER M 6 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL M 68 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS M 8 " --> pdb=" O VAL M 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE M 5 " --> pdb=" O GLN M 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE M 135 " --> pdb=" O ILE M 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE M 7 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL M 137 " --> pdb=" O ILE M 7 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL M 9 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N HIS M 139 " --> pdb=" O VAL M 9 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N SER M 165 " --> pdb=" O PHE M 135 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N VAL M 137 " --> pdb=" O SER M 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU M 167 " --> pdb=" O VAL M 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS M 139 " --> pdb=" O LEU M 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE M 169 " --> pdb=" O HIS M 139 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N CYS M 200 " --> pdb=" O GLU M 168 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER M 170 " --> pdb=" O CYS M 200 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE M 202 " --> pdb=" O SER M 170 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR M 172 " --> pdb=" O PHE M 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL M 204 " --> pdb=" O TYR M 172 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 53 through 55 Processing sheet with id= AM, first strand: chain 'M' and resid 269 through 273 removed outlier: 5.878A pdb=" N LYS M 352 " --> pdb=" O LEU M 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR M 319 " --> pdb=" O LYS M 352 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N GLY M 354 " --> pdb=" O TYR M 319 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY M 321 " --> pdb=" O GLY M 354 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'N' and resid 92 through 94 removed outlier: 7.868A pdb=" N VAL N 93 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU N 67 " --> pdb=" O VAL N 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE N 66 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS N 6 " --> pdb=" O ILE N 66 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL N 68 " --> pdb=" O HIS N 6 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN N 8 " --> pdb=" O VAL N 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL N 5 " --> pdb=" O GLN N 133 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE N 135 " --> pdb=" O VAL N 5 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE N 7 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU N 137 " --> pdb=" O ILE N 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA N 9 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS N 139 " --> pdb=" O ALA N 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE N 165 " --> pdb=" O PHE N 135 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU N 137 " --> pdb=" O ILE N 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN N 167 " --> pdb=" O LEU N 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS N 139 " --> pdb=" O ASN N 167 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE N 169 " --> pdb=" O HIS N 139 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLU N 200 " --> pdb=" O THR N 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER N 170 " --> pdb=" O GLU N 200 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR N 202 " --> pdb=" O SER N 170 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 53 through 56 Processing sheet with id= AP, first strand: chain 'N' and resid 269 through 273 Processing sheet with id= AQ, first strand: chain 'O' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE O 93 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE O 67 " --> pdb=" O ILE O 93 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL O 66 " --> pdb=" O CYS O 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER O 6 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL O 68 " --> pdb=" O SER O 6 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS O 8 " --> pdb=" O VAL O 68 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N ILE O 5 " --> pdb=" O GLN O 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE O 135 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE O 7 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL O 137 " --> pdb=" O ILE O 7 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL O 9 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N HIS O 139 " --> pdb=" O VAL O 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER O 165 " --> pdb=" O PHE O 135 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL O 137 " --> pdb=" O SER O 165 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU O 167 " --> pdb=" O VAL O 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS O 139 " --> pdb=" O LEU O 167 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N PHE O 169 " --> pdb=" O HIS O 139 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS O 200 " --> pdb=" O GLU O 168 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER O 170 " --> pdb=" O CYS O 200 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE O 202 " --> pdb=" O SER O 170 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR O 172 " --> pdb=" O PHE O 202 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL O 204 " --> pdb=" O TYR O 172 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'O' and resid 53 through 55 Processing sheet with id= AS, first strand: chain 'O' and resid 269 through 273 removed outlier: 5.878A pdb=" N LYS O 352 " --> pdb=" O LEU O 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR O 319 " --> pdb=" O LYS O 352 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY O 354 " --> pdb=" O TYR O 319 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY O 321 " --> pdb=" O GLY O 354 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'P' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL P 93 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU P 67 " --> pdb=" O VAL P 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE P 66 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS P 6 " --> pdb=" O ILE P 66 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL P 68 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN P 8 " --> pdb=" O VAL P 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL P 5 " --> pdb=" O GLN P 133 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N PHE P 135 " --> pdb=" O VAL P 5 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE P 7 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LEU P 137 " --> pdb=" O ILE P 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA P 9 " --> pdb=" O LEU P 137 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N HIS P 139 " --> pdb=" O ALA P 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE P 165 " --> pdb=" O PHE P 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU P 137 " --> pdb=" O ILE P 165 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASN P 167 " --> pdb=" O LEU P 137 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N HIS P 139 " --> pdb=" O ASN P 167 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE P 169 " --> pdb=" O HIS P 139 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU P 200 " --> pdb=" O THR P 168 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER P 170 " --> pdb=" O GLU P 200 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N TYR P 202 " --> pdb=" O SER P 170 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'P' and resid 53 through 56 Processing sheet with id= AV, first strand: chain 'P' and resid 269 through 273 Processing sheet with id= AW, first strand: chain 'Q' and resid 92 through 94 removed outlier: 7.864A pdb=" N ILE Q 93 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N PHE Q 67 " --> pdb=" O ILE Q 93 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N VAL Q 66 " --> pdb=" O CYS Q 4 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER Q 6 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL Q 68 " --> pdb=" O SER Q 6 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS Q 8 " --> pdb=" O VAL Q 68 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ILE Q 5 " --> pdb=" O GLN Q 133 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE Q 135 " --> pdb=" O ILE Q 5 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE Q 7 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL Q 137 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N VAL Q 9 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N HIS Q 139 " --> pdb=" O VAL Q 9 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N SER Q 165 " --> pdb=" O PHE Q 135 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL Q 137 " --> pdb=" O SER Q 165 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU Q 167 " --> pdb=" O VAL Q 137 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS Q 139 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE Q 169 " --> pdb=" O HIS Q 139 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N CYS Q 200 " --> pdb=" O GLU Q 168 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N SER Q 170 " --> pdb=" O CYS Q 200 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE Q 202 " --> pdb=" O SER Q 170 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N TYR Q 172 " --> pdb=" O PHE Q 202 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N VAL Q 204 " --> pdb=" O TYR Q 172 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 53 through 55 Processing sheet with id= AY, first strand: chain 'Q' and resid 269 through 273 removed outlier: 5.878A pdb=" N LYS Q 352 " --> pdb=" O LEU Q 317 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N TYR Q 319 " --> pdb=" O LYS Q 352 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY Q 354 " --> pdb=" O TYR Q 319 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N GLY Q 321 " --> pdb=" O GLY Q 354 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'R' and resid 92 through 94 removed outlier: 7.869A pdb=" N VAL R 93 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU R 67 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N ILE R 66 " --> pdb=" O ILE R 4 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N HIS R 6 " --> pdb=" O ILE R 66 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL R 68 " --> pdb=" O HIS R 6 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN R 8 " --> pdb=" O VAL R 68 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL R 5 " --> pdb=" O GLN R 133 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE R 135 " --> pdb=" O VAL R 5 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ILE R 7 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU R 137 " --> pdb=" O ILE R 7 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA R 9 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N HIS R 139 " --> pdb=" O ALA R 9 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE R 165 " --> pdb=" O PHE R 135 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU R 137 " --> pdb=" O ILE R 165 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASN R 167 " --> pdb=" O LEU R 137 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N HIS R 139 " --> pdb=" O ASN R 167 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE R 169 " --> pdb=" O HIS R 139 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N GLU R 200 " --> pdb=" O THR R 168 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N SER R 170 " --> pdb=" O GLU R 200 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N TYR R 202 " --> pdb=" O SER R 170 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'R' and resid 53 through 56 Processing sheet with id= BB, first strand: chain 'R' and resid 269 through 273 2493 hydrogen bonds defined for protein. 6534 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: 20.64 Time building geometry restraints manager: 21.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 16794 1.32 - 1.45: 17588 1.45 - 1.58: 27178 1.58 - 1.70: 54 1.70 - 1.83: 648 Bond restraints: 62262 Sorted by residual: bond pdb=" CA GLY Q 265 " pdb=" C GLY Q 265 " ideal model delta sigma weight residual 1.519 1.273 0.246 1.25e-02 6.40e+03 3.86e+02 bond pdb=" CA GLY M 265 " pdb=" C GLY M 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.85e+02 bond pdb=" CA GLY I 265 " pdb=" C GLY I 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.84e+02 bond pdb=" CA GLY E 265 " pdb=" C GLY E 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.84e+02 bond pdb=" CA GLY G 265 " pdb=" C GLY G 265 " ideal model delta sigma weight residual 1.519 1.274 0.245 1.25e-02 6.40e+03 3.83e+02 ... (remaining 62257 not shown) Histogram of bond angle deviations from ideal: 92.93 - 103.57: 1355 103.57 - 114.21: 35287 114.21 - 124.84: 45596 124.84 - 135.48: 2317 135.48 - 146.12: 27 Bond angle restraints: 84582 Sorted by residual: angle pdb=" C ARG G 264 " pdb=" N GLY G 265 " pdb=" CA GLY G 265 " ideal model delta sigma weight residual 121.45 101.49 19.96 1.06e+00 8.90e-01 3.55e+02 angle pdb=" C ARG O 264 " pdb=" N GLY O 265 " pdb=" CA GLY O 265 " ideal model delta sigma weight residual 121.45 101.49 19.96 1.06e+00 8.90e-01 3.55e+02 angle pdb=" C ARG K 264 " pdb=" N GLY K 265 " pdb=" CA GLY K 265 " ideal model delta sigma weight residual 121.45 101.50 19.95 1.06e+00 8.90e-01 3.54e+02 angle pdb=" C ARG E 264 " pdb=" N GLY E 265 " pdb=" CA GLY E 265 " ideal model delta sigma weight residual 121.45 101.50 19.95 1.06e+00 8.90e-01 3.54e+02 angle pdb=" C ARG Q 264 " pdb=" N GLY Q 265 " pdb=" CA GLY Q 265 " ideal model delta sigma weight residual 121.45 101.50 19.95 1.06e+00 8.90e-01 3.54e+02 ... (remaining 84577 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 36333 35.89 - 71.77: 585 71.77 - 107.66: 54 107.66 - 143.55: 18 143.55 - 179.43: 27 Dihedral angle restraints: 37017 sinusoidal: 14850 harmonic: 22167 Sorted by residual: dihedral pdb=" CA LEU L 248 " pdb=" C LEU L 248 " pdb=" N ASN L 249 " pdb=" CA ASN L 249 " ideal model delta harmonic sigma weight residual -180.00 -133.85 -46.15 0 5.00e+00 4.00e-02 8.52e+01 dihedral pdb=" CA LEU F 248 " pdb=" C LEU F 248 " pdb=" N ASN F 249 " pdb=" CA ASN F 249 " ideal model delta harmonic sigma weight residual 180.00 -133.86 -46.14 0 5.00e+00 4.00e-02 8.51e+01 dihedral pdb=" CA LEU B 248 " pdb=" C LEU B 248 " pdb=" N ASN B 249 " pdb=" CA ASN B 249 " ideal model delta harmonic sigma weight residual -180.00 -133.91 -46.09 0 5.00e+00 4.00e-02 8.50e+01 ... (remaining 37014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 6801 0.133 - 0.266: 1869 0.266 - 0.399: 384 0.399 - 0.532: 126 0.532 - 0.665: 36 Chirality restraints: 9216 Sorted by residual: chirality pdb=" CA HIS M 266 " pdb=" N HIS M 266 " pdb=" C HIS M 266 " pdb=" CB HIS M 266 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA HIS Q 266 " pdb=" N HIS Q 266 " pdb=" C HIS Q 266 " pdb=" CB HIS Q 266 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 chirality pdb=" CA HIS O 266 " pdb=" N HIS O 266 " pdb=" C HIS O 266 " pdb=" CB HIS O 266 " both_signs ideal model delta sigma weight residual False 2.51 1.85 0.66 2.00e-01 2.50e+01 1.10e+01 ... (remaining 9213 not shown) Planarity restraints: 11043 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER Q 439 " 0.032 2.00e-02 2.50e+03 6.32e-02 4.00e+01 pdb=" C SER Q 439 " -0.109 2.00e-02 2.50e+03 pdb=" O SER Q 439 " 0.039 2.00e-02 2.50e+03 pdb=" OXT SER Q 439 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 439 " 0.032 2.00e-02 2.50e+03 6.31e-02 3.99e+01 pdb=" C SER M 439 " -0.109 2.00e-02 2.50e+03 pdb=" O SER M 439 " 0.039 2.00e-02 2.50e+03 pdb=" OXT SER M 439 " 0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O 439 " 0.032 2.00e-02 2.50e+03 6.31e-02 3.98e+01 pdb=" C SER O 439 " -0.109 2.00e-02 2.50e+03 pdb=" O SER O 439 " 0.039 2.00e-02 2.50e+03 pdb=" OXT SER O 439 " 0.039 2.00e-02 2.50e+03 ... (remaining 11040 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 2935 2.64 - 3.20: 63278 3.20 - 3.77: 109021 3.77 - 4.33: 147546 4.33 - 4.90: 228325 Nonbonded interactions: 551105 Sorted by model distance: nonbonded pdb="MG MG K 502 " pdb=" O HOH K 601 " model vdw 2.069 2.170 nonbonded pdb="MG MG A 502 " pdb=" O HOH A 601 " model vdw 2.070 2.170 nonbonded pdb="MG MG E 502 " pdb=" O HOH E 601 " model vdw 2.070 2.170 nonbonded pdb="MG MG G 502 " pdb=" O HOH G 601 " model vdw 2.070 2.170 nonbonded pdb="MG MG M 502 " pdb=" O HOH M 601 " model vdw 2.070 2.170 ... (remaining 551100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 3.170 Check model and map are aligned: 0.660 Set scattering table: 0.410 Process input model: 128.080 Find NCS groups from input model: 3.650 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 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 : 0.021 0.257 62262 Z= 1.367 Angle : 2.641 21.911 84582 Z= 1.765 Chirality : 0.139 0.665 9216 Planarity : 0.008 0.063 11043 Dihedral : 14.012 179.431 22788 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.59 % Allowed : 3.07 % Favored : 96.34 % Rotamer: Outliers : 0.14 % Allowed : 0.69 % Favored : 99.17 % Cbeta Deviations : 0.90 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.09), residues: 7632 helix: -0.74 (0.07), residues: 3564 sheet: 0.75 (0.14), residues: 1170 loop : -1.08 (0.11), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP K 21 HIS 0.012 0.002 HIS Q 139 PHE 0.038 0.004 PHE K 49 TYR 0.077 0.010 TYR F 61 ARG 0.007 0.001 ARG N 284 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2868 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 2859 time to evaluate : 5.413 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: 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: 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: 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: 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: 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: 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: 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: 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: 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 outliers start: 9 outliers final: 0 residues processed: 2859 average time/residue: 0.6493 time to fit residues: 3025.5812 Evaluate side-chains 1407 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1407 time to evaluate : 5.326 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.1657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 638 optimal weight: 20.0000 chunk 573 optimal weight: 8.9990 chunk 317 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 386 optimal weight: 20.0000 chunk 306 optimal weight: 20.0000 chunk 592 optimal weight: 7.9990 chunk 229 optimal weight: 8.9990 chunk 360 optimal weight: 8.9990 chunk 441 optimal weight: 8.9990 chunk 686 optimal weight: 30.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 96 GLN B 136 GLN B 266 HIS C 8 HIS ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 133 GLN C 356 ASN D 96 GLN D 193 GLN D 309 HIS ** E 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 96 GLN F 193 GLN F 309 HIS G 61 HIS G 133 GLN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 258 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 GLN H 139 HIS H 193 GLN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 HIS ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN I 356 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 11 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 193 GLN ** J 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 133 GLN K 258 ASN K 300 ASN ** K 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS K 356 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 11 GLN ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 193 GLN M 35 GLN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 301 GLN N 37 HIS N 96 GLN ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN O 233 GLN O 301 GLN P 96 GLN P 193 GLN ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 349 ASN P 433 GLN ** Q 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 233 GLN Q 293 ASN Q 301 GLN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 HIS R 96 GLN R 136 GLN R 349 ASN ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 62262 Z= 0.266 Angle : 0.733 9.508 84582 Z= 0.387 Chirality : 0.047 0.219 9216 Planarity : 0.006 0.139 11043 Dihedral : 12.543 169.544 8595 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.26 % Allowed : 2.80 % Favored : 96.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.10), residues: 7632 helix: 0.26 (0.08), residues: 3474 sheet: 1.13 (0.17), residues: 990 loop : -0.21 (0.12), residues: 3168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP O 21 HIS 0.014 0.002 HIS M 309 PHE 0.028 0.002 PHE I 255 TYR 0.029 0.003 TYR O 224 ARG 0.017 0.001 ARG R 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2008 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1991 time to evaluate : 5.333 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: 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: 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: 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: 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: 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: 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: 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: 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 outliers start: 17 outliers final: 1 residues processed: 2000 average time/residue: 0.6377 time to fit residues: 2132.7138 Evaluate side-chains 1266 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1265 time to evaluate : 5.284 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4459 time to fit residues: 7.9199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 381 optimal weight: 50.0000 chunk 213 optimal weight: 50.0000 chunk 571 optimal weight: 40.0000 chunk 467 optimal weight: 9.9990 chunk 189 optimal weight: 0.3980 chunk 687 optimal weight: 9.9990 chunk 742 optimal weight: 30.0000 chunk 612 optimal weight: 40.0000 chunk 682 optimal weight: 40.0000 chunk 234 optimal weight: 4.9990 chunk 551 optimal weight: 20.0000 overall best weight: 9.0790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 35 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS ** G 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 294 GLN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 101 ASN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 294 GLN J 300 ASN J 349 ASN ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 258 ASN M 309 HIS N 229 HIS ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 309 HIS O 35 GLN ** O 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 HIS P 249 ASN P 281 GLN P 349 ASN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 349 ASN ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7179 moved from start: 0.6245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 62262 Z= 0.240 Angle : 0.672 10.106 84582 Z= 0.350 Chirality : 0.045 0.260 9216 Planarity : 0.005 0.114 11043 Dihedral : 11.797 170.392 8595 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 22.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.28 % Allowed : 2.60 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.10), residues: 7632 helix: 0.22 (0.08), residues: 3420 sheet: 0.92 (0.16), residues: 1107 loop : 0.09 (0.12), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP J 21 HIS 0.012 0.001 HIS C 8 PHE 0.043 0.002 PHE F 395 TYR 0.023 0.002 TYR B 61 ARG 0.009 0.001 ARG D 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1702 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1684 time to evaluate : 5.441 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: 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: 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: 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: 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: 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: 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: 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 outliers start: 18 outliers final: 3 residues processed: 1690 average time/residue: 0.6056 time to fit residues: 1716.4794 Evaluate side-chains 1159 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1156 time to evaluate : 5.315 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5287 time to fit residues: 9.8630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 679 optimal weight: 6.9990 chunk 517 optimal weight: 40.0000 chunk 356 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 328 optimal weight: 5.9990 chunk 461 optimal weight: 20.0000 chunk 690 optimal weight: 50.0000 chunk 730 optimal weight: 50.0000 chunk 360 optimal weight: 7.9990 chunk 654 optimal weight: 9.9990 chunk 196 optimal weight: 40.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS D 193 GLN ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 HIS J 186 ASN J 281 GLN ** J 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** K 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 HIS ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 GLN M 309 HIS ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 HIS Q 35 GLN ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.6908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 62262 Z= 0.203 Angle : 0.631 12.243 84582 Z= 0.326 Chirality : 0.045 0.240 9216 Planarity : 0.005 0.078 11043 Dihedral : 11.192 168.704 8595 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 0.12 % Allowed : 2.90 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.47 (0.10), residues: 7632 helix: 0.36 (0.09), residues: 3420 sheet: 1.10 (0.16), residues: 1134 loop : 0.16 (0.12), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP R 21 HIS 0.020 0.001 HIS M 28 PHE 0.040 0.002 PHE D 262 TYR 0.034 0.002 TYR N 161 ARG 0.009 0.001 ARG E 390 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1663 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1655 time to evaluate : 5.289 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: 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 2 residues processed: 1659 average time/residue: 0.5993 time to fit residues: 1660.8912 Evaluate side-chains 1163 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1161 time to evaluate : 5.373 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.5264 time to fit residues: 9.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 608 optimal weight: 8.9990 chunk 414 optimal weight: 50.0000 chunk 10 optimal weight: 5.9990 chunk 544 optimal weight: 50.0000 chunk 301 optimal weight: 8.9990 chunk 623 optimal weight: 40.0000 chunk 505 optimal weight: 20.0000 chunk 0 optimal weight: 80.0000 chunk 373 optimal weight: 9.9990 chunk 655 optimal weight: 10.0000 chunk 184 optimal weight: 30.0000 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 176 GLN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS N 266 HIS ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 85 GLN O 197 HIS O 285 GLN P 37 HIS P 247 GLN ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.7436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 62262 Z= 0.219 Angle : 0.631 10.319 84582 Z= 0.326 Chirality : 0.045 0.229 9216 Planarity : 0.005 0.099 11043 Dihedral : 10.919 172.632 8595 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.09 % Allowed : 2.11 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.54 (0.10), residues: 7632 helix: 0.39 (0.09), residues: 3438 sheet: 1.00 (0.15), residues: 1215 loop : 0.27 (0.13), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP R 21 HIS 0.010 0.001 HIS I 266 PHE 0.026 0.002 PHE A 49 TYR 0.033 0.002 TYR K 24 ARG 0.010 0.001 ARG B 79 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1557 time to evaluate : 5.375 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: 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: 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: 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: 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: 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: 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 outliers start: 6 outliers final: 3 residues processed: 1560 average time/residue: 0.5981 time to fit residues: 1566.3645 Evaluate side-chains 1134 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1131 time to evaluate : 5.301 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.5135 time to fit residues: 9.7854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 245 optimal weight: 40.0000 chunk 658 optimal weight: 30.0000 chunk 144 optimal weight: 5.9990 chunk 429 optimal weight: 20.0000 chunk 180 optimal weight: 9.9990 chunk 731 optimal weight: 0.0370 chunk 607 optimal weight: 9.9990 chunk 338 optimal weight: 0.5980 chunk 60 optimal weight: 40.0000 chunk 241 optimal weight: 30.0000 chunk 384 optimal weight: 7.9990 overall best weight: 4.9264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 ASN B 281 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** D 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 192 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 249 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS F 339 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 61 HIS ** K 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 GLN M 309 HIS N 266 HIS N 294 GLN O 285 GLN O 293 ASN ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 197 HIS Q 283 HIS ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.7829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 62262 Z= 0.179 Angle : 0.609 10.019 84582 Z= 0.311 Chirality : 0.045 0.228 9216 Planarity : 0.005 0.074 11043 Dihedral : 10.484 178.349 8595 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.09 % Allowed : 1.71 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.56 (0.10), residues: 7632 helix: 0.41 (0.09), residues: 3474 sheet: 1.14 (0.15), residues: 1152 loop : 0.22 (0.12), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.003 TRP R 21 HIS 0.009 0.001 HIS H 107 PHE 0.023 0.001 PHE F 395 TYR 0.027 0.001 TYR K 24 ARG 0.007 0.000 ARG P 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1571 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1565 time to evaluate : 5.321 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: 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 1567 average time/residue: 0.5978 time to fit residues: 1578.9286 Evaluate side-chains 1159 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1158 time to evaluate : 5.280 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.5187 time to fit residues: 7.9730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 705 optimal weight: 0.0060 chunk 82 optimal weight: 40.0000 chunk 416 optimal weight: 6.9990 chunk 534 optimal weight: 40.0000 chunk 413 optimal weight: 5.9990 chunk 615 optimal weight: 40.0000 chunk 408 optimal weight: 30.0000 chunk 728 optimal weight: 50.0000 chunk 456 optimal weight: 10.0000 chunk 444 optimal weight: 6.9990 chunk 336 optimal weight: 40.0000 overall best weight: 6.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 ASN A 266 HIS ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 249 ASN B 309 HIS C 11 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 37 HIS D 192 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS D 424 ASN F 37 HIS ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 101 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 HIS N 300 ASN O 226 ASN O 285 GLN ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 283 HIS ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.8186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 62262 Z= 0.186 Angle : 0.625 12.626 84582 Z= 0.317 Chirality : 0.045 0.181 9216 Planarity : 0.005 0.059 11043 Dihedral : 10.116 175.118 8595 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.11 % Allowed : 1.25 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.44 (0.10), residues: 7632 helix: 0.35 (0.09), residues: 3519 sheet: 0.79 (0.15), residues: 1260 loop : 0.22 (0.13), residues: 2853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP R 21 HIS 0.022 0.001 HIS L 28 PHE 0.036 0.001 PHE M 49 TYR 0.037 0.002 TYR D 202 ARG 0.008 0.001 ARG L 320 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1519 time to evaluate : 5.356 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: 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: 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: 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: 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: 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 outliers start: 7 outliers final: 1 residues processed: 1521 average time/residue: 0.6266 time to fit residues: 1617.4891 Evaluate side-chains 1112 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1111 time to evaluate : 5.367 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4524 time to fit residues: 8.0443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 450 optimal weight: 50.0000 chunk 290 optimal weight: 20.0000 chunk 435 optimal weight: 30.0000 chunk 219 optimal weight: 50.0000 chunk 143 optimal weight: 5.9990 chunk 141 optimal weight: 30.0000 chunk 463 optimal weight: 7.9990 chunk 496 optimal weight: 8.9990 chunk 360 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 572 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 136 GLN ** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 37 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 ASN F 37 HIS ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 393 HIS ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 229 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 309 HIS ** N 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN ** O 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 249 ASN ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 176 GLN Q 283 HIS ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.8524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 62262 Z= 0.204 Angle : 0.640 9.951 84582 Z= 0.331 Chirality : 0.045 0.258 9216 Planarity : 0.005 0.063 11043 Dihedral : 9.750 170.982 8595 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 21.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.03 % Allowed : 0.92 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.35 (0.10), residues: 7632 helix: 0.32 (0.09), residues: 3519 sheet: 0.87 (0.15), residues: 1197 loop : 0.06 (0.12), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP R 21 HIS 0.009 0.001 HIS Q 283 PHE 0.039 0.002 PHE F 395 TYR 0.030 0.002 TYR I 432 ARG 0.010 0.001 ARG J 278 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1480 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1478 time to evaluate : 5.335 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 1479 average time/residue: 0.5939 time to fit residues: 1483.0544 Evaluate side-chains 1035 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1035 time to evaluate : 5.365 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 662 optimal weight: 8.9990 chunk 698 optimal weight: 7.9990 chunk 636 optimal weight: 40.0000 chunk 679 optimal weight: 8.9990 chunk 697 optimal weight: 7.9990 chunk 408 optimal weight: 50.0000 chunk 295 optimal weight: 8.9990 chunk 533 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 613 optimal weight: 20.0000 chunk 642 optimal weight: 50.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 136 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS F 37 HIS ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN G 197 HIS ** G 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 309 HIS ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 HIS O 226 ASN P 37 HIS P 249 ASN ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.8797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 62262 Z= 0.199 Angle : 0.644 11.589 84582 Z= 0.331 Chirality : 0.045 0.274 9216 Planarity : 0.005 0.064 11043 Dihedral : 9.477 168.880 8595 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 21.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.06 % Allowed : 0.55 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.37 (0.10), residues: 7632 helix: 0.39 (0.09), residues: 3465 sheet: 0.67 (0.15), residues: 1224 loop : 0.09 (0.12), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.003 TRP R 21 HIS 0.011 0.001 HIS E 266 PHE 0.032 0.001 PHE J 395 TYR 0.029 0.002 TYR E 83 ARG 0.010 0.001 ARG M 123 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1469 time to evaluate : 5.380 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: 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: 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: 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: 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: 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 outliers start: 4 outliers final: 0 residues processed: 1470 average time/residue: 0.5960 time to fit residues: 1481.7582 Evaluate side-chains 1068 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1068 time to evaluate : 5.737 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 676 optimal weight: 9.9990 chunk 445 optimal weight: 10.0000 chunk 718 optimal weight: 9.9990 chunk 438 optimal weight: 30.0000 chunk 340 optimal weight: 40.0000 chunk 499 optimal weight: 10.0000 chunk 753 optimal weight: 0.6980 chunk 693 optimal weight: 40.0000 chunk 599 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 chunk 463 optimal weight: 20.0000 overall best weight: 7.9390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 37 HIS B 136 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 193 GLN ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 206 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN P 37 HIS P 249 ASN ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 266 HIS ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.9063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 62262 Z= 0.204 Angle : 0.650 9.461 84582 Z= 0.334 Chirality : 0.046 0.225 9216 Planarity : 0.005 0.074 11043 Dihedral : 9.206 167.718 8595 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.05 % Allowed : 0.40 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 0.34 (0.10), residues: 7632 helix: 0.35 (0.09), residues: 3510 sheet: 0.47 (0.15), residues: 1278 loop : 0.20 (0.13), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.003 TRP R 21 HIS 0.008 0.001 HIS I 28 PHE 0.045 0.002 PHE J 395 TYR 0.025 0.002 TYR K 24 ARG 0.013 0.001 ARG P 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15264 Ramachandran restraints generated. 7632 Oldfield, 0 Emsley, 7632 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1440 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1437 time to evaluate : 5.526 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: 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: 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: 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: 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: 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 outliers start: 3 outliers final: 0 residues processed: 1438 average time/residue: 0.6102 time to fit residues: 1492.0714 Evaluate side-chains 1050 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1050 time to evaluate : 5.309 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.2793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 756 random chunks: chunk 367 optimal weight: 2.9990 chunk 476 optimal weight: 50.0000 chunk 638 optimal weight: 6.9990 chunk 183 optimal weight: 7.9990 chunk 553 optimal weight: 10.0000 chunk 88 optimal weight: 0.4980 chunk 166 optimal weight: 30.0000 chunk 600 optimal weight: 30.0000 chunk 251 optimal weight: 7.9990 chunk 616 optimal weight: 7.9990 chunk 76 optimal weight: 9.9990 overall best weight: 5.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 ASN ** F 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS G 128 GLN G 228 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN H 249 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 18 ASN ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 247 GLN K 101 ASN K 380 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN O 226 ASN ** O 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 37 HIS ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 14 ASN R 309 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.076812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.062301 restraints weight = 214194.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.065224 restraints weight = 128339.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.067383 restraints weight = 84808.246| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.9248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 62262 Z= 0.186 Angle : 0.651 12.246 84582 Z= 0.332 Chirality : 0.046 0.272 9216 Planarity : 0.005 0.077 11043 Dihedral : 8.974 167.088 8595 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 20.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.06 % Allowed : 0.31 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.36 (0.10), residues: 7632 helix: 0.40 (0.09), residues: 3474 sheet: 0.48 (0.14), residues: 1278 loop : 0.16 (0.13), residues: 2880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.003 TRP R 21 HIS 0.020 0.001 HIS O 61 PHE 0.043 0.001 PHE J 395 TYR 0.024 0.001 TYR K 24 ARG 0.012 0.001 ARG P 48 =============================================================================== Job complete usr+sys time: 21833.73 seconds wall clock time: 381 minutes 47.36 seconds (22907.36 seconds total)