Starting phenix.real_space_refine on Tue Mar 12 01:14:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/03_2024/3j6f_5896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/03_2024/3j6f_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_5896/03_2024/3j6f_5896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/03_2024/3j6f_5896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/03_2024/3j6f_5896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j6f_5896/03_2024/3j6f_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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 22.69, per 1000 atoms: 0.37 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: 18.68 Conformation dependent library (CDL) restraints added in 8.1 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: 8.74 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: 20.29 Time building geometry restraints manager: 20.41 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: 0.060 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: 0.040 Extract box with map and model: 3.020 Check model and map are aligned: 0.650 Set scattering table: 0.420 Process input model: 121.050 Find NCS groups from input model: 3.600 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:2.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.730 ------------------------------------------------------------------------------- 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 : 5.104 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 REVERT: A 5 ILE cc_start: 0.7973 (mt) cc_final: 0.7711 (mm) REVERT: A 21 TRP cc_start: 0.8672 (m100) cc_final: 0.8467 (m100) REVERT: A 26 LEU cc_start: 0.9097 (mt) cc_final: 0.8859 (mm) REVERT: A 33 ASP cc_start: 0.5831 (p0) cc_final: 0.5549 (t0) REVERT: A 53 PHE cc_start: 0.8519 (m-80) cc_final: 0.7259 (m-80) REVERT: A 66 VAL cc_start: 0.8854 (t) cc_final: 0.8064 (t) REVERT: A 122 ILE cc_start: 0.9175 (mt) cc_final: 0.8944 (mt) REVERT: A 171 ILE cc_start: 0.8487 (mm) cc_final: 0.8165 (mp) REVERT: A 188 ILE cc_start: 0.9289 (mm) cc_final: 0.8775 (tt) REVERT: A 209 ILE cc_start: 0.9406 (mt) cc_final: 0.8334 (mm) REVERT: A 227 LEU cc_start: 0.9209 (mt) cc_final: 0.8539 (mm) REVERT: A 230 LEU cc_start: 0.8941 (tp) cc_final: 0.8507 (tp) REVERT: A 242 LEU cc_start: 0.7333 (mt) cc_final: 0.6575 (mt) REVERT: A 248 LEU cc_start: 0.6718 (mt) cc_final: 0.5907 (mp) REVERT: A 302 MET cc_start: 0.7693 (mmm) cc_final: 0.7133 (tpt) REVERT: A 352 LYS cc_start: 0.8121 (tptt) cc_final: 0.7902 (tptp) REVERT: A 378 LEU cc_start: 0.8176 (mt) cc_final: 0.7560 (mt) REVERT: A 409 VAL cc_start: 0.8724 (t) cc_final: 0.8426 (p) REVERT: A 431 ASP cc_start: 0.8306 (m-30) cc_final: 0.7463 (m-30) REVERT: B 20 PHE cc_start: 0.8697 (t80) cc_final: 0.8295 (t80) REVERT: B 21 TRP cc_start: 0.8186 (m100) cc_final: 0.7661 (m100) REVERT: B 24 ILE cc_start: 0.9538 (mm) cc_final: 0.9141 (mm) REVERT: B 60 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8494 (mmtt) REVERT: B 66 ILE cc_start: 0.9074 (mt) cc_final: 0.8807 (mm) REVERT: B 67 LEU cc_start: 0.8450 (mt) cc_final: 0.8214 (mt) REVERT: B 70 LEU cc_start: 0.8233 (mt) cc_final: 0.7621 (mp) REVERT: B 91 ASN cc_start: 0.8668 (m-40) cc_final: 0.8294 (m110) REVERT: B 93 VAL cc_start: 0.9277 (t) cc_final: 0.8846 (t) REVERT: B 137 LEU cc_start: 0.7290 (mp) cc_final: 0.6831 (mt) REVERT: B 169 PHE cc_start: 0.6656 (m-80) cc_final: 0.5552 (m-10) REVERT: B 217 LEU cc_start: 0.8635 (mt) cc_final: 0.7847 (mt) REVERT: B 230 LEU cc_start: 0.8622 (mt) cc_final: 0.8267 (tt) REVERT: B 235 MET cc_start: 0.8477 (mtp) cc_final: 0.7956 (mtp) REVERT: B 239 THR cc_start: 0.9134 (p) cc_final: 0.8523 (t) REVERT: B 240 THR cc_start: 0.3590 (t) cc_final: 0.3056 (t) REVERT: B 267 PHE cc_start: 0.7821 (m-80) cc_final: 0.7540 (m-80) REVERT: B 378 ILE cc_start: 0.7809 (mt) cc_final: 0.7427 (mp) REVERT: B 398 MET cc_start: 0.7020 (mtm) cc_final: 0.6467 (mtm) REVERT: C 8 HIS cc_start: 0.5152 (m-70) cc_final: 0.4882 (m90) REVERT: C 60 LYS cc_start: 0.7912 (mmtt) cc_final: 0.7326 (pttt) REVERT: C 75 ILE cc_start: 0.9108 (mm) cc_final: 0.8597 (tt) REVERT: C 153 LEU cc_start: 0.9162 (tp) cc_final: 0.8709 (tt) REVERT: C 157 LEU cc_start: 0.9090 (mt) cc_final: 0.8487 (mt) REVERT: C 188 ILE cc_start: 0.9298 (mm) cc_final: 0.8942 (tt) REVERT: C 227 LEU cc_start: 0.9370 (mt) cc_final: 0.9037 (mt) REVERT: C 290 GLU cc_start: 0.6188 (tp30) cc_final: 0.5911 (tp30) REVERT: C 347 CYS cc_start: 0.6338 (t) cc_final: 0.6114 (t) REVERT: C 378 LEU cc_start: 0.8406 (mt) cc_final: 0.7674 (mt) REVERT: D 60 LYS cc_start: 0.8386 (mmtt) cc_final: 0.8075 (ttmt) REVERT: D 66 ILE cc_start: 0.8380 (mt) cc_final: 0.8112 (mm) REVERT: D 75 MET cc_start: 0.7484 (mmm) cc_final: 0.7103 (mmm) REVERT: D 137 LEU cc_start: 0.7610 (mp) cc_final: 0.7252 (mt) REVERT: D 157 ILE cc_start: 0.8650 (mt) cc_final: 0.8220 (mt) REVERT: D 163 ASP cc_start: 0.7382 (p0) cc_final: 0.7057 (p0) REVERT: D 169 PHE cc_start: 0.6373 (m-80) cc_final: 0.5611 (m-10) REVERT: D 239 THR cc_start: 0.9341 (p) cc_final: 0.9131 (t) REVERT: D 333 LEU cc_start: 0.8868 (tp) cc_final: 0.7604 (tt) REVERT: D 347 ILE cc_start: 0.9236 (mt) cc_final: 0.8963 (mp) REVERT: E 24 TYR cc_start: 0.7792 (m-80) cc_final: 0.6724 (m-80) REVERT: E 53 PHE cc_start: 0.8174 (m-80) cc_final: 0.7182 (m-80) REVERT: E 66 VAL cc_start: 0.8375 (t) cc_final: 0.8123 (p) REVERT: E 75 ILE cc_start: 0.8760 (mm) cc_final: 0.8387 (mm) REVERT: E 135 PHE cc_start: 0.7694 (p90) cc_final: 0.7491 (p90) REVERT: E 157 LEU cc_start: 0.8597 (mt) cc_final: 0.7973 (mt) REVERT: E 171 ILE cc_start: 0.8932 (mm) cc_final: 0.8503 (mp) REVERT: E 227 LEU cc_start: 0.9230 (mt) cc_final: 0.8408 (mm) REVERT: E 230 LEU cc_start: 0.8742 (tp) cc_final: 0.8329 (tp) REVERT: E 231 ILE cc_start: 0.9385 (mt) cc_final: 0.9020 (tt) REVERT: E 242 LEU cc_start: 0.7004 (mt) cc_final: 0.6506 (mt) REVERT: E 248 LEU cc_start: 0.6361 (mt) cc_final: 0.5924 (mt) REVERT: E 302 MET cc_start: 0.8624 (mmm) cc_final: 0.7696 (mmm) REVERT: E 318 LEU cc_start: 0.7384 (tp) cc_final: 0.6488 (tp) REVERT: E 335 ILE cc_start: 0.8650 (pt) cc_final: 0.8210 (mm) REVERT: E 352 LYS cc_start: 0.8843 (tptt) cc_final: 0.8603 (tptt) REVERT: E 363 VAL cc_start: 0.8313 (t) cc_final: 0.8010 (p) REVERT: E 378 LEU cc_start: 0.7777 (mt) cc_final: 0.6302 (mt) REVERT: E 428 LEU cc_start: 0.8711 (tp) cc_final: 0.8125 (tp) REVERT: F 24 ILE cc_start: 0.9544 (mm) cc_final: 0.9067 (mm) REVERT: F 67 LEU cc_start: 0.8474 (mt) cc_final: 0.7316 (mt) REVERT: F 157 ILE cc_start: 0.8767 (mt) cc_final: 0.8003 (mm) REVERT: F 163 ASP cc_start: 0.7229 (p0) cc_final: 0.6700 (p0) REVERT: F 179 ASP cc_start: 0.7809 (m-30) cc_final: 0.7384 (p0) REVERT: F 239 THR cc_start: 0.9177 (p) cc_final: 0.8608 (t) REVERT: F 252 LEU cc_start: 0.8680 (tp) cc_final: 0.8049 (tp) REVERT: F 259 MET cc_start: 0.7036 (mmm) cc_final: 0.6682 (mmm) REVERT: F 265 LEU cc_start: 0.9391 (mt) cc_final: 0.9029 (mp) REVERT: F 267 PHE cc_start: 0.7574 (m-80) cc_final: 0.6705 (m-80) REVERT: F 329 ASP cc_start: 0.7846 (m-30) cc_final: 0.7451 (m-30) REVERT: F 378 ILE cc_start: 0.6761 (mt) cc_final: 0.6368 (mp) REVERT: F 405 LEU cc_start: 0.8776 (mt) cc_final: 0.8348 (mt) REVERT: F 432 TYR cc_start: 0.8210 (m-80) cc_final: 0.7528 (m-80) REVERT: G 5 ILE cc_start: 0.8284 (mt) cc_final: 0.7764 (mm) REVERT: G 25 CYS cc_start: 0.7622 (m) cc_final: 0.7211 (m) REVERT: G 26 LEU cc_start: 0.9032 (mt) cc_final: 0.7654 (mt) REVERT: G 66 VAL cc_start: 0.8184 (t) cc_final: 0.7851 (p) REVERT: G 75 ILE cc_start: 0.9280 (mm) cc_final: 0.8596 (tt) REVERT: G 125 LEU cc_start: 0.9173 (mt) cc_final: 0.8958 (mm) REVERT: G 153 LEU cc_start: 0.8846 (tp) cc_final: 0.8535 (tt) REVERT: G 167 LEU cc_start: 0.7296 (mt) cc_final: 0.6351 (mt) REVERT: G 217 LEU cc_start: 0.8127 (mt) cc_final: 0.6473 (mt) REVERT: G 242 LEU cc_start: 0.7838 (mt) cc_final: 0.6419 (mt) REVERT: G 248 LEU cc_start: 0.8205 (mt) cc_final: 0.7931 (mm) REVERT: G 259 LEU cc_start: 0.6967 (mt) cc_final: 0.6715 (mt) REVERT: G 269 LEU cc_start: 0.8059 (mt) cc_final: 0.7855 (mt) REVERT: G 288 VAL cc_start: 0.8810 (t) cc_final: 0.8193 (t) REVERT: G 317 LEU cc_start: 0.8867 (mt) cc_final: 0.8568 (mm) REVERT: G 318 LEU cc_start: 0.7448 (tp) cc_final: 0.7224 (tp) REVERT: G 376 CYS cc_start: 0.7891 (t) cc_final: 0.6942 (t) REVERT: G 378 LEU cc_start: 0.7358 (mt) cc_final: 0.6897 (mt) REVERT: G 388 TRP cc_start: 0.6777 (m100) cc_final: 0.5889 (m100) REVERT: G 409 VAL cc_start: 0.8631 (t) cc_final: 0.8340 (p) REVERT: H 20 PHE cc_start: 0.8395 (t80) cc_final: 0.7949 (t80) REVERT: H 24 ILE cc_start: 0.9233 (mm) cc_final: 0.8994 (mm) REVERT: H 28 HIS cc_start: 0.7885 (m-70) cc_final: 0.7275 (m90) REVERT: H 60 LYS cc_start: 0.8154 (mmtt) cc_final: 0.7271 (ptmt) REVERT: H 212 ILE cc_start: 0.9071 (mt) cc_final: 0.8207 (mt) REVERT: H 230 LEU cc_start: 0.8563 (mt) cc_final: 0.8335 (mm) REVERT: H 232 SER cc_start: 0.8001 (p) cc_final: 0.7700 (p) REVERT: H 351 VAL cc_start: 0.9353 (t) cc_final: 0.9111 (p) REVERT: I 25 CYS cc_start: 0.7518 (m) cc_final: 0.7270 (m) REVERT: I 26 LEU cc_start: 0.9154 (mt) cc_final: 0.8947 (mm) REVERT: I 53 PHE cc_start: 0.7475 (m-80) cc_final: 0.6620 (m-80) REVERT: I 66 VAL cc_start: 0.8267 (t) cc_final: 0.7548 (p) REVERT: I 74 VAL cc_start: 0.8678 (t) cc_final: 0.8054 (t) REVERT: I 122 ILE cc_start: 0.8887 (mt) cc_final: 0.8392 (mt) REVERT: I 138 PHE cc_start: 0.6805 (m-80) cc_final: 0.6180 (m-80) REVERT: I 171 ILE cc_start: 0.8548 (mm) cc_final: 0.8298 (mm) REVERT: I 205 ASP cc_start: 0.8587 (t0) cc_final: 0.8322 (t0) REVERT: I 209 ILE cc_start: 0.9423 (mt) cc_final: 0.9069 (mm) REVERT: I 217 LEU cc_start: 0.7933 (mt) cc_final: 0.6312 (mt) REVERT: I 227 LEU cc_start: 0.9332 (mt) cc_final: 0.8863 (mt) REVERT: I 230 LEU cc_start: 0.8553 (tp) cc_final: 0.8323 (tp) REVERT: I 234 ILE cc_start: 0.8985 (mt) cc_final: 0.8686 (mt) REVERT: I 238 ILE cc_start: 0.8438 (mt) cc_final: 0.7715 (tp) REVERT: I 248 LEU cc_start: 0.8678 (mt) cc_final: 0.7863 (mp) REVERT: I 258 ASN cc_start: 0.6870 (m-40) cc_final: 0.5909 (m-40) REVERT: I 262 TYR cc_start: 0.7193 (m-80) cc_final: 0.6760 (m-80) REVERT: I 288 VAL cc_start: 0.8854 (t) cc_final: 0.8503 (m) REVERT: I 317 LEU cc_start: 0.8951 (mt) cc_final: 0.8292 (mt) REVERT: I 318 LEU cc_start: 0.7823 (tp) cc_final: 0.7063 (tp) REVERT: I 335 ILE cc_start: 0.8563 (pt) cc_final: 0.8208 (tp) REVERT: I 376 CYS cc_start: 0.7976 (t) cc_final: 0.7604 (t) REVERT: I 378 LEU cc_start: 0.8382 (mt) cc_final: 0.7960 (mt) REVERT: J 6 HIS cc_start: 0.7206 (t70) cc_final: 0.6969 (t-90) REVERT: J 24 ILE cc_start: 0.9199 (mm) cc_final: 0.8223 (mm) REVERT: J 87 PHE cc_start: 0.8354 (m-80) cc_final: 0.7862 (m-80) REVERT: J 141 LEU cc_start: 0.7394 (mt) cc_final: 0.6697 (mt) REVERT: J 216 THR cc_start: 0.7787 (p) cc_final: 0.6515 (p) REVERT: J 351 VAL cc_start: 0.9360 (t) cc_final: 0.9049 (p) REVERT: J 352 LYS cc_start: 0.8395 (mmtt) cc_final: 0.8009 (tmtt) REVERT: J 388 PHE cc_start: 0.6057 (m-10) cc_final: 0.4680 (m-80) REVERT: J 435 TYR cc_start: 0.7833 (m-80) cc_final: 0.7372 (m-80) REVERT: K 7 ILE cc_start: 0.9281 (mt) cc_final: 0.8968 (mp) REVERT: K 25 CYS cc_start: 0.8262 (m) cc_final: 0.7618 (m) REVERT: K 33 ASP cc_start: 0.6178 (p0) cc_final: 0.5698 (t0) REVERT: K 122 ILE cc_start: 0.8714 (mt) cc_final: 0.7555 (mt) REVERT: K 125 LEU cc_start: 0.8432 (mt) cc_final: 0.7792 (mm) REVERT: K 129 CYS cc_start: 0.8142 (m) cc_final: 0.7892 (m) REVERT: K 167 LEU cc_start: 0.7888 (mt) cc_final: 0.7629 (mt) REVERT: K 205 ASP cc_start: 0.8530 (t0) cc_final: 0.7876 (t0) REVERT: K 217 LEU cc_start: 0.8236 (mt) cc_final: 0.7117 (mt) REVERT: K 242 LEU cc_start: 0.7331 (mt) cc_final: 0.6376 (mp) REVERT: K 248 LEU cc_start: 0.8843 (mt) cc_final: 0.8560 (mp) REVERT: K 252 LEU cc_start: 0.7157 (mt) cc_final: 0.6955 (mt) REVERT: K 262 TYR cc_start: 0.6900 (m-80) cc_final: 0.6500 (m-80) REVERT: K 288 VAL cc_start: 0.9276 (t) cc_final: 0.8336 (m) REVERT: K 292 THR cc_start: 0.8856 (p) cc_final: 0.8647 (p) REVERT: K 325 PRO cc_start: 0.7591 (Cg_exo) cc_final: 0.6990 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8668 (pt) cc_final: 0.8006 (tp) REVERT: K 347 CYS cc_start: 0.5514 (t) cc_final: 0.4669 (t) REVERT: K 355 ILE cc_start: 0.9146 (mt) cc_final: 0.8686 (tp) REVERT: K 431 ASP cc_start: 0.6654 (m-30) cc_final: 0.6223 (m-30) REVERT: L 24 ILE cc_start: 0.9116 (mm) cc_final: 0.8673 (mm) REVERT: L 288 VAL cc_start: 0.8466 (t) cc_final: 0.8012 (t) REVERT: L 291 LEU cc_start: 0.9167 (mt) cc_final: 0.7927 (mt) REVERT: L 329 ASP cc_start: 0.7481 (m-30) cc_final: 0.7194 (m-30) REVERT: L 352 LYS cc_start: 0.9373 (mmtt) cc_final: 0.8221 (tmtt) REVERT: L 355 VAL cc_start: 0.6607 (t) cc_final: 0.6380 (m) REVERT: L 395 PHE cc_start: 0.7978 (t80) cc_final: 0.7342 (t80) REVERT: M 5 ILE cc_start: 0.8422 (mt) cc_final: 0.7660 (mm) REVERT: M 53 PHE cc_start: 0.6912 (m-80) cc_final: 0.6413 (m-80) REVERT: M 74 VAL cc_start: 0.8986 (t) cc_final: 0.8078 (t) REVERT: M 75 ILE cc_start: 0.8866 (mm) cc_final: 0.8547 (tt) REVERT: M 137 VAL cc_start: 0.8711 (t) cc_final: 0.8448 (p) REVERT: M 171 ILE cc_start: 0.8027 (mm) cc_final: 0.7724 (mp) REVERT: M 227 LEU cc_start: 0.9291 (mt) cc_final: 0.8801 (mm) REVERT: M 230 LEU cc_start: 0.8440 (tp) cc_final: 0.8139 (tp) REVERT: M 231 ILE cc_start: 0.9194 (mt) cc_final: 0.8789 (mm) REVERT: M 238 ILE cc_start: 0.8463 (mt) cc_final: 0.8073 (tt) REVERT: M 275 VAL cc_start: 0.8692 (t) cc_final: 0.8386 (t) REVERT: M 322 ASP cc_start: 0.7014 (t0) cc_final: 0.6597 (t70) REVERT: M 335 ILE cc_start: 0.8329 (pt) cc_final: 0.7844 (tp) REVERT: M 428 LEU cc_start: 0.8509 (tp) cc_final: 0.8302 (tp) REVERT: N 7 ILE cc_start: 0.8880 (mt) cc_final: 0.8174 (mm) REVERT: N 8 GLN cc_start: 0.6748 (mt0) cc_final: 0.6044 (mt0) REVERT: N 21 TRP cc_start: 0.8281 (m100) cc_final: 0.7816 (m100) REVERT: N 42 LEU cc_start: 0.8843 (mt) cc_final: 0.8333 (mt) REVERT: N 90 ASP cc_start: 0.6848 (m-30) cc_final: 0.6619 (m-30) REVERT: N 92 PHE cc_start: 0.8367 (m-80) cc_final: 0.8035 (m-80) REVERT: N 115 VAL cc_start: 0.8914 (t) cc_final: 0.8675 (p) REVERT: N 230 LEU cc_start: 0.8794 (mt) cc_final: 0.8555 (mt) REVERT: N 235 MET cc_start: 0.7968 (mtp) cc_final: 0.7551 (ttm) REVERT: N 252 LEU cc_start: 0.7895 (tp) cc_final: 0.7585 (tp) REVERT: N 255 LEU cc_start: 0.6940 (tp) cc_final: 0.6376 (tp) REVERT: N 266 HIS cc_start: 0.7700 (p90) cc_final: 0.7462 (p-80) REVERT: N 288 VAL cc_start: 0.9417 (t) cc_final: 0.9160 (t) REVERT: N 297 ASP cc_start: 0.7855 (t0) cc_final: 0.7543 (t0) REVERT: N 314 THR cc_start: 0.6986 (p) cc_final: 0.6262 (p) REVERT: N 315 VAL cc_start: 0.7574 (t) cc_final: 0.7130 (t) REVERT: N 333 LEU cc_start: 0.8786 (tp) cc_final: 0.8178 (tt) REVERT: N 378 ILE cc_start: 0.7480 (mt) cc_final: 0.7266 (mp) REVERT: O 21 TRP cc_start: 0.8323 (m100) cc_final: 0.7899 (m100) REVERT: O 53 PHE cc_start: 0.7240 (m-80) cc_final: 0.6648 (m-80) REVERT: O 74 VAL cc_start: 0.8757 (t) cc_final: 0.7430 (t) REVERT: O 118 VAL cc_start: 0.8905 (t) cc_final: 0.8541 (t) REVERT: O 152 LEU cc_start: 0.8475 (tp) cc_final: 0.8199 (tp) REVERT: O 171 ILE cc_start: 0.7971 (mm) cc_final: 0.7732 (mm) REVERT: O 230 LEU cc_start: 0.8078 (tp) cc_final: 0.7644 (tp) REVERT: O 231 ILE cc_start: 0.9225 (mt) cc_final: 0.8546 (tt) REVERT: O 242 LEU cc_start: 0.6201 (mt) cc_final: 0.5301 (mt) REVERT: O 275 VAL cc_start: 0.8784 (t) cc_final: 0.8226 (t) REVERT: O 286 LEU cc_start: 0.8250 (mt) cc_final: 0.7103 (mt) REVERT: O 378 LEU cc_start: 0.8802 (mt) cc_final: 0.8568 (mt) REVERT: O 398 MET cc_start: 0.6906 (mtp) cc_final: 0.6684 (mmm) REVERT: P 7 ILE cc_start: 0.9139 (mt) cc_final: 0.8919 (mm) REVERT: P 24 ILE cc_start: 0.9449 (mm) cc_final: 0.9149 (mm) REVERT: P 86 ILE cc_start: 0.9006 (tt) cc_final: 0.8577 (tt) REVERT: P 108 TYR cc_start: 0.7462 (t80) cc_final: 0.6669 (t80) REVERT: P 154 ILE cc_start: 0.8310 (mt) cc_final: 0.7971 (mt) REVERT: P 201 THR cc_start: 0.7704 (t) cc_final: 0.7013 (p) REVERT: P 221 THR cc_start: 0.8350 (p) cc_final: 0.8128 (p) REVERT: P 259 MET cc_start: 0.7460 (mmm) cc_final: 0.7008 (mmt) REVERT: P 333 LEU cc_start: 0.9021 (tp) cc_final: 0.8029 (tt) REVERT: P 378 ILE cc_start: 0.8158 (mt) cc_final: 0.7631 (mp) REVERT: P 384 ILE cc_start: 0.8076 (mt) cc_final: 0.7755 (mm) REVERT: P 428 LEU cc_start: 0.8559 (mt) cc_final: 0.7768 (mt) REVERT: Q 53 PHE cc_start: 0.6806 (m-80) cc_final: 0.6509 (m-80) REVERT: Q 66 VAL cc_start: 0.8368 (t) cc_final: 0.7914 (t) REVERT: Q 171 ILE cc_start: 0.7949 (mm) cc_final: 0.7491 (mm) REVERT: Q 231 ILE cc_start: 0.9388 (mt) cc_final: 0.9041 (tt) REVERT: Q 286 LEU cc_start: 0.8272 (mt) cc_final: 0.7579 (mt) REVERT: Q 315 CYS cc_start: 0.7397 (t) cc_final: 0.5389 (t) REVERT: Q 317 LEU cc_start: 0.6841 (mt) cc_final: 0.5959 (mm) REVERT: Q 378 LEU cc_start: 0.7791 (mt) cc_final: 0.6884 (mt) REVERT: Q 398 MET cc_start: 0.7109 (mtp) cc_final: 0.6731 (mmm) REVERT: Q 407 TRP cc_start: 0.7900 (m100) cc_final: 0.7467 (m100) REVERT: Q 431 ASP cc_start: 0.6681 (m-30) cc_final: 0.6328 (m-30) REVERT: R 7 ILE cc_start: 0.8953 (mt) cc_final: 0.8663 (mm) REVERT: R 67 LEU cc_start: 0.8266 (mt) cc_final: 0.7167 (mm) REVERT: R 92 PHE cc_start: 0.7476 (m-80) cc_final: 0.7123 (m-80) REVERT: R 108 TYR cc_start: 0.7360 (t80) cc_final: 0.6781 (t80) REVERT: R 171 VAL cc_start: 0.8784 (t) cc_final: 0.8424 (t) REVERT: R 230 LEU cc_start: 0.8928 (mt) cc_final: 0.8682 (mm) REVERT: R 235 MET cc_start: 0.7932 (mtp) cc_final: 0.7729 (ttm) REVERT: R 248 LEU cc_start: 0.8007 (mt) cc_final: 0.7801 (mt) REVERT: R 254 LYS cc_start: 0.7625 (tttt) cc_final: 0.7127 (ttmt) REVERT: R 259 MET cc_start: 0.7927 (mmm) cc_final: 0.7250 (mmt) REVERT: R 260 VAL cc_start: 0.9275 (t) cc_final: 0.9022 (t) REVERT: R 275 LEU cc_start: 0.9578 (tp) cc_final: 0.9359 (tp) REVERT: R 378 ILE cc_start: 0.7369 (mt) cc_final: 0.6973 (mp) outliers start: 9 outliers final: 0 residues processed: 2859 average time/residue: 0.6390 time to fit residues: 2971.6895 Evaluate side-chains 1481 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1481 time to evaluate : 5.115 ------------------------------------------------------------------------------- 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: 10.0000 chunk 317 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 chunk 386 optimal weight: 30.0000 chunk 306 optimal weight: 20.0000 chunk 592 optimal weight: 8.9990 chunk 229 optimal weight: 7.9990 chunk 360 optimal weight: 7.9990 chunk 441 optimal weight: 7.9990 chunk 686 optimal weight: 30.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 96 GLN ** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS ** C 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 356 ASN D 96 GLN D 193 GLN D 249 ASN D 309 HIS ** E 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 309 HIS G 61 HIS G 133 GLN 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 61 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 101 ASN ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 301 GLN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.4939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 62262 Z= 0.252 Angle : 0.729 9.060 84582 Z= 0.386 Chirality : 0.047 0.201 9216 Planarity : 0.006 0.139 11043 Dihedral : 12.579 170.057 8595 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.21 % Allowed : 2.64 % Favored : 97.14 % 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: 0.24 (0.10), residues: 7632 helix: 0.35 (0.08), residues: 3438 sheet: 1.17 (0.17), residues: 990 loop : -0.23 (0.12), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP J 103 HIS 0.012 0.002 HIS F 309 PHE 0.027 0.002 PHE B 244 TYR 0.027 0.002 TYR M 24 ARG 0.015 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: 14 poor density : 1994 time to evaluate : 5.219 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: A 16 ILE cc_start: 0.8641 (pt) cc_final: 0.8389 (pt) REVERT: A 21 TRP cc_start: 0.8539 (m100) cc_final: 0.8281 (m100) REVERT: A 53 PHE cc_start: 0.8000 (m-80) cc_final: 0.7296 (m-80) REVERT: A 157 LEU cc_start: 0.8975 (mt) cc_final: 0.8516 (mt) REVERT: A 234 ILE cc_start: 0.9265 (mt) cc_final: 0.9051 (tt) REVERT: A 258 ASN cc_start: 0.6247 (m-40) cc_final: 0.5347 (t0) REVERT: A 282 TYR cc_start: 0.6170 (m-80) cc_final: 0.5826 (m-80) REVERT: A 291 ILE cc_start: 0.9133 (mt) cc_final: 0.8126 (tp) REVERT: A 296 PHE cc_start: 0.7564 (m-80) cc_final: 0.7131 (m-10) REVERT: A 300 ASN cc_start: 0.8457 (p0) cc_final: 0.7995 (p0) REVERT: A 317 LEU cc_start: 0.7875 (mt) cc_final: 0.7389 (mt) REVERT: A 335 ILE cc_start: 0.8487 (tp) cc_final: 0.8215 (tp) REVERT: A 352 LYS cc_start: 0.8206 (tptt) cc_final: 0.7780 (tptp) REVERT: A 408 TYR cc_start: 0.5666 (m-80) cc_final: 0.5315 (m-80) REVERT: B 20 PHE cc_start: 0.8460 (t80) cc_final: 0.7906 (t80) REVERT: B 67 LEU cc_start: 0.9078 (mt) cc_final: 0.8709 (mt) REVERT: B 124 LYS cc_start: 0.8985 (pptt) cc_final: 0.8662 (pttm) REVERT: B 139 HIS cc_start: 0.8195 (p90) cc_final: 0.7380 (p90) REVERT: B 165 ILE cc_start: 0.8772 (mt) cc_final: 0.7912 (mt) REVERT: B 166 MET cc_start: 0.8241 (mmp) cc_final: 0.7906 (mmm) REVERT: B 268 PHE cc_start: 0.6338 (m-80) cc_final: 0.5984 (m-80) REVERT: B 335 VAL cc_start: 0.9101 (t) cc_final: 0.8827 (t) REVERT: B 422 GLU cc_start: 0.8963 (pt0) cc_final: 0.8462 (pp20) REVERT: C 21 TRP cc_start: 0.7449 (m100) cc_final: 0.6499 (m100) REVERT: C 60 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7722 (tttt) REVERT: C 75 ILE cc_start: 0.9036 (mm) cc_final: 0.7626 (tt) REVERT: C 78 VAL cc_start: 0.9291 (t) cc_final: 0.9002 (t) REVERT: C 125 LEU cc_start: 0.8509 (mt) cc_final: 0.8060 (tp) REVERT: C 154 MET cc_start: 0.6862 (tpt) cc_final: 0.6645 (tpp) REVERT: C 157 LEU cc_start: 0.9173 (mt) cc_final: 0.8892 (pp) REVERT: C 167 LEU cc_start: 0.6483 (mt) cc_final: 0.5896 (mt) REVERT: C 193 THR cc_start: 0.8425 (p) cc_final: 0.8220 (t) REVERT: C 200 CYS cc_start: 0.6398 (t) cc_final: 0.5497 (p) REVERT: C 217 LEU cc_start: 0.8701 (mm) cc_final: 0.8464 (mm) REVERT: C 292 THR cc_start: 0.8905 (t) cc_final: 0.8622 (t) REVERT: C 378 LEU cc_start: 0.7339 (mt) cc_final: 0.7076 (mt) REVERT: D 108 TYR cc_start: 0.6684 (t80) cc_final: 0.6071 (t80) REVERT: D 154 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8277 (mm) REVERT: D 165 ILE cc_start: 0.8672 (mt) cc_final: 0.8442 (mt) REVERT: D 239 THR cc_start: 0.9284 (p) cc_final: 0.8133 (t) REVERT: D 260 VAL cc_start: 0.8580 (t) cc_final: 0.8227 (t) REVERT: D 265 LEU cc_start: 0.9371 (mt) cc_final: 0.9034 (mp) REVERT: D 302 MET cc_start: 0.7178 (mtm) cc_final: 0.6958 (mtt) REVERT: D 380 ASN cc_start: 0.8380 (t0) cc_final: 0.7993 (t0) REVERT: D 395 PHE cc_start: 0.8459 (t80) cc_final: 0.8231 (t80) REVERT: D 405 LEU cc_start: 0.8466 (mt) cc_final: 0.8145 (mt) REVERT: D 420 GLU cc_start: 0.7131 (tm-30) cc_final: 0.6669 (tm-30) REVERT: D 435 TYR cc_start: 0.6084 (m-80) cc_final: 0.5551 (m-80) REVERT: E 14 VAL cc_start: 0.9194 (t) cc_final: 0.8990 (p) REVERT: E 16 ILE cc_start: 0.8823 (pt) cc_final: 0.8540 (pt) REVERT: E 23 LEU cc_start: 0.8612 (tp) cc_final: 0.8395 (tp) REVERT: E 25 CYS cc_start: 0.7495 (m) cc_final: 0.7292 (m) REVERT: E 33 ASP cc_start: 0.7873 (p0) cc_final: 0.7626 (p0) REVERT: E 53 PHE cc_start: 0.6946 (m-80) cc_final: 0.6228 (m-80) REVERT: E 92 LEU cc_start: 0.8499 (mm) cc_final: 0.8173 (mt) REVERT: E 177 VAL cc_start: 0.8539 (t) cc_final: 0.8306 (p) REVERT: E 218 ASP cc_start: 0.7172 (m-30) cc_final: 0.5685 (m-30) REVERT: E 227 LEU cc_start: 0.8917 (mt) cc_final: 0.8452 (mp) REVERT: E 228 ASN cc_start: 0.8405 (m-40) cc_final: 0.7895 (p0) REVERT: E 282 TYR cc_start: 0.5415 (m-80) cc_final: 0.5082 (m-80) REVERT: E 291 ILE cc_start: 0.9186 (mt) cc_final: 0.8248 (tp) REVERT: E 302 MET cc_start: 0.7917 (mmm) cc_final: 0.7507 (mtt) REVERT: E 335 ILE cc_start: 0.8974 (pt) cc_final: 0.7739 (tp) REVERT: E 352 LYS cc_start: 0.9128 (tptt) cc_final: 0.8748 (tptp) REVERT: F 123 ARG cc_start: 0.7373 (ttm110) cc_final: 0.7165 (ttm110) REVERT: F 139 HIS cc_start: 0.8131 (p90) cc_final: 0.6905 (p90) REVERT: F 163 ASP cc_start: 0.7006 (p0) cc_final: 0.6503 (p0) REVERT: F 212 ILE cc_start: 0.8636 (mt) cc_final: 0.8327 (tp) REVERT: F 239 THR cc_start: 0.9392 (p) cc_final: 0.8923 (t) REVERT: F 248 LEU cc_start: 0.6999 (mt) cc_final: 0.6698 (mm) REVERT: F 286 LEU cc_start: 0.7975 (mt) cc_final: 0.7469 (mt) REVERT: F 327 GLU cc_start: 0.7678 (tp30) cc_final: 0.7155 (tm-30) REVERT: F 329 ASP cc_start: 0.7595 (m-30) cc_final: 0.7390 (m-30) REVERT: F 332 MET cc_start: 0.6595 (tmm) cc_final: 0.6169 (tmm) REVERT: F 398 MET cc_start: 0.8017 (mtp) cc_final: 0.6831 (ptm) REVERT: F 432 TYR cc_start: 0.7985 (m-80) cc_final: 0.7279 (m-80) REVERT: G 5 ILE cc_start: 0.8384 (mt) cc_final: 0.7889 (mm) REVERT: G 16 ILE cc_start: 0.8120 (pt) cc_final: 0.7828 (pt) REVERT: G 25 CYS cc_start: 0.7569 (m) cc_final: 0.6267 (m) REVERT: G 75 ILE cc_start: 0.9250 (mm) cc_final: 0.8341 (tt) REVERT: G 122 ILE cc_start: 0.8425 (mt) cc_final: 0.8153 (mt) REVERT: G 138 PHE cc_start: 0.5726 (m-80) cc_final: 0.5512 (m-80) REVERT: G 209 ILE cc_start: 0.9254 (mm) cc_final: 0.8795 (mm) REVERT: G 217 LEU cc_start: 0.7637 (mt) cc_final: 0.7344 (mt) REVERT: G 376 CYS cc_start: 0.6808 (t) cc_final: 0.6035 (t) REVERT: G 378 LEU cc_start: 0.8096 (mt) cc_final: 0.6933 (mt) REVERT: H 5 VAL cc_start: 0.8664 (t) cc_final: 0.8401 (t) REVERT: H 19 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8392 (mmmt) REVERT: H 24 ILE cc_start: 0.8999 (mm) cc_final: 0.8491 (tp) REVERT: H 28 HIS cc_start: 0.7291 (m-70) cc_final: 0.6187 (m170) REVERT: H 60 LYS cc_start: 0.7387 (mmtt) cc_final: 0.7175 (pttt) REVERT: H 86 ILE cc_start: 0.8920 (tt) cc_final: 0.8433 (tt) REVERT: H 132 LEU cc_start: 0.8957 (tp) cc_final: 0.8550 (tp) REVERT: H 166 MET cc_start: 0.7733 (mmp) cc_final: 0.7497 (mmm) REVERT: H 213 CYS cc_start: 0.7021 (p) cc_final: 0.6642 (p) REVERT: H 432 TYR cc_start: 0.6731 (m-80) cc_final: 0.5934 (m-80) REVERT: I 53 PHE cc_start: 0.6719 (m-80) cc_final: 0.5986 (m-80) REVERT: I 83 TYR cc_start: 0.5845 (m-10) cc_final: 0.5444 (m-10) REVERT: I 124 LYS cc_start: 0.8456 (ttpp) cc_final: 0.8178 (ttpp) REVERT: I 138 PHE cc_start: 0.6546 (m-80) cc_final: 0.5036 (m-80) REVERT: I 158 SER cc_start: 0.8833 (p) cc_final: 0.8600 (t) REVERT: I 172 TYR cc_start: 0.6415 (t80) cc_final: 0.5665 (t80) REVERT: I 212 ILE cc_start: 0.9161 (mt) cc_final: 0.8960 (mt) REVERT: I 227 LEU cc_start: 0.9126 (mt) cc_final: 0.8885 (mt) REVERT: I 377 MET cc_start: 0.7484 (tmm) cc_final: 0.6803 (tmm) REVERT: I 391 LEU cc_start: 0.7718 (mt) cc_final: 0.7435 (mt) REVERT: J 21 TRP cc_start: 0.7819 (m100) cc_final: 0.7532 (m100) REVERT: J 24 ILE cc_start: 0.9059 (mm) cc_final: 0.8321 (tp) REVERT: J 67 LEU cc_start: 0.8097 (mt) cc_final: 0.6890 (mt) REVERT: J 120 ASP cc_start: 0.7057 (t70) cc_final: 0.6696 (t0) REVERT: J 122 VAL cc_start: 0.9296 (t) cc_final: 0.8827 (t) REVERT: J 124 LYS cc_start: 0.7939 (pttp) cc_final: 0.7734 (pttt) REVERT: J 169 PHE cc_start: 0.7067 (m-80) cc_final: 0.6556 (m-10) REVERT: J 216 THR cc_start: 0.7862 (p) cc_final: 0.6131 (t) REVERT: J 242 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.7916 (mt) REVERT: J 333 LEU cc_start: 0.7793 (mt) cc_final: 0.7170 (mt) REVERT: K 16 ILE cc_start: 0.8778 (pt) cc_final: 0.8489 (pt) REVERT: K 33 ASP cc_start: 0.6511 (p0) cc_final: 0.6130 (t0) REVERT: K 66 VAL cc_start: 0.7851 (p) cc_final: 0.7573 (m) REVERT: K 86 LEU cc_start: 0.8644 (tp) cc_final: 0.8403 (tp) REVERT: K 122 ILE cc_start: 0.8228 (mt) cc_final: 0.7626 (mt) REVERT: K 191 THR cc_start: 0.8347 (m) cc_final: 0.8110 (m) REVERT: K 227 LEU cc_start: 0.9192 (mt) cc_final: 0.8556 (mp) REVERT: K 252 LEU cc_start: 0.7597 (mt) cc_final: 0.7393 (mt) REVERT: K 258 ASN cc_start: 0.7448 (m110) cc_final: 0.7067 (t0) REVERT: K 279 GLU cc_start: 0.7928 (mp0) cc_final: 0.7310 (mp0) REVERT: K 280 LYS cc_start: 0.7839 (mtmt) cc_final: 0.6882 (mmmt) REVERT: K 288 VAL cc_start: 0.9000 (t) cc_final: 0.8406 (m) REVERT: K 292 THR cc_start: 0.8984 (p) cc_final: 0.8768 (p) REVERT: K 322 ASP cc_start: 0.6951 (t70) cc_final: 0.6420 (m-30) REVERT: K 325 PRO cc_start: 0.7846 (Cg_exo) cc_final: 0.7437 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8696 (pt) cc_final: 0.8141 (tp) REVERT: K 352 LYS cc_start: 0.7577 (tptt) cc_final: 0.6995 (tptt) REVERT: K 391 LEU cc_start: 0.7903 (mt) cc_final: 0.7667 (mt) REVERT: K 425 MET cc_start: 0.7497 (ttt) cc_final: 0.7225 (ttp) REVERT: L 24 ILE cc_start: 0.8695 (mm) cc_final: 0.8080 (pt) REVERT: L 33 THR cc_start: 0.7026 (p) cc_final: 0.6756 (p) REVERT: L 86 ILE cc_start: 0.8943 (mt) cc_final: 0.8255 (mt) REVERT: L 153 LEU cc_start: 0.8799 (tp) cc_final: 0.8559 (mt) REVERT: L 181 VAL cc_start: 0.6271 (t) cc_final: 0.5800 (t) REVERT: L 239 THR cc_start: 0.9238 (t) cc_final: 0.8758 (t) REVERT: L 291 LEU cc_start: 0.8511 (mt) cc_final: 0.7937 (mt) REVERT: L 333 LEU cc_start: 0.8515 (mt) cc_final: 0.7415 (mt) REVERT: L 334 ASN cc_start: 0.7851 (m110) cc_final: 0.7327 (m110) REVERT: L 395 PHE cc_start: 0.8044 (t80) cc_final: 0.7760 (t80) REVERT: L 413 MET cc_start: 0.6947 (mtt) cc_final: 0.6674 (mtt) REVERT: M 21 TRP cc_start: 0.7713 (m100) cc_final: 0.7393 (m100) REVERT: M 23 LEU cc_start: 0.8626 (tp) cc_final: 0.7559 (tp) REVERT: M 101 ASN cc_start: 0.7757 (t0) cc_final: 0.7518 (t0) REVERT: M 171 ILE cc_start: 0.8139 (mm) cc_final: 0.7870 (mm) REVERT: M 175 PRO cc_start: 0.5675 (Cg_endo) cc_final: 0.4383 (Cg_exo) REVERT: M 230 LEU cc_start: 0.8459 (tp) cc_final: 0.7921 (tp) REVERT: M 269 LEU cc_start: 0.8079 (mt) cc_final: 0.7842 (mt) REVERT: M 317 LEU cc_start: 0.6510 (mt) cc_final: 0.6021 (mm) REVERT: M 335 ILE cc_start: 0.7940 (pt) cc_final: 0.7273 (tp) REVERT: M 378 LEU cc_start: 0.7900 (mt) cc_final: 0.7532 (mt) REVERT: M 413 MET cc_start: 0.8433 (mmm) cc_final: 0.8120 (mmm) REVERT: M 425 MET cc_start: 0.8199 (ttp) cc_final: 0.7472 (ptm) REVERT: N 193 GLN cc_start: 0.7539 (mm110) cc_final: 0.6513 (tt0) REVERT: N 295 MET cc_start: 0.8155 (ppp) cc_final: 0.7931 (ppp) REVERT: N 314 THR cc_start: 0.7271 (p) cc_final: 0.6951 (p) REVERT: N 315 VAL cc_start: 0.7052 (t) cc_final: 0.6722 (t) REVERT: N 325 MET cc_start: 0.6412 (mtt) cc_final: 0.6160 (mtt) REVERT: N 378 ILE cc_start: 0.7605 (mt) cc_final: 0.7146 (mp) REVERT: N 384 ILE cc_start: 0.8571 (mp) cc_final: 0.8338 (mp) REVERT: N 425 MET cc_start: 0.8632 (tpp) cc_final: 0.7997 (tpt) REVERT: O 3 GLU cc_start: 0.7360 (mp0) cc_final: 0.7113 (mp0) REVERT: O 21 TRP cc_start: 0.8549 (m100) cc_final: 0.7445 (m100) REVERT: O 24 TYR cc_start: 0.6504 (m-80) cc_final: 0.5530 (m-80) REVERT: O 66 VAL cc_start: 0.8186 (t) cc_final: 0.7876 (t) REVERT: O 76 ASP cc_start: 0.8626 (m-30) cc_final: 0.8133 (t0) REVERT: O 127 ASP cc_start: 0.7489 (t0) cc_final: 0.7233 (t0) REVERT: O 230 LEU cc_start: 0.8059 (tp) cc_final: 0.7243 (tp) REVERT: O 269 LEU cc_start: 0.8558 (mt) cc_final: 0.8061 (mt) REVERT: O 306 ASP cc_start: 0.7043 (t0) cc_final: 0.6765 (t70) REVERT: P 42 LEU cc_start: 0.8191 (mt) cc_final: 0.7961 (mp) REVERT: P 86 ILE cc_start: 0.9007 (tt) cc_final: 0.8461 (tt) REVERT: P 108 TYR cc_start: 0.7587 (t80) cc_final: 0.7183 (t80) REVERT: P 118 VAL cc_start: 0.8892 (t) cc_final: 0.8573 (t) REVERT: P 124 LYS cc_start: 0.8521 (ttpp) cc_final: 0.8263 (ptmt) REVERT: P 163 ASP cc_start: 0.8301 (p0) cc_final: 0.7731 (p0) REVERT: P 201 THR cc_start: 0.7488 (t) cc_final: 0.6957 (p) REVERT: P 217 LEU cc_start: 0.7299 (tp) cc_final: 0.6657 (tp) REVERT: P 259 MET cc_start: 0.7415 (mmm) cc_final: 0.7148 (mmt) REVERT: P 288 VAL cc_start: 0.9018 (t) cc_final: 0.8729 (t) REVERT: P 314 THR cc_start: 0.7687 (p) cc_final: 0.7365 (p) REVERT: P 425 MET cc_start: 0.8668 (tpp) cc_final: 0.8252 (tpp) REVERT: Q 52 PHE cc_start: 0.6414 (m-10) cc_final: 0.6142 (m-10) REVERT: Q 66 VAL cc_start: 0.8148 (t) cc_final: 0.7854 (t) REVERT: Q 86 LEU cc_start: 0.8385 (tp) cc_final: 0.8142 (tp) REVERT: Q 214 ARG cc_start: 0.5973 (ptp-170) cc_final: 0.5760 (ptp-170) REVERT: R 22 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6218 (tm-30) REVERT: R 42 LEU cc_start: 0.9186 (mt) cc_final: 0.8906 (mp) REVERT: R 115 VAL cc_start: 0.9102 (p) cc_final: 0.8717 (p) REVERT: R 118 VAL cc_start: 0.8704 (t) cc_final: 0.8449 (t) REVERT: R 165 ILE cc_start: 0.8788 (mt) cc_final: 0.8101 (mt) REVERT: R 166 MET cc_start: 0.7322 (mmm) cc_final: 0.6811 (mmm) REVERT: R 194 LEU cc_start: 0.8491 (tt) cc_final: 0.7481 (tp) REVERT: R 235 MET cc_start: 0.6821 (mtp) cc_final: 0.6525 (ttm) REVERT: R 259 MET cc_start: 0.8168 (mmm) cc_final: 0.7857 (mmt) REVERT: R 315 VAL cc_start: 0.7071 (t) cc_final: 0.6849 (t) REVERT: R 425 MET cc_start: 0.8557 (tpp) cc_final: 0.8212 (tpp) outliers start: 14 outliers final: 1 residues processed: 2004 average time/residue: 0.5898 time to fit residues: 1967.1751 Evaluate side-chains 1346 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1343 time to evaluate : 5.141 ------------------------------------------------------------------------------- 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: 40.0000 chunk 571 optimal weight: 40.0000 chunk 467 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 687 optimal weight: 50.0000 chunk 742 optimal weight: 50.0000 chunk 612 optimal weight: 50.0000 chunk 682 optimal weight: 40.0000 chunk 234 optimal weight: 6.9990 chunk 551 optimal weight: 30.0000 overall best weight: 20.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 101 ASN A 176 GLN ** A 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 309 HIS C 8 HIS ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 176 GLN C 293 ASN D 91 ASN D 107 HIS ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 309 HIS G 176 GLN G 285 GLN G 293 ASN G 342 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 393 HIS ** J 8 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 309 HIS ** 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 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 176 GLN M 197 HIS M 258 ASN ** M 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 229 HIS ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 309 HIS ** N 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 35 GLN O 85 GLN O 197 HIS O 226 ASN ** O 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 249 ASN ** P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 281 GLN P 334 ASN P 349 ASN ** P 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 35 GLN Q 197 HIS Q 380 ASN R 14 ASN ** R 136 GLN ** 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: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.6641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 62262 Z= 0.384 Angle : 0.804 11.923 84582 Z= 0.429 Chirality : 0.048 0.267 9216 Planarity : 0.006 0.110 11043 Dihedral : 12.248 172.237 8595 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 29.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.23 % Allowed : 3.59 % Favored : 96.18 % 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: -0.19 (0.09), residues: 7632 helix: -0.23 (0.08), residues: 3492 sheet: 1.14 (0.16), residues: 1026 loop : -0.25 (0.12), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP F 346 HIS 0.015 0.003 HIS I 266 PHE 0.033 0.003 PHE J 92 TYR 0.029 0.003 TYR L 224 ARG 0.039 0.001 ARG G 339 *********************** 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 1592 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1577 time to evaluate : 5.287 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: A 21 TRP cc_start: 0.8991 (m100) cc_final: 0.8152 (m100) REVERT: A 53 PHE cc_start: 0.7610 (m-80) cc_final: 0.7065 (m-80) REVERT: A 123 ARG cc_start: 0.6793 (tpp-160) cc_final: 0.6219 (ttm-80) REVERT: A 135 PHE cc_start: 0.5684 (OUTLIER) cc_final: 0.5429 (p90) REVERT: A 157 LEU cc_start: 0.8784 (mt) cc_final: 0.8426 (mt) REVERT: A 209 ILE cc_start: 0.9059 (mp) cc_final: 0.8803 (mp) REVERT: A 217 LEU cc_start: 0.8653 (mm) cc_final: 0.8132 (mm) REVERT: A 258 ASN cc_start: 0.6416 (m-40) cc_final: 0.6160 (t0) REVERT: A 296 PHE cc_start: 0.7741 (m-80) cc_final: 0.7485 (m-10) REVERT: A 300 ASN cc_start: 0.8998 (p0) cc_final: 0.7980 (m-40) REVERT: A 335 ILE cc_start: 0.8471 (tp) cc_final: 0.8135 (tp) REVERT: A 347 CYS cc_start: 0.8306 (p) cc_final: 0.8026 (p) REVERT: A 352 LYS cc_start: 0.8716 (tptt) cc_final: 0.8460 (tptp) REVERT: A 408 TYR cc_start: 0.5979 (m-80) cc_final: 0.5279 (m-80) REVERT: B 21 TRP cc_start: 0.7937 (m100) cc_final: 0.7463 (m100) REVERT: B 60 LYS cc_start: 0.9102 (mmtt) cc_final: 0.8810 (mmtt) REVERT: B 67 LEU cc_start: 0.8753 (mt) cc_final: 0.8477 (mt) REVERT: B 124 LYS cc_start: 0.8574 (pptt) cc_final: 0.8310 (ptmt) REVERT: B 165 ILE cc_start: 0.8516 (mt) cc_final: 0.8186 (mt) REVERT: B 275 LEU cc_start: 0.8758 (mt) cc_final: 0.8498 (mt) REVERT: B 302 MET cc_start: 0.7343 (mpp) cc_final: 0.7071 (mpp) REVERT: B 326 LYS cc_start: 0.7686 (tppt) cc_final: 0.7447 (tptp) REVERT: B 422 GLU cc_start: 0.9139 (pt0) cc_final: 0.8581 (pp20) REVERT: C 21 TRP cc_start: 0.7898 (m100) cc_final: 0.7140 (m100) REVERT: C 75 ILE cc_start: 0.9116 (mm) cc_final: 0.7828 (tt) REVERT: C 230 LEU cc_start: 0.8713 (tp) cc_final: 0.8369 (tp) REVERT: C 257 THR cc_start: 0.7772 (p) cc_final: 0.7489 (p) REVERT: C 292 THR cc_start: 0.9180 (t) cc_final: 0.8801 (p) REVERT: D 75 MET cc_start: 0.7734 (mmm) cc_final: 0.7247 (tpt) REVERT: D 163 ASP cc_start: 0.8048 (p0) cc_final: 0.7796 (p0) REVERT: D 232 SER cc_start: 0.8710 (t) cc_final: 0.8498 (t) REVERT: D 264 ARG cc_start: 0.6186 (mtt180) cc_final: 0.5633 (mtt180) REVERT: D 283 TYR cc_start: 0.7153 (m-10) cc_final: 0.6730 (m-10) REVERT: D 302 MET cc_start: 0.7054 (mtm) cc_final: 0.6407 (mtt) REVERT: D 333 LEU cc_start: 0.8171 (mt) cc_final: 0.7903 (mt) REVERT: D 405 LEU cc_start: 0.8863 (mt) cc_final: 0.8414 (mt) REVERT: E 21 TRP cc_start: 0.8527 (m100) cc_final: 0.8315 (m100) REVERT: E 141 PHE cc_start: 0.3732 (m-10) cc_final: 0.3425 (m-10) REVERT: E 227 LEU cc_start: 0.8971 (mt) cc_final: 0.8172 (mp) REVERT: E 262 TYR cc_start: 0.7630 (m-10) cc_final: 0.7361 (m-10) REVERT: E 288 VAL cc_start: 0.8511 (m) cc_final: 0.8180 (m) REVERT: E 352 LYS cc_start: 0.9281 (tptt) cc_final: 0.8998 (tptp) REVERT: F 66 ILE cc_start: 0.8844 (mm) cc_final: 0.8587 (mm) REVERT: F 163 ASP cc_start: 0.7881 (p0) cc_final: 0.6964 (p0) REVERT: F 166 MET cc_start: 0.7763 (mmp) cc_final: 0.7121 (mmm) REVERT: F 212 ILE cc_start: 0.9003 (mt) cc_final: 0.8733 (tp) REVERT: F 239 THR cc_start: 0.9374 (p) cc_final: 0.9089 (t) REVERT: F 243 ARG cc_start: 0.8522 (mtm110) cc_final: 0.7757 (mtm110) REVERT: F 326 LYS cc_start: 0.7676 (tttm) cc_final: 0.6473 (ttpp) REVERT: G 25 CYS cc_start: 0.7216 (m) cc_final: 0.6662 (m) REVERT: G 36 MET cc_start: 0.4480 (ttm) cc_final: 0.2733 (ttm) REVERT: G 127 ASP cc_start: 0.6594 (m-30) cc_final: 0.6290 (m-30) REVERT: G 138 PHE cc_start: 0.6735 (m-80) cc_final: 0.6254 (m-80) REVERT: G 212 ILE cc_start: 0.9344 (mt) cc_final: 0.9013 (mt) REVERT: G 217 LEU cc_start: 0.7982 (mt) cc_final: 0.7437 (mt) REVERT: H 21 TRP cc_start: 0.7358 (m100) cc_final: 0.6410 (m100) REVERT: H 28 HIS cc_start: 0.7007 (m-70) cc_final: 0.6638 (m170) REVERT: H 239 THR cc_start: 0.9147 (t) cc_final: 0.8844 (t) REVERT: H 257 VAL cc_start: 0.9145 (t) cc_final: 0.8888 (p) REVERT: I 36 MET cc_start: 0.4750 (ttm) cc_final: 0.2702 (ttm) REVERT: I 53 PHE cc_start: 0.7080 (m-80) cc_final: 0.6322 (m-80) REVERT: I 83 TYR cc_start: 0.5571 (m-10) cc_final: 0.5170 (m-10) REVERT: I 127 ASP cc_start: 0.6545 (m-30) cc_final: 0.6098 (m-30) REVERT: I 138 PHE cc_start: 0.6745 (m-80) cc_final: 0.5700 (m-80) REVERT: I 167 LEU cc_start: 0.8215 (tp) cc_final: 0.7870 (tp) REVERT: I 227 LEU cc_start: 0.9019 (mt) cc_final: 0.8327 (mp) REVERT: I 291 ILE cc_start: 0.8238 (mt) cc_final: 0.7868 (mt) REVERT: J 20 PHE cc_start: 0.8278 (t80) cc_final: 0.7974 (t80) REVERT: J 21 TRP cc_start: 0.7883 (m100) cc_final: 0.6779 (m100) REVERT: J 131 CYS cc_start: 0.4797 (m) cc_final: 0.4556 (m) REVERT: J 165 ILE cc_start: 0.7912 (pt) cc_final: 0.7401 (pt) REVERT: J 166 MET cc_start: 0.6461 (mmp) cc_final: 0.6260 (mmm) REVERT: J 323 MET cc_start: 0.8734 (mpp) cc_final: 0.8292 (mpp) REVERT: J 428 LEU cc_start: 0.8547 (tp) cc_final: 0.8192 (mm) REVERT: K 23 LEU cc_start: 0.8616 (tp) cc_final: 0.8370 (tp) REVERT: K 33 ASP cc_start: 0.6454 (p0) cc_final: 0.5868 (t0) REVERT: K 122 ILE cc_start: 0.8262 (mt) cc_final: 0.7943 (mt) REVERT: K 169 PHE cc_start: 0.6699 (m-80) cc_final: 0.6226 (m-80) REVERT: K 227 LEU cc_start: 0.9236 (mt) cc_final: 0.8479 (mp) REVERT: K 260 VAL cc_start: 0.8248 (t) cc_final: 0.7927 (t) REVERT: K 279 GLU cc_start: 0.8142 (mp0) cc_final: 0.7342 (mp0) REVERT: K 280 LYS cc_start: 0.7969 (mtmt) cc_final: 0.7743 (mmmt) REVERT: K 291 ILE cc_start: 0.8838 (mt) cc_final: 0.8340 (mm) REVERT: K 302 MET cc_start: 0.6214 (mpp) cc_final: 0.4245 (mpp) REVERT: K 322 ASP cc_start: 0.7441 (t70) cc_final: 0.6700 (m-30) REVERT: K 325 PRO cc_start: 0.8615 (Cg_exo) cc_final: 0.8176 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8973 (pt) cc_final: 0.8485 (tp) REVERT: K 378 LEU cc_start: 0.6585 (mt) cc_final: 0.6370 (mt) REVERT: L 21 TRP cc_start: 0.7533 (m100) cc_final: 0.6669 (m100) REVERT: L 103 TRP cc_start: 0.6768 (t-100) cc_final: 0.6000 (t-100) REVERT: L 120 ASP cc_start: 0.7245 (t70) cc_final: 0.6683 (t70) REVERT: L 269 MET cc_start: 0.5660 (ttt) cc_final: 0.5333 (tpp) REVERT: L 291 LEU cc_start: 0.8510 (mt) cc_final: 0.8024 (mt) REVERT: L 327 GLU cc_start: 0.6725 (tm-30) cc_final: 0.6217 (tm-30) REVERT: L 330 GLU cc_start: 0.7283 (tp30) cc_final: 0.6834 (tp30) REVERT: L 334 ASN cc_start: 0.8270 (m110) cc_final: 0.7594 (m110) REVERT: L 373 MET cc_start: 0.7843 (ptp) cc_final: 0.7530 (ptp) REVERT: L 395 PHE cc_start: 0.8417 (t80) cc_final: 0.8126 (t80) REVERT: M 21 TRP cc_start: 0.8000 (m100) cc_final: 0.7440 (m100) REVERT: M 23 LEU cc_start: 0.8409 (tp) cc_final: 0.7797 (tp) REVERT: M 101 ASN cc_start: 0.7336 (t0) cc_final: 0.7065 (t0) REVERT: M 118 VAL cc_start: 0.9076 (t) cc_final: 0.8830 (t) REVERT: M 231 ILE cc_start: 0.8902 (mt) cc_final: 0.8629 (mm) REVERT: M 275 VAL cc_start: 0.8731 (m) cc_final: 0.8275 (m) REVERT: M 286 LEU cc_start: 0.7978 (mt) cc_final: 0.7608 (mt) REVERT: M 291 ILE cc_start: 0.8522 (mt) cc_final: 0.8291 (mt) REVERT: M 335 ILE cc_start: 0.8275 (pt) cc_final: 0.7905 (tp) REVERT: M 398 MET cc_start: 0.7244 (ptt) cc_final: 0.6531 (ptt) REVERT: M 413 MET cc_start: 0.8490 (mmm) cc_final: 0.8192 (mmm) REVERT: N 19 LYS cc_start: 0.8525 (tptp) cc_final: 0.7991 (tptp) REVERT: N 21 TRP cc_start: 0.8740 (m100) cc_final: 0.8201 (m100) REVERT: N 132 LEU cc_start: 0.8522 (mm) cc_final: 0.8285 (mt) REVERT: N 163 ASP cc_start: 0.8881 (p0) cc_final: 0.8296 (p0) REVERT: N 171 VAL cc_start: 0.9047 (t) cc_final: 0.8790 (t) REVERT: N 213 CYS cc_start: 0.7883 (p) cc_final: 0.7574 (p) REVERT: N 259 MET cc_start: 0.7579 (mmm) cc_final: 0.7115 (mmp) REVERT: N 269 MET cc_start: 0.7881 (tpp) cc_final: 0.7442 (tpt) REVERT: N 315 VAL cc_start: 0.7418 (t) cc_final: 0.7206 (t) REVERT: N 398 MET cc_start: 0.7996 (ptm) cc_final: 0.7472 (mtm) REVERT: N 425 MET cc_start: 0.8477 (tpp) cc_final: 0.8249 (tpp) REVERT: O 21 TRP cc_start: 0.8637 (m100) cc_final: 0.8023 (m100) REVERT: O 23 LEU cc_start: 0.8342 (tp) cc_final: 0.7489 (tp) REVERT: O 76 ASP cc_start: 0.8653 (m-30) cc_final: 0.8306 (t0) REVERT: O 152 LEU cc_start: 0.8981 (tp) cc_final: 0.8766 (tp) REVERT: O 275 VAL cc_start: 0.9395 (m) cc_final: 0.9114 (m) REVERT: O 293 ASN cc_start: 0.7773 (m110) cc_final: 0.7435 (m110) REVERT: O 306 ASP cc_start: 0.7473 (t0) cc_final: 0.7130 (t70) REVERT: O 317 LEU cc_start: 0.7215 (mt) cc_final: 0.6583 (mt) REVERT: P 86 ILE cc_start: 0.9015 (tt) cc_final: 0.8616 (tt) REVERT: P 163 ASP cc_start: 0.8949 (p0) cc_final: 0.8593 (p0) REVERT: P 179 ASP cc_start: 0.8759 (m-30) cc_final: 0.8528 (m-30) REVERT: P 199 ASP cc_start: 0.6637 (t70) cc_final: 0.6214 (t70) REVERT: P 201 THR cc_start: 0.6933 (t) cc_final: 0.6407 (p) REVERT: P 254 LYS cc_start: 0.6410 (tttt) cc_final: 0.5926 (mttt) REVERT: P 259 MET cc_start: 0.7775 (mmm) cc_final: 0.7061 (mmm) REVERT: P 314 THR cc_start: 0.7843 (p) cc_final: 0.7215 (p) REVERT: P 326 LYS cc_start: 0.8515 (ttmt) cc_final: 0.8039 (tppt) REVERT: P 333 LEU cc_start: 0.8016 (tt) cc_final: 0.7738 (tt) REVERT: P 425 MET cc_start: 0.7899 (tpp) cc_final: 0.7552 (ttt) REVERT: Q 23 LEU cc_start: 0.8642 (tp) cc_final: 0.8098 (tp) REVERT: Q 25 CYS cc_start: 0.8132 (m) cc_final: 0.7757 (m) REVERT: Q 214 ARG cc_start: 0.5787 (ptp-170) cc_final: 0.5096 (ptp-110) REVERT: Q 425 MET cc_start: 0.8736 (ppp) cc_final: 0.8314 (ppp) REVERT: R 115 VAL cc_start: 0.9412 (p) cc_final: 0.9134 (p) REVERT: R 165 ILE cc_start: 0.8485 (mt) cc_final: 0.8098 (mt) REVERT: R 179 ASP cc_start: 0.8806 (m-30) cc_final: 0.8194 (m-30) REVERT: R 259 MET cc_start: 0.7477 (mmm) cc_final: 0.7026 (mmt) REVERT: R 332 MET cc_start: 0.5728 (tmm) cc_final: 0.5280 (tmm) outliers start: 15 outliers final: 4 residues processed: 1589 average time/residue: 0.5887 time to fit residues: 1566.2870 Evaluate side-chains 1151 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1146 time to evaluate : 5.180 ------------------------------------------------------------------------------- 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: 0.9990 chunk 517 optimal weight: 40.0000 chunk 356 optimal weight: 4.9990 chunk 76 optimal weight: 2.9990 chunk 328 optimal weight: 50.0000 chunk 461 optimal weight: 10.0000 chunk 690 optimal weight: 40.0000 chunk 730 optimal weight: 30.0000 chunk 360 optimal weight: 7.9990 chunk 654 optimal weight: 30.0000 chunk 196 optimal weight: 40.0000 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 293 ASN ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN B 309 HIS C 8 HIS ** C 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 258 ASN ** C 293 ASN ** 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 293 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 281 GLN J 349 ASN K 61 HIS ** K 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 309 HIS ** K 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 393 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 HIS ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 226 ASN ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 228 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: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.7120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 62262 Z= 0.185 Angle : 0.628 10.284 84582 Z= 0.323 Chirality : 0.045 0.271 9216 Planarity : 0.005 0.135 11043 Dihedral : 11.646 176.368 8595 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 20.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.12 % Allowed : 2.48 % Favored : 97.40 % 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: 0.29 (0.08), residues: 3438 sheet: 0.93 (0.15), residues: 1134 loop : 0.11 (0.12), residues: 3060 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP F 346 HIS 0.009 0.001 HIS C 8 PHE 0.032 0.002 PHE J 92 TYR 0.022 0.002 TYR F 435 ARG 0.018 0.001 ARG K 422 *********************** 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 1656 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 1648 time to evaluate : 5.239 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: A 21 TRP cc_start: 0.9026 (m100) cc_final: 0.8232 (m100) REVERT: A 33 ASP cc_start: 0.6903 (p0) cc_final: 0.6002 (t0) REVERT: A 53 PHE cc_start: 0.8313 (m-80) cc_final: 0.7084 (m-80) REVERT: A 75 ILE cc_start: 0.9440 (mm) cc_final: 0.8887 (tt) REVERT: A 217 LEU cc_start: 0.8568 (mm) cc_final: 0.8239 (mm) REVERT: A 291 ILE cc_start: 0.9312 (mt) cc_final: 0.8109 (tp) REVERT: A 300 ASN cc_start: 0.8892 (p0) cc_final: 0.8642 (p0) REVERT: A 317 LEU cc_start: 0.8294 (mt) cc_final: 0.7889 (mt) REVERT: A 352 LYS cc_start: 0.8525 (tptt) cc_final: 0.8155 (tptp) REVERT: A 408 TYR cc_start: 0.5718 (m-80) cc_final: 0.4795 (m-80) REVERT: B 67 LEU cc_start: 0.8667 (mt) cc_final: 0.8386 (mt) REVERT: B 129 CYS cc_start: 0.8247 (p) cc_final: 0.8018 (p) REVERT: B 139 HIS cc_start: 0.8270 (p90) cc_final: 0.7348 (p-80) REVERT: B 165 ILE cc_start: 0.8334 (mt) cc_final: 0.7774 (mt) REVERT: B 199 ASP cc_start: 0.8987 (m-30) cc_final: 0.8065 (m-30) REVERT: B 215 ARG cc_start: 0.7315 (tmm160) cc_final: 0.6702 (ttp80) REVERT: B 239 THR cc_start: 0.9255 (t) cc_final: 0.9029 (m) REVERT: B 268 PHE cc_start: 0.6904 (m-80) cc_final: 0.6405 (m-80) REVERT: B 356 CYS cc_start: 0.3154 (p) cc_final: 0.2520 (p) REVERT: B 422 GLU cc_start: 0.8991 (pt0) cc_final: 0.8543 (pp20) REVERT: B 432 TYR cc_start: 0.6921 (m-10) cc_final: 0.6092 (m-80) REVERT: C 21 TRP cc_start: 0.7631 (m100) cc_final: 0.6847 (m100) REVERT: C 60 LYS cc_start: 0.8058 (mmtt) cc_final: 0.7453 (tttt) REVERT: C 75 ILE cc_start: 0.8938 (mm) cc_final: 0.7475 (tt) REVERT: C 196 GLU cc_start: 0.7864 (mp0) cc_final: 0.7650 (mp0) REVERT: C 230 LEU cc_start: 0.8862 (tp) cc_final: 0.8302 (tp) REVERT: C 295 CYS cc_start: 0.9149 (t) cc_final: 0.8793 (t) REVERT: D 75 MET cc_start: 0.7641 (mmm) cc_final: 0.7257 (tpt) REVERT: D 108 TYR cc_start: 0.4890 (t80) cc_final: 0.4352 (t80) REVERT: D 154 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8540 (mm) REVERT: D 163 ASP cc_start: 0.7755 (p0) cc_final: 0.7092 (p0) REVERT: D 165 ILE cc_start: 0.8025 (mt) cc_final: 0.7498 (mt) REVERT: D 302 MET cc_start: 0.7207 (mtm) cc_final: 0.6909 (mtt) REVERT: D 333 LEU cc_start: 0.7912 (mt) cc_final: 0.7656 (mt) REVERT: D 405 LEU cc_start: 0.8570 (mt) cc_final: 0.8350 (mt) REVERT: E 21 TRP cc_start: 0.8587 (m100) cc_final: 0.8203 (m100) REVERT: E 53 PHE cc_start: 0.7512 (m-80) cc_final: 0.6705 (m-80) REVERT: E 75 ILE cc_start: 0.9072 (mm) cc_final: 0.8756 (mm) REVERT: E 177 VAL cc_start: 0.8369 (t) cc_final: 0.8108 (p) REVERT: E 228 ASN cc_start: 0.8440 (m-40) cc_final: 0.7540 (p0) REVERT: E 262 TYR cc_start: 0.7358 (m-10) cc_final: 0.7037 (m-80) REVERT: E 291 ILE cc_start: 0.9255 (mt) cc_final: 0.8010 (tp) REVERT: E 300 ASN cc_start: 0.7900 (p0) cc_final: 0.7443 (p0) REVERT: E 352 LYS cc_start: 0.9177 (tptt) cc_final: 0.8912 (tptp) REVERT: F 66 ILE cc_start: 0.8474 (mm) cc_final: 0.8258 (mm) REVERT: F 139 HIS cc_start: 0.7941 (p90) cc_final: 0.6378 (p90) REVERT: F 163 ASP cc_start: 0.7235 (p0) cc_final: 0.6279 (p0) REVERT: F 212 ILE cc_start: 0.9198 (mt) cc_final: 0.8688 (tp) REVERT: G 16 ILE cc_start: 0.8249 (pt) cc_final: 0.7708 (pt) REVERT: G 25 CYS cc_start: 0.6889 (m) cc_final: 0.6280 (m) REVERT: G 53 PHE cc_start: 0.7367 (m-80) cc_final: 0.7001 (m-80) REVERT: G 132 LEU cc_start: 0.5566 (tt) cc_final: 0.5259 (tt) REVERT: G 154 MET cc_start: 0.6557 (ttt) cc_final: 0.6309 (ttt) REVERT: G 269 LEU cc_start: 0.7277 (mt) cc_final: 0.6883 (mt) REVERT: G 313 MET cc_start: 0.5025 (mpp) cc_final: 0.4429 (mmm) REVERT: G 431 ASP cc_start: 0.7501 (m-30) cc_final: 0.6687 (m-30) REVERT: H 21 TRP cc_start: 0.7449 (m100) cc_final: 0.6209 (m100) REVERT: H 53 TYR cc_start: 0.5446 (m-10) cc_final: 0.4538 (m-80) REVERT: H 132 LEU cc_start: 0.8923 (tp) cc_final: 0.8479 (tp) REVERT: H 138 THR cc_start: 0.6600 (p) cc_final: 0.6356 (p) REVERT: H 165 ILE cc_start: 0.7805 (pt) cc_final: 0.7535 (pt) REVERT: H 213 CYS cc_start: 0.6564 (p) cc_final: 0.6234 (p) REVERT: H 257 VAL cc_start: 0.9182 (t) cc_final: 0.8879 (p) REVERT: H 288 VAL cc_start: 0.8843 (t) cc_final: 0.8356 (t) REVERT: I 53 PHE cc_start: 0.6840 (m-80) cc_final: 0.6153 (m-80) REVERT: I 127 ASP cc_start: 0.6211 (m-30) cc_final: 0.5553 (m-30) REVERT: I 138 PHE cc_start: 0.5835 (m-80) cc_final: 0.5236 (m-80) REVERT: I 167 LEU cc_start: 0.8121 (tp) cc_final: 0.7791 (tp) REVERT: I 209 ILE cc_start: 0.9143 (mm) cc_final: 0.8906 (mm) REVERT: I 227 LEU cc_start: 0.8950 (mt) cc_final: 0.8422 (mt) REVERT: I 271 THR cc_start: 0.5673 (m) cc_final: 0.4215 (m) REVERT: I 286 LEU cc_start: 0.7710 (mt) cc_final: 0.7149 (mt) REVERT: I 376 CYS cc_start: 0.7428 (t) cc_final: 0.7210 (t) REVERT: I 377 MET cc_start: 0.7513 (tmm) cc_final: 0.6452 (tmm) REVERT: J 16 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9014 (tp) REVERT: J 19 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8839 (mmmt) REVERT: J 21 TRP cc_start: 0.7460 (m100) cc_final: 0.7137 (m100) REVERT: J 53 TYR cc_start: 0.6599 (m-80) cc_final: 0.6397 (m-80) REVERT: J 55 GLU cc_start: 0.5183 (tp30) cc_final: 0.4761 (tp30) REVERT: J 92 PHE cc_start: 0.7856 (m-80) cc_final: 0.7592 (m-80) REVERT: J 103 TRP cc_start: 0.7146 (t-100) cc_final: 0.6442 (t-100) REVERT: J 132 LEU cc_start: 0.8424 (mm) cc_final: 0.8166 (mm) REVERT: J 138 THR cc_start: 0.7011 (p) cc_final: 0.5887 (p) REVERT: J 165 ILE cc_start: 0.7466 (pt) cc_final: 0.6925 (pt) REVERT: J 169 PHE cc_start: 0.6706 (m-80) cc_final: 0.6304 (m-80) REVERT: J 333 LEU cc_start: 0.8346 (mt) cc_final: 0.8023 (mt) REVERT: J 349 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8248 (t0) REVERT: J 428 LEU cc_start: 0.8418 (tp) cc_final: 0.8134 (mm) REVERT: K 16 ILE cc_start: 0.8415 (pt) cc_final: 0.8197 (pt) REVERT: K 23 LEU cc_start: 0.8620 (tp) cc_final: 0.8379 (tp) REVERT: K 33 ASP cc_start: 0.5955 (p0) cc_final: 0.5610 (t0) REVERT: K 120 ASP cc_start: 0.7367 (m-30) cc_final: 0.4771 (t70) REVERT: K 122 ILE cc_start: 0.7872 (mt) cc_final: 0.7647 (mt) REVERT: K 169 PHE cc_start: 0.6172 (m-80) cc_final: 0.5938 (m-80) REVERT: K 227 LEU cc_start: 0.9206 (mt) cc_final: 0.8954 (mt) REVERT: K 279 GLU cc_start: 0.8208 (mp0) cc_final: 0.7467 (mp0) REVERT: K 280 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7678 (mmmt) REVERT: K 288 VAL cc_start: 0.8949 (m) cc_final: 0.8543 (p) REVERT: K 291 ILE cc_start: 0.8588 (mt) cc_final: 0.8245 (mt) REVERT: K 322 ASP cc_start: 0.7084 (t70) cc_final: 0.6731 (m-30) REVERT: K 325 PRO cc_start: 0.8553 (Cg_exo) cc_final: 0.8218 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8855 (pt) cc_final: 0.8146 (tp) REVERT: K 425 MET cc_start: 0.6386 (ttt) cc_final: 0.6003 (tpp) REVERT: L 21 TRP cc_start: 0.7437 (m100) cc_final: 0.6351 (m100) REVERT: L 86 ILE cc_start: 0.8470 (mt) cc_final: 0.7831 (pt) REVERT: L 154 ILE cc_start: 0.8641 (mt) cc_final: 0.8370 (mt) REVERT: L 191 VAL cc_start: 0.9070 (t) cc_final: 0.8757 (t) REVERT: L 288 VAL cc_start: 0.8647 (t) cc_final: 0.8007 (t) REVERT: L 327 GLU cc_start: 0.6425 (tm-30) cc_final: 0.6147 (tm-30) REVERT: L 330 GLU cc_start: 0.7286 (tp30) cc_final: 0.6925 (tp30) REVERT: L 334 ASN cc_start: 0.8210 (m110) cc_final: 0.7911 (m110) REVERT: L 338 LYS cc_start: 0.7686 (mtmm) cc_final: 0.7249 (ptmt) REVERT: L 425 MET cc_start: 0.7394 (ttt) cc_final: 0.7103 (ttt) REVERT: L 428 LEU cc_start: 0.7685 (pp) cc_final: 0.7480 (pp) REVERT: M 21 TRP cc_start: 0.7985 (m100) cc_final: 0.7530 (m100) REVERT: M 23 LEU cc_start: 0.8188 (tp) cc_final: 0.7611 (tp) REVERT: M 101 ASN cc_start: 0.7429 (t0) cc_final: 0.7064 (t0) REVERT: M 123 ARG cc_start: 0.7449 (mmm-85) cc_final: 0.7196 (mmm-85) REVERT: M 231 ILE cc_start: 0.8564 (mt) cc_final: 0.8034 (mm) REVERT: M 317 LEU cc_start: 0.7096 (mt) cc_final: 0.6577 (mm) REVERT: M 335 ILE cc_start: 0.8248 (pt) cc_final: 0.7861 (tp) REVERT: M 398 MET cc_start: 0.7033 (ptt) cc_final: 0.6401 (ptt) REVERT: M 413 MET cc_start: 0.8896 (mmm) cc_final: 0.8527 (mmm) REVERT: M 425 MET cc_start: 0.7971 (ptm) cc_final: 0.7569 (ptm) REVERT: M 430 LYS cc_start: 0.8153 (mmpt) cc_final: 0.7812 (mmmt) REVERT: N 132 LEU cc_start: 0.8292 (mm) cc_final: 0.8014 (mt) REVERT: N 163 ASP cc_start: 0.8591 (p0) cc_final: 0.7812 (p0) REVERT: N 213 CYS cc_start: 0.7642 (p) cc_final: 0.7173 (p) REVERT: N 229 HIS cc_start: 0.7319 (t70) cc_final: 0.7077 (t-90) REVERT: N 248 LEU cc_start: 0.7927 (mt) cc_final: 0.7640 (mt) REVERT: N 269 MET cc_start: 0.7827 (tpp) cc_final: 0.7579 (tpt) REVERT: N 315 VAL cc_start: 0.6950 (t) cc_final: 0.6550 (t) REVERT: N 355 VAL cc_start: 0.5751 (t) cc_final: 0.5337 (t) REVERT: N 391 ILE cc_start: 0.8893 (mm) cc_final: 0.8667 (mm) REVERT: N 405 LEU cc_start: 0.7954 (tp) cc_final: 0.7614 (tp) REVERT: N 413 MET cc_start: 0.6133 (mmt) cc_final: 0.5523 (mmp) REVERT: N 425 MET cc_start: 0.7943 (ttt) cc_final: 0.7736 (tpp) REVERT: N 432 TYR cc_start: 0.7354 (m-10) cc_final: 0.6900 (m-10) REVERT: O 21 TRP cc_start: 0.8530 (m100) cc_final: 0.7982 (m100) REVERT: O 23 LEU cc_start: 0.8017 (tp) cc_final: 0.7587 (tp) REVERT: O 74 VAL cc_start: 0.7906 (p) cc_final: 0.6935 (m) REVERT: O 75 ILE cc_start: 0.9521 (mm) cc_final: 0.9314 (mm) REVERT: O 76 ASP cc_start: 0.7758 (m-30) cc_final: 0.7382 (t0) REVERT: O 152 LEU cc_start: 0.9018 (tp) cc_final: 0.8665 (tp) REVERT: O 293 ASN cc_start: 0.7631 (m110) cc_final: 0.7429 (m110) REVERT: O 425 MET cc_start: 0.8405 (ppp) cc_final: 0.7834 (ppp) REVERT: P 67 LEU cc_start: 0.8710 (mm) cc_final: 0.8463 (mm) REVERT: P 86 ILE cc_start: 0.8908 (tt) cc_final: 0.8513 (tt) REVERT: P 163 ASP cc_start: 0.8633 (p0) cc_final: 0.7974 (p0) REVERT: P 166 MET cc_start: 0.6573 (ptt) cc_final: 0.4457 (ptt) REVERT: P 193 GLN cc_start: 0.8161 (mm110) cc_final: 0.7735 (mm110) REVERT: P 259 MET cc_start: 0.7519 (mmm) cc_final: 0.6907 (mmt) REVERT: P 292 THR cc_start: 0.8043 (p) cc_final: 0.7315 (p) REVERT: P 333 LEU cc_start: 0.7761 (tt) cc_final: 0.7387 (mt) REVERT: P 334 ASN cc_start: 0.6956 (m110) cc_final: 0.6540 (m-40) REVERT: Q 25 CYS cc_start: 0.7544 (m) cc_final: 0.7331 (m) REVERT: Q 76 ASP cc_start: 0.8137 (m-30) cc_final: 0.7769 (t0) REVERT: Q 230 LEU cc_start: 0.8535 (tp) cc_final: 0.8263 (tp) REVERT: Q 414 GLU cc_start: 0.7929 (tm-30) cc_final: 0.7703 (tm-30) REVERT: Q 429 GLU cc_start: 0.6695 (mm-30) cc_final: 0.6364 (mm-30) REVERT: Q 431 ASP cc_start: 0.6375 (m-30) cc_final: 0.5886 (m-30) REVERT: R 115 VAL cc_start: 0.9201 (p) cc_final: 0.8720 (p) REVERT: R 259 MET cc_start: 0.7303 (mmm) cc_final: 0.6765 (mmm) REVERT: R 266 HIS cc_start: 0.8028 (p-80) cc_final: 0.7729 (p-80) REVERT: R 269 MET cc_start: 0.4648 (tpt) cc_final: 0.4257 (tpt) REVERT: R 276 THR cc_start: 0.7359 (p) cc_final: 0.6854 (p) REVERT: R 398 MET cc_start: 0.7921 (ptt) cc_final: 0.6706 (ptt) outliers start: 8 outliers final: 3 residues processed: 1654 average time/residue: 0.5839 time to fit residues: 1610.1377 Evaluate side-chains 1194 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1188 time to evaluate : 5.157 ------------------------------------------------------------------------------- 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: 10.0000 chunk 414 optimal weight: 50.0000 chunk 10 optimal weight: 20.0000 chunk 544 optimal weight: 50.0000 chunk 301 optimal weight: 50.0000 chunk 623 optimal weight: 0.0050 chunk 505 optimal weight: 8.9990 chunk 0 optimal weight: 80.0000 chunk 373 optimal weight: 30.0000 chunk 655 optimal weight: 20.0000 chunk 184 optimal weight: 8.9990 overall best weight: 9.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN A 266 HIS ** 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** C 101 ASN C 128 GLN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 339 ASN ** G 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 186 ASN J 229 HIS ** J 249 ASN ** 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 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 301 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** ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 HIS ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN P 247 GLN ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 283 HIS ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.7614 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= 0.218 Angle : 0.637 9.304 84582 Z= 0.332 Chirality : 0.045 0.250 9216 Planarity : 0.005 0.068 11043 Dihedral : 11.391 179.920 8595 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.05 % Allowed : 2.17 % Favored : 97.78 % 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: 0.36 (0.10), residues: 7632 helix: 0.29 (0.08), residues: 3492 sheet: 0.93 (0.16), residues: 1125 loop : 0.13 (0.12), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP R 21 HIS 0.010 0.001 HIS M 61 PHE 0.032 0.002 PHE J 262 TYR 0.031 0.002 TYR N 161 ARG 0.010 0.001 ARG R 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 1536 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1533 time to evaluate : 5.310 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: A 21 TRP cc_start: 0.8823 (m100) cc_final: 0.8163 (m100) REVERT: A 53 PHE cc_start: 0.8224 (m-80) cc_final: 0.6880 (m-80) REVERT: A 217 LEU cc_start: 0.8599 (mm) cc_final: 0.8349 (mm) REVERT: A 291 ILE cc_start: 0.9321 (mt) cc_final: 0.8235 (tp) REVERT: A 297 GLU cc_start: 0.8470 (pt0) cc_final: 0.7991 (pt0) REVERT: A 300 ASN cc_start: 0.8900 (p0) cc_final: 0.8624 (p0) REVERT: A 317 LEU cc_start: 0.8165 (mt) cc_final: 0.7732 (mt) REVERT: A 335 ILE cc_start: 0.8036 (tp) cc_final: 0.7809 (tp) REVERT: A 352 LYS cc_start: 0.9000 (tptt) cc_final: 0.8439 (tptp) REVERT: A 408 TYR cc_start: 0.5866 (m-80) cc_final: 0.5057 (m-10) REVERT: B 90 ASP cc_start: 0.6362 (t0) cc_final: 0.6087 (t0) REVERT: B 91 ASN cc_start: 0.7983 (m110) cc_final: 0.7733 (m110) REVERT: B 119 LEU cc_start: 0.8187 (mt) cc_final: 0.7822 (mt) REVERT: B 139 HIS cc_start: 0.8310 (p90) cc_final: 0.7238 (p-80) REVERT: B 165 ILE cc_start: 0.8366 (mt) cc_final: 0.8075 (mt) REVERT: B 215 ARG cc_start: 0.7290 (tmm160) cc_final: 0.6846 (ttp80) REVERT: B 262 PHE cc_start: 0.8421 (t80) cc_final: 0.8106 (t80) REVERT: B 268 PHE cc_start: 0.6726 (m-80) cc_final: 0.6490 (m-80) REVERT: B 302 MET cc_start: 0.7403 (mpp) cc_final: 0.7133 (mpp) REVERT: B 422 GLU cc_start: 0.8935 (pt0) cc_final: 0.8543 (pp20) REVERT: B 432 TYR cc_start: 0.6892 (m-10) cc_final: 0.6218 (m-80) REVERT: C 21 TRP cc_start: 0.7735 (m100) cc_final: 0.7406 (m100) REVERT: C 60 LYS cc_start: 0.8212 (mmtt) cc_final: 0.7567 (tttt) REVERT: C 75 ILE cc_start: 0.8726 (mm) cc_final: 0.7155 (tt) REVERT: C 230 LEU cc_start: 0.8658 (tp) cc_final: 0.8441 (tp) REVERT: C 295 CYS cc_start: 0.8889 (t) cc_final: 0.8539 (t) REVERT: C 317 LEU cc_start: 0.7808 (mt) cc_final: 0.7563 (mt) REVERT: C 425 MET cc_start: 0.8355 (ppp) cc_final: 0.8133 (ppp) REVERT: D 75 MET cc_start: 0.7625 (mmm) cc_final: 0.7132 (mmm) REVERT: D 123 ARG cc_start: 0.8024 (mtm-85) cc_final: 0.7738 (ptp-110) REVERT: D 132 LEU cc_start: 0.8743 (mm) cc_final: 0.8516 (mm) REVERT: D 163 ASP cc_start: 0.7986 (p0) cc_final: 0.7410 (p0) REVERT: D 165 ILE cc_start: 0.7966 (mt) cc_final: 0.7280 (mt) REVERT: D 292 THR cc_start: 0.8057 (t) cc_final: 0.6841 (t) REVERT: D 302 MET cc_start: 0.7106 (mtm) cc_final: 0.6733 (mtt) REVERT: D 333 LEU cc_start: 0.7925 (mt) cc_final: 0.7651 (mt) REVERT: D 369 ARG cc_start: 0.7911 (tmm-80) cc_final: 0.7632 (tmm-80) REVERT: D 405 LEU cc_start: 0.8684 (mt) cc_final: 0.8241 (mt) REVERT: D 416 MET cc_start: 0.5477 (mmp) cc_final: 0.5275 (mmm) REVERT: E 21 TRP cc_start: 0.8586 (m100) cc_final: 0.8372 (m100) REVERT: E 23 LEU cc_start: 0.8631 (tp) cc_final: 0.8411 (tp) REVERT: E 36 MET cc_start: 0.3193 (tmm) cc_final: 0.2700 (tmm) REVERT: E 61 HIS cc_start: 0.6524 (m-70) cc_final: 0.5711 (m-70) REVERT: E 228 ASN cc_start: 0.8356 (m-40) cc_final: 0.7383 (p0) REVERT: E 291 ILE cc_start: 0.9143 (mt) cc_final: 0.8154 (tt) REVERT: E 344 VAL cc_start: 0.7917 (m) cc_final: 0.6804 (p) REVERT: F 116 ASP cc_start: 0.7898 (m-30) cc_final: 0.7336 (m-30) REVERT: F 139 HIS cc_start: 0.7482 (p90) cc_final: 0.6105 (p90) REVERT: F 166 MET cc_start: 0.8283 (mmp) cc_final: 0.7707 (mmm) REVERT: F 243 ARG cc_start: 0.8257 (mtm110) cc_final: 0.7682 (mtm110) REVERT: F 326 LYS cc_start: 0.8018 (ttpt) cc_final: 0.7484 (ttpp) REVERT: G 16 ILE cc_start: 0.8152 (pt) cc_final: 0.7913 (pt) REVERT: G 75 ILE cc_start: 0.9003 (mm) cc_final: 0.8046 (tt) REVERT: G 214 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6924 (ptp-110) REVERT: G 269 LEU cc_start: 0.7066 (mt) cc_final: 0.6693 (mt) REVERT: H 21 TRP cc_start: 0.7558 (m100) cc_final: 0.6544 (m100) REVERT: H 66 ILE cc_start: 0.8596 (mm) cc_final: 0.8341 (mm) REVERT: H 132 LEU cc_start: 0.9014 (tp) cc_final: 0.8500 (tp) REVERT: H 138 THR cc_start: 0.6324 (p) cc_final: 0.5961 (p) REVERT: H 165 ILE cc_start: 0.7713 (pt) cc_final: 0.7234 (pt) REVERT: H 257 VAL cc_start: 0.9290 (t) cc_final: 0.8980 (p) REVERT: H 301 MET cc_start: 0.7679 (ppp) cc_final: 0.6472 (ppp) REVERT: I 53 PHE cc_start: 0.6901 (m-80) cc_final: 0.6432 (m-80) REVERT: I 127 ASP cc_start: 0.6735 (m-30) cc_final: 0.6089 (m-30) REVERT: I 138 PHE cc_start: 0.6100 (m-80) cc_final: 0.5640 (m-80) REVERT: I 167 LEU cc_start: 0.7972 (tp) cc_final: 0.7758 (tp) REVERT: I 217 LEU cc_start: 0.7182 (mm) cc_final: 0.6702 (mm) REVERT: I 271 THR cc_start: 0.6020 (m) cc_final: 0.4543 (m) REVERT: I 286 LEU cc_start: 0.7353 (mt) cc_final: 0.6049 (mt) REVERT: I 377 MET cc_start: 0.7366 (tmm) cc_final: 0.6437 (tmm) REVERT: J 21 TRP cc_start: 0.7541 (m100) cc_final: 0.7210 (m100) REVERT: J 60 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8712 (mmmt) REVERT: J 103 TRP cc_start: 0.7108 (t-100) cc_final: 0.6698 (t-100) REVERT: J 132 LEU cc_start: 0.8451 (mm) cc_final: 0.8200 (mm) REVERT: J 165 ILE cc_start: 0.7516 (pt) cc_final: 0.7090 (pt) REVERT: J 169 PHE cc_start: 0.6900 (m-80) cc_final: 0.6043 (m-80) REVERT: J 327 GLU cc_start: 0.8337 (pt0) cc_final: 0.8113 (pt0) REVERT: J 356 CYS cc_start: 0.0356 (t) cc_final: 0.0044 (t) REVERT: J 420 GLU cc_start: 0.6550 (tp30) cc_final: 0.6336 (mt-10) REVERT: J 428 LEU cc_start: 0.8527 (tp) cc_final: 0.8140 (mm) REVERT: K 23 LEU cc_start: 0.8659 (tp) cc_final: 0.8249 (tp) REVERT: K 33 ASP cc_start: 0.5995 (p0) cc_final: 0.5670 (t0) REVERT: K 120 ASP cc_start: 0.7486 (m-30) cc_final: 0.4798 (t70) REVERT: K 132 LEU cc_start: 0.7717 (tp) cc_final: 0.7403 (tp) REVERT: K 169 PHE cc_start: 0.6405 (m-80) cc_final: 0.6148 (m-80) REVERT: K 279 GLU cc_start: 0.8296 (mp0) cc_final: 0.7524 (mp0) REVERT: K 288 VAL cc_start: 0.9040 (m) cc_final: 0.8582 (p) REVERT: K 291 ILE cc_start: 0.8725 (mt) cc_final: 0.8210 (mm) REVERT: K 325 PRO cc_start: 0.8686 (Cg_exo) cc_final: 0.8340 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8899 (pt) cc_final: 0.8236 (tp) REVERT: K 352 LYS cc_start: 0.8434 (tptt) cc_final: 0.7931 (tppt) REVERT: L 21 TRP cc_start: 0.7600 (m100) cc_final: 0.6210 (m100) REVERT: L 120 ASP cc_start: 0.7294 (t70) cc_final: 0.6848 (t70) REVERT: L 239 THR cc_start: 0.9227 (m) cc_final: 0.8887 (t) REVERT: L 330 GLU cc_start: 0.7150 (tp30) cc_final: 0.6930 (tp30) REVERT: L 334 ASN cc_start: 0.8288 (m110) cc_final: 0.7821 (m110) REVERT: L 395 PHE cc_start: 0.8107 (t80) cc_final: 0.7858 (t80) REVERT: L 425 MET cc_start: 0.7498 (ttt) cc_final: 0.7191 (ttt) REVERT: M 16 ILE cc_start: 0.8816 (mt) cc_final: 0.8605 (mt) REVERT: M 21 TRP cc_start: 0.8397 (m100) cc_final: 0.7541 (m100) REVERT: M 23 LEU cc_start: 0.8208 (tp) cc_final: 0.7704 (tp) REVERT: M 101 ASN cc_start: 0.7516 (t0) cc_final: 0.7205 (t0) REVERT: M 231 ILE cc_start: 0.8580 (mt) cc_final: 0.8143 (mm) REVERT: M 291 ILE cc_start: 0.8041 (mt) cc_final: 0.7662 (mt) REVERT: M 335 ILE cc_start: 0.8502 (pt) cc_final: 0.7895 (tp) REVERT: M 413 MET cc_start: 0.8910 (mmm) cc_final: 0.8543 (mmm) REVERT: N 163 ASP cc_start: 0.8660 (p0) cc_final: 0.7760 (p0) REVERT: N 171 VAL cc_start: 0.8930 (t) cc_final: 0.8625 (t) REVERT: N 248 LEU cc_start: 0.8380 (mt) cc_final: 0.8007 (mt) REVERT: N 259 MET cc_start: 0.7840 (mmt) cc_final: 0.6556 (mmt) REVERT: N 268 PHE cc_start: 0.7675 (m-10) cc_final: 0.7203 (m-80) REVERT: N 288 VAL cc_start: 0.9004 (t) cc_final: 0.8780 (t) REVERT: N 355 VAL cc_start: 0.6508 (t) cc_final: 0.6038 (t) REVERT: N 384 ILE cc_start: 0.8599 (mp) cc_final: 0.8355 (mp) REVERT: N 413 MET cc_start: 0.6255 (mmt) cc_final: 0.5856 (mmp) REVERT: N 425 MET cc_start: 0.7975 (ttt) cc_final: 0.7670 (tpp) REVERT: O 21 TRP cc_start: 0.8731 (m100) cc_final: 0.8162 (m100) REVERT: O 23 LEU cc_start: 0.8343 (tp) cc_final: 0.7852 (tp) REVERT: O 54 SER cc_start: 0.4140 (t) cc_final: 0.3566 (t) REVERT: O 66 VAL cc_start: 0.7683 (t) cc_final: 0.7394 (t) REVERT: O 152 LEU cc_start: 0.9119 (tp) cc_final: 0.8771 (tp) REVERT: O 255 PHE cc_start: 0.6439 (m-10) cc_final: 0.5969 (m-10) REVERT: O 275 VAL cc_start: 0.9029 (m) cc_final: 0.8587 (m) REVERT: O 293 ASN cc_start: 0.7828 (m110) cc_final: 0.7622 (m110) REVERT: O 373 ARG cc_start: 0.8793 (ptp90) cc_final: 0.8232 (mtp180) REVERT: O 413 MET cc_start: 0.8400 (mmm) cc_final: 0.8086 (mmp) REVERT: P 86 ILE cc_start: 0.9024 (tt) cc_final: 0.8802 (tp) REVERT: P 163 ASP cc_start: 0.8822 (p0) cc_final: 0.8525 (p0) REVERT: P 166 MET cc_start: 0.4990 (ptt) cc_final: 0.4649 (ptt) REVERT: P 249 ASN cc_start: 0.8629 (m110) cc_final: 0.8242 (p0) REVERT: P 259 MET cc_start: 0.7329 (mmm) cc_final: 0.6967 (mmt) REVERT: P 262 PHE cc_start: 0.7748 (m-80) cc_final: 0.7152 (m-80) REVERT: P 292 THR cc_start: 0.7917 (p) cc_final: 0.7230 (p) REVERT: P 333 LEU cc_start: 0.7605 (tt) cc_final: 0.7301 (tp) REVERT: P 425 MET cc_start: 0.7952 (tpp) cc_final: 0.7024 (tpp) REVERT: Q 25 CYS cc_start: 0.7652 (m) cc_final: 0.7211 (m) REVERT: Q 152 LEU cc_start: 0.9133 (tp) cc_final: 0.8759 (tp) REVERT: Q 214 ARG cc_start: 0.5886 (ptp-170) cc_final: 0.5685 (ptp-110) REVERT: Q 317 LEU cc_start: 0.7118 (mt) cc_final: 0.6543 (mm) REVERT: Q 398 MET cc_start: 0.7635 (mtp) cc_final: 0.6308 (mmp) REVERT: Q 431 ASP cc_start: 0.6540 (m-30) cc_final: 0.5647 (m-30) REVERT: R 115 VAL cc_start: 0.9209 (p) cc_final: 0.8839 (p) REVERT: R 259 MET cc_start: 0.7304 (mmm) cc_final: 0.6716 (mmm) REVERT: R 269 MET cc_start: 0.4645 (tpt) cc_final: 0.4286 (tpt) outliers start: 3 outliers final: 1 residues processed: 1536 average time/residue: 0.5856 time to fit residues: 1511.6812 Evaluate side-chains 1122 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1121 time to evaluate : 5.178 ------------------------------------------------------------------------------- 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: 6.9990 chunk 658 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 chunk 429 optimal weight: 50.0000 chunk 180 optimal weight: 10.0000 chunk 731 optimal weight: 20.0000 chunk 607 optimal weight: 7.9990 chunk 338 optimal weight: 0.0470 chunk 60 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 384 optimal weight: 40.0000 overall best weight: 6.4088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 136 GLN C 128 GLN C 133 GLN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 300 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 197 ASN ** 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** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 HIS ** H 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN J 247 GLN ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 266 HIS ** N 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 266 HIS P 282 GLN Q 197 HIS Q 283 HIS ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.7975 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= 0.184 Angle : 0.611 9.302 84582 Z= 0.315 Chirality : 0.045 0.222 9216 Planarity : 0.005 0.060 11043 Dihedral : 10.960 177.118 8595 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 20.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.03 % Allowed : 1.82 % Favored : 98.15 % 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: 0.45 (0.10), residues: 7632 helix: 0.39 (0.09), residues: 3528 sheet: 0.85 (0.15), residues: 1188 loop : 0.18 (0.13), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP R 21 HIS 0.008 0.001 HIS Q 283 PHE 0.025 0.001 PHE J 92 TYR 0.030 0.002 TYR N 161 ARG 0.012 0.001 ARG F 278 *********************** 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 1542 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1540 time to evaluate : 5.164 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: A 21 TRP cc_start: 0.8755 (m100) cc_final: 0.8087 (m100) REVERT: A 33 ASP cc_start: 0.7014 (p0) cc_final: 0.6003 (t0) REVERT: A 53 PHE cc_start: 0.8250 (m-80) cc_final: 0.6993 (m-80) REVERT: A 217 LEU cc_start: 0.8515 (mm) cc_final: 0.8298 (mm) REVERT: A 291 ILE cc_start: 0.9291 (mt) cc_final: 0.8227 (tp) REVERT: A 297 GLU cc_start: 0.8565 (pt0) cc_final: 0.8356 (pt0) REVERT: A 300 ASN cc_start: 0.8762 (p0) cc_final: 0.8457 (p0) REVERT: A 317 LEU cc_start: 0.8380 (mt) cc_final: 0.7898 (mt) REVERT: A 398 MET cc_start: 0.7560 (mtp) cc_final: 0.7336 (mmp) REVERT: A 408 TYR cc_start: 0.5948 (m-80) cc_final: 0.5298 (m-80) REVERT: B 16 ILE cc_start: 0.9165 (mt) cc_final: 0.8934 (mt) REVERT: B 21 TRP cc_start: 0.7864 (m100) cc_final: 0.7654 (m-10) REVERT: B 119 LEU cc_start: 0.8065 (mt) cc_final: 0.7804 (mt) REVERT: B 139 HIS cc_start: 0.7990 (p90) cc_final: 0.6943 (p90) REVERT: B 228 ASN cc_start: 0.8646 (m-40) cc_final: 0.8156 (m-40) REVERT: B 262 PHE cc_start: 0.8274 (t80) cc_final: 0.8031 (t80) REVERT: B 267 PHE cc_start: 0.6508 (m-80) cc_final: 0.5646 (m-80) REVERT: B 268 PHE cc_start: 0.7002 (m-80) cc_final: 0.6744 (m-80) REVERT: B 269 MET cc_start: 0.7397 (ttt) cc_final: 0.6727 (ttm) REVERT: B 422 GLU cc_start: 0.8901 (pt0) cc_final: 0.8590 (pp20) REVERT: B 432 TYR cc_start: 0.5792 (m-10) cc_final: 0.5354 (m-80) REVERT: C 60 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7726 (tttt) REVERT: C 75 ILE cc_start: 0.8569 (mm) cc_final: 0.7289 (tt) REVERT: C 295 CYS cc_start: 0.8740 (t) cc_final: 0.8508 (t) REVERT: D 75 MET cc_start: 0.7644 (mmm) cc_final: 0.7347 (tpp) REVERT: D 119 LEU cc_start: 0.9003 (mt) cc_final: 0.8392 (mt) REVERT: D 163 ASP cc_start: 0.8023 (p0) cc_final: 0.7398 (p0) REVERT: D 165 ILE cc_start: 0.8008 (mt) cc_final: 0.7517 (mt) REVERT: D 262 PHE cc_start: 0.8327 (m-80) cc_final: 0.8078 (m-80) REVERT: D 333 LEU cc_start: 0.7656 (mt) cc_final: 0.7431 (mt) REVERT: D 369 ARG cc_start: 0.7803 (tmm-80) cc_final: 0.7507 (tmm-80) REVERT: D 378 ILE cc_start: 0.6437 (mp) cc_final: 0.5959 (mp) REVERT: D 405 LEU cc_start: 0.8693 (mt) cc_final: 0.8316 (mt) REVERT: D 416 MET cc_start: 0.5225 (mmp) cc_final: 0.5001 (mmm) REVERT: E 21 TRP cc_start: 0.8718 (m100) cc_final: 0.8228 (m100) REVERT: E 23 LEU cc_start: 0.8610 (tp) cc_final: 0.8223 (tp) REVERT: E 53 PHE cc_start: 0.7970 (m-80) cc_final: 0.7212 (m-80) REVERT: E 75 ILE cc_start: 0.9150 (mm) cc_final: 0.8906 (mm) REVERT: E 291 ILE cc_start: 0.9176 (mt) cc_final: 0.8091 (tt) REVERT: E 344 VAL cc_start: 0.8171 (m) cc_final: 0.6695 (p) REVERT: F 66 ILE cc_start: 0.8439 (mm) cc_final: 0.8004 (mm) REVERT: F 139 HIS cc_start: 0.8076 (p90) cc_final: 0.6913 (p90) REVERT: F 166 MET cc_start: 0.8239 (mmp) cc_final: 0.7547 (mmm) REVERT: F 369 ARG cc_start: 0.8201 (tmm-80) cc_final: 0.7884 (tmm-80) REVERT: F 432 TYR cc_start: 0.6443 (m-10) cc_final: 0.6052 (m-10) REVERT: G 33 ASP cc_start: 0.5869 (p0) cc_final: 0.5345 (p0) REVERT: G 218 ASP cc_start: 0.5558 (m-30) cc_final: 0.5208 (m-30) REVERT: G 280 LYS cc_start: 0.7034 (mtmm) cc_final: 0.6605 (ptmt) REVERT: H 19 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8577 (mmmt) REVERT: H 21 TRP cc_start: 0.7606 (m100) cc_final: 0.7112 (m100) REVERT: H 67 LEU cc_start: 0.7428 (mt) cc_final: 0.6972 (mt) REVERT: H 132 LEU cc_start: 0.8896 (tp) cc_final: 0.8370 (tp) REVERT: H 165 ILE cc_start: 0.7424 (pt) cc_final: 0.7025 (pt) REVERT: H 176 LYS cc_start: 0.7628 (mmmt) cc_final: 0.6095 (tmtt) REVERT: H 213 CYS cc_start: 0.6304 (p) cc_final: 0.5939 (p) REVERT: H 220 THR cc_start: 0.8197 (p) cc_final: 0.7926 (m) REVERT: H 257 VAL cc_start: 0.9203 (t) cc_final: 0.8936 (p) REVERT: H 269 MET cc_start: 0.4822 (ptt) cc_final: 0.4232 (ptt) REVERT: H 288 VAL cc_start: 0.8732 (t) cc_final: 0.8493 (t) REVERT: H 301 MET cc_start: 0.7590 (ppp) cc_final: 0.6758 (ppp) REVERT: I 53 PHE cc_start: 0.6934 (m-80) cc_final: 0.6527 (m-80) REVERT: I 127 ASP cc_start: 0.6986 (m-30) cc_final: 0.6576 (m-30) REVERT: I 138 PHE cc_start: 0.6300 (m-80) cc_final: 0.5637 (m-80) REVERT: I 271 THR cc_start: 0.6218 (m) cc_final: 0.4633 (m) REVERT: I 286 LEU cc_start: 0.7137 (mt) cc_final: 0.6010 (mt) REVERT: I 335 ILE cc_start: 0.9144 (pt) cc_final: 0.8141 (mm) REVERT: I 377 MET cc_start: 0.7459 (tmm) cc_final: 0.6260 (tmm) REVERT: I 422 ARG cc_start: 0.7817 (pmt-80) cc_final: 0.7558 (tmm-80) REVERT: J 60 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7907 (mmmt) REVERT: J 75 MET cc_start: 0.6435 (tpt) cc_final: 0.5681 (tpt) REVERT: J 76 ASP cc_start: 0.5922 (m-30) cc_final: 0.5312 (m-30) REVERT: J 138 THR cc_start: 0.7104 (p) cc_final: 0.6768 (p) REVERT: J 165 ILE cc_start: 0.7617 (pt) cc_final: 0.7135 (pt) REVERT: J 182 VAL cc_start: 0.8993 (m) cc_final: 0.8707 (t) REVERT: J 333 LEU cc_start: 0.8458 (mt) cc_final: 0.8240 (mt) REVERT: J 349 ASN cc_start: 0.8852 (t0) cc_final: 0.8321 (t0) REVERT: J 357 ASP cc_start: 0.5169 (t0) cc_final: 0.4863 (t0) REVERT: J 425 MET cc_start: 0.6808 (ttt) cc_final: 0.6134 (tpp) REVERT: K 16 ILE cc_start: 0.8349 (pt) cc_final: 0.8091 (pt) REVERT: K 23 LEU cc_start: 0.8587 (tp) cc_final: 0.8297 (tp) REVERT: K 33 ASP cc_start: 0.6620 (p0) cc_final: 0.6251 (t0) REVERT: K 78 VAL cc_start: 0.8434 (t) cc_final: 0.7785 (t) REVERT: K 120 ASP cc_start: 0.7626 (m-30) cc_final: 0.6819 (t70) REVERT: K 169 PHE cc_start: 0.6023 (m-80) cc_final: 0.5514 (m-80) REVERT: K 209 ILE cc_start: 0.8747 (mm) cc_final: 0.8482 (mm) REVERT: K 279 GLU cc_start: 0.8085 (mp0) cc_final: 0.7611 (mp0) REVERT: K 288 VAL cc_start: 0.8952 (m) cc_final: 0.8518 (p) REVERT: K 291 ILE cc_start: 0.8696 (mt) cc_final: 0.8366 (mt) REVERT: K 325 PRO cc_start: 0.8683 (Cg_exo) cc_final: 0.8346 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8926 (pt) cc_final: 0.8310 (tp) REVERT: K 352 LYS cc_start: 0.8458 (tptt) cc_final: 0.8202 (tppt) REVERT: L 21 TRP cc_start: 0.7572 (m100) cc_final: 0.6208 (m100) REVERT: L 103 TRP cc_start: 0.6356 (t60) cc_final: 0.6147 (t60) REVERT: L 120 ASP cc_start: 0.7569 (t70) cc_final: 0.6730 (t70) REVERT: L 124 LYS cc_start: 0.6934 (ptpp) cc_final: 0.6693 (pttt) REVERT: L 132 LEU cc_start: 0.8020 (tp) cc_final: 0.7749 (tp) REVERT: L 163 ASP cc_start: 0.7265 (p0) cc_final: 0.6949 (p0) REVERT: L 373 MET cc_start: 0.8123 (ptm) cc_final: 0.7500 (ptp) REVERT: L 395 PHE cc_start: 0.8034 (t80) cc_final: 0.7487 (t80) REVERT: L 425 MET cc_start: 0.7459 (ttt) cc_final: 0.7053 (ttt) REVERT: M 16 ILE cc_start: 0.8708 (mt) cc_final: 0.8496 (mt) REVERT: M 21 TRP cc_start: 0.8427 (m100) cc_final: 0.7695 (m100) REVERT: M 23 LEU cc_start: 0.8227 (tp) cc_final: 0.8007 (tp) REVERT: M 101 ASN cc_start: 0.7423 (t0) cc_final: 0.7144 (t0) REVERT: M 118 VAL cc_start: 0.9127 (t) cc_final: 0.8924 (t) REVERT: M 231 ILE cc_start: 0.8581 (mt) cc_final: 0.8251 (mm) REVERT: M 335 ILE cc_start: 0.8283 (pt) cc_final: 0.7826 (tp) REVERT: M 413 MET cc_start: 0.8917 (mmm) cc_final: 0.8501 (mmm) REVERT: N 154 ILE cc_start: 0.8621 (tp) cc_final: 0.8400 (tp) REVERT: N 163 ASP cc_start: 0.8802 (p0) cc_final: 0.7849 (p0) REVERT: N 213 CYS cc_start: 0.6748 (p) cc_final: 0.6437 (p) REVERT: N 259 MET cc_start: 0.7653 (mmm) cc_final: 0.6673 (mmt) REVERT: N 268 PHE cc_start: 0.7622 (m-10) cc_final: 0.7169 (m-80) REVERT: N 288 VAL cc_start: 0.9050 (t) cc_final: 0.8717 (t) REVERT: N 384 ILE cc_start: 0.8702 (mp) cc_final: 0.8435 (mm) REVERT: N 413 MET cc_start: 0.6208 (mmt) cc_final: 0.5884 (mmp) REVERT: N 425 MET cc_start: 0.8076 (ttt) cc_final: 0.7623 (tpp) REVERT: O 21 TRP cc_start: 0.8534 (m100) cc_final: 0.7862 (m100) REVERT: O 23 LEU cc_start: 0.8203 (tp) cc_final: 0.7691 (tp) REVERT: O 152 LEU cc_start: 0.9155 (tp) cc_final: 0.8775 (tp) REVERT: O 214 ARG cc_start: 0.4872 (ptp-170) cc_final: 0.4501 (ptp-110) REVERT: O 255 PHE cc_start: 0.6501 (m-10) cc_final: 0.6025 (m-10) REVERT: O 279 GLU cc_start: 0.6592 (tm-30) cc_final: 0.6271 (tm-30) REVERT: P 19 LYS cc_start: 0.7681 (tmtt) cc_final: 0.7414 (tptm) REVERT: P 21 TRP cc_start: 0.8708 (m100) cc_final: 0.8271 (m100) REVERT: P 22 GLU cc_start: 0.7981 (tm-30) cc_final: 0.6127 (tm-30) REVERT: P 67 LEU cc_start: 0.8449 (mm) cc_final: 0.8002 (mm) REVERT: P 165 ILE cc_start: 0.7696 (mt) cc_final: 0.7311 (mt) REVERT: P 166 MET cc_start: 0.5194 (ptt) cc_final: 0.4119 (ptt) REVERT: P 259 MET cc_start: 0.7562 (mmm) cc_final: 0.7221 (mmt) REVERT: P 262 PHE cc_start: 0.8625 (m-80) cc_final: 0.8337 (m-80) REVERT: P 292 THR cc_start: 0.7966 (p) cc_final: 0.7320 (p) REVERT: P 326 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8108 (ttpp) REVERT: P 333 LEU cc_start: 0.7508 (tt) cc_final: 0.7156 (tp) REVERT: P 425 MET cc_start: 0.7763 (ttt) cc_final: 0.7309 (tpp) REVERT: Q 55 GLU cc_start: 0.7733 (tp30) cc_final: 0.7464 (tp30) REVERT: Q 86 LEU cc_start: 0.8499 (tp) cc_final: 0.8266 (tp) REVERT: Q 154 MET cc_start: 0.7578 (tmm) cc_final: 0.7224 (tmm) REVERT: Q 398 MET cc_start: 0.7577 (mtp) cc_final: 0.6222 (mmp) REVERT: R 115 VAL cc_start: 0.9182 (p) cc_final: 0.8824 (p) REVERT: R 120 ASP cc_start: 0.7559 (m-30) cc_final: 0.7277 (m-30) REVERT: R 135 PHE cc_start: 0.8506 (m-80) cc_final: 0.8304 (m-80) REVERT: R 259 MET cc_start: 0.7305 (mmm) cc_final: 0.6792 (mmm) REVERT: R 398 MET cc_start: 0.6739 (ptt) cc_final: 0.6138 (ptt) outliers start: 2 outliers final: 1 residues processed: 1541 average time/residue: 0.5698 time to fit residues: 1471.6074 Evaluate side-chains 1114 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1113 time to evaluate : 5.107 ------------------------------------------------------------------------------- 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: 0.0020 chunk 82 optimal weight: 20.0000 chunk 416 optimal weight: 10.0000 chunk 534 optimal weight: 30.0000 chunk 413 optimal weight: 0.5980 chunk 615 optimal weight: 4.9990 chunk 408 optimal weight: 0.4980 chunk 728 optimal weight: 50.0000 chunk 456 optimal weight: 30.0000 chunk 444 optimal weight: 20.0000 chunk 336 optimal weight: 7.9990 overall best weight: 2.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 GLN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 216 ASN ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 HIS ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 ASN ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN H 249 ASN ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 309 HIS ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 ASN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 301 GLN K 309 HIS ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 128 GLN M 309 HIS ** N 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 294 GLN P 406 HIS Q 176 GLN Q 283 HIS ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 282 GLN ** R 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.8286 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= 0.175 Angle : 0.619 11.350 84582 Z= 0.315 Chirality : 0.045 0.232 9216 Planarity : 0.005 0.086 11043 Dihedral : 10.447 179.356 8595 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.06 % Allowed : 1.27 % Favored : 98.67 % 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: 0.52 (0.10), residues: 7632 helix: 0.45 (0.09), residues: 3528 sheet: 0.77 (0.15), residues: 1260 loop : 0.25 (0.13), residues: 2844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.003 TRP R 21 HIS 0.012 0.001 HIS H 107 PHE 0.023 0.001 PHE E 49 TYR 0.043 0.001 TYR P 161 ARG 0.011 0.001 ARG F 123 *********************** 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 1563 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1559 time to evaluate : 5.253 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: A 21 TRP cc_start: 0.8719 (m100) cc_final: 0.8107 (m100) REVERT: A 33 ASP cc_start: 0.7019 (p0) cc_final: 0.6645 (t0) REVERT: A 53 PHE cc_start: 0.8202 (m-80) cc_final: 0.7185 (m-80) REVERT: A 75 ILE cc_start: 0.9515 (mm) cc_final: 0.8649 (tt) REVERT: A 179 THR cc_start: 0.7176 (m) cc_final: 0.6936 (m) REVERT: A 291 ILE cc_start: 0.9303 (mt) cc_final: 0.8147 (tp) REVERT: A 302 MET cc_start: 0.7092 (mpp) cc_final: 0.6783 (mpp) REVERT: A 347 CYS cc_start: 0.7099 (p) cc_final: 0.6794 (p) REVERT: A 355 ILE cc_start: 0.8790 (pt) cc_final: 0.8445 (pt) REVERT: A 435 VAL cc_start: 0.9268 (t) cc_final: 0.9026 (t) REVERT: B 21 TRP cc_start: 0.7969 (m100) cc_final: 0.7643 (m100) REVERT: B 51 VAL cc_start: 0.8547 (t) cc_final: 0.8255 (m) REVERT: B 67 LEU cc_start: 0.8290 (mm) cc_final: 0.8085 (mm) REVERT: B 119 LEU cc_start: 0.8016 (mt) cc_final: 0.7611 (mt) REVERT: B 129 CYS cc_start: 0.8143 (p) cc_final: 0.7941 (p) REVERT: B 139 HIS cc_start: 0.7846 (p90) cc_final: 0.6788 (p90) REVERT: B 217 LEU cc_start: 0.8989 (mm) cc_final: 0.8468 (mm) REVERT: B 267 PHE cc_start: 0.6470 (m-80) cc_final: 0.6200 (m-10) REVERT: B 269 MET cc_start: 0.7695 (ttt) cc_final: 0.6755 (ttm) REVERT: B 356 CYS cc_start: 0.1854 (p) cc_final: 0.1469 (p) REVERT: B 398 MET cc_start: 0.7349 (ptt) cc_final: 0.7076 (ptt) REVERT: B 422 GLU cc_start: 0.8880 (pt0) cc_final: 0.8461 (pp20) REVERT: C 60 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7551 (tttt) REVERT: C 75 ILE cc_start: 0.8506 (mm) cc_final: 0.7205 (tt) REVERT: C 217 LEU cc_start: 0.8915 (mm) cc_final: 0.8590 (mm) REVERT: D 19 LYS cc_start: 0.8321 (mmmm) cc_final: 0.8118 (mmmt) REVERT: D 119 LEU cc_start: 0.8913 (mt) cc_final: 0.8180 (mt) REVERT: D 137 LEU cc_start: 0.7735 (tt) cc_final: 0.7417 (mp) REVERT: D 138 THR cc_start: 0.5375 (m) cc_final: 0.4367 (m) REVERT: D 165 ILE cc_start: 0.7815 (mt) cc_final: 0.7281 (mt) REVERT: D 199 ASP cc_start: 0.8453 (m-30) cc_final: 0.7951 (m-30) REVERT: D 302 MET cc_start: 0.8507 (ptp) cc_final: 0.8229 (ptp) REVERT: D 405 LEU cc_start: 0.8573 (mt) cc_final: 0.8295 (mt) REVERT: E 21 TRP cc_start: 0.8568 (m100) cc_final: 0.7896 (m100) REVERT: E 23 LEU cc_start: 0.8546 (tp) cc_final: 0.7892 (tp) REVERT: E 53 PHE cc_start: 0.7727 (m-80) cc_final: 0.7228 (m-80) REVERT: E 129 CYS cc_start: 0.7393 (t) cc_final: 0.7167 (t) REVERT: E 291 ILE cc_start: 0.9065 (mt) cc_final: 0.7860 (tt) REVERT: E 344 VAL cc_start: 0.7757 (m) cc_final: 0.6556 (p) REVERT: E 347 CYS cc_start: 0.8012 (p) cc_final: 0.7311 (p) REVERT: F 66 ILE cc_start: 0.8486 (mm) cc_final: 0.7911 (mm) REVERT: F 116 ASP cc_start: 0.7766 (m-30) cc_final: 0.7057 (m-30) REVERT: F 119 LEU cc_start: 0.8890 (pp) cc_final: 0.8632 (pp) REVERT: F 163 ASP cc_start: 0.7249 (p0) cc_final: 0.6154 (p0) REVERT: F 166 MET cc_start: 0.7987 (mmp) cc_final: 0.7643 (mmm) REVERT: G 200 CYS cc_start: 0.7996 (t) cc_final: 0.7704 (t) REVERT: G 269 LEU cc_start: 0.7004 (mt) cc_final: 0.6614 (mt) REVERT: G 295 CYS cc_start: 0.8876 (m) cc_final: 0.8386 (m) REVERT: G 388 TRP cc_start: 0.7043 (m100) cc_final: 0.6840 (m100) REVERT: H 5 VAL cc_start: 0.8580 (t) cc_final: 0.8212 (t) REVERT: H 19 LYS cc_start: 0.8819 (mmmt) cc_final: 0.8456 (mmmt) REVERT: H 21 TRP cc_start: 0.7676 (m100) cc_final: 0.7068 (m100) REVERT: H 67 LEU cc_start: 0.7371 (mt) cc_final: 0.6792 (mt) REVERT: H 132 LEU cc_start: 0.8904 (tp) cc_final: 0.8445 (tp) REVERT: H 165 ILE cc_start: 0.7186 (pt) cc_final: 0.6913 (pt) REVERT: H 176 LYS cc_start: 0.7526 (mmmt) cc_final: 0.5988 (tmtt) REVERT: H 257 VAL cc_start: 0.9160 (t) cc_final: 0.8928 (p) REVERT: H 288 VAL cc_start: 0.8630 (t) cc_final: 0.6810 (t) REVERT: H 301 MET cc_start: 0.7417 (ppp) cc_final: 0.6304 (ppp) REVERT: H 332 MET cc_start: 0.8053 (mmp) cc_final: 0.7695 (mmm) REVERT: I 53 PHE cc_start: 0.7069 (m-80) cc_final: 0.6213 (m-80) REVERT: I 138 PHE cc_start: 0.5721 (m-80) cc_final: 0.5439 (m-80) REVERT: I 211 ASP cc_start: 0.6873 (t0) cc_final: 0.6125 (t0) REVERT: I 217 LEU cc_start: 0.7876 (mm) cc_final: 0.7329 (mm) REVERT: I 227 LEU cc_start: 0.8571 (mm) cc_final: 0.8224 (mm) REVERT: I 230 LEU cc_start: 0.8988 (tp) cc_final: 0.8748 (tp) REVERT: I 271 THR cc_start: 0.6168 (m) cc_final: 0.5809 (m) REVERT: I 286 LEU cc_start: 0.6988 (mt) cc_final: 0.5820 (mt) REVERT: I 300 ASN cc_start: 0.6865 (m110) cc_final: 0.6496 (m110) REVERT: I 335 ILE cc_start: 0.9132 (pt) cc_final: 0.8201 (mm) REVERT: J 21 TRP cc_start: 0.7653 (m100) cc_final: 0.7448 (m100) REVERT: J 55 GLU cc_start: 0.5137 (tp30) cc_final: 0.4431 (pm20) REVERT: J 60 LYS cc_start: 0.7932 (mmtt) cc_final: 0.7041 (mmmt) REVERT: J 165 ILE cc_start: 0.7435 (pt) cc_final: 0.6951 (pt) REVERT: J 327 GLU cc_start: 0.7863 (pt0) cc_final: 0.7138 (pt0) REVERT: J 349 ASN cc_start: 0.8787 (t0) cc_final: 0.8144 (t0) REVERT: J 352 LYS cc_start: 0.7947 (mmtt) cc_final: 0.7637 (tttp) REVERT: J 371 LEU cc_start: 0.7241 (mm) cc_final: 0.7019 (mm) REVERT: J 425 MET cc_start: 0.6585 (ttt) cc_final: 0.5774 (tpp) REVERT: K 16 ILE cc_start: 0.8150 (pt) cc_final: 0.7791 (pt) REVERT: K 23 LEU cc_start: 0.8438 (tp) cc_final: 0.8217 (tp) REVERT: K 33 ASP cc_start: 0.6114 (p0) cc_final: 0.5814 (t0) REVERT: K 78 VAL cc_start: 0.8432 (t) cc_final: 0.8069 (t) REVERT: K 116 ASP cc_start: 0.7297 (p0) cc_final: 0.6705 (p0) REVERT: K 120 ASP cc_start: 0.8204 (m-30) cc_final: 0.7038 (t70) REVERT: K 149 PHE cc_start: 0.6917 (t80) cc_final: 0.6076 (t80) REVERT: K 169 PHE cc_start: 0.6327 (m-80) cc_final: 0.6111 (m-80) REVERT: K 227 LEU cc_start: 0.8527 (mm) cc_final: 0.8196 (mm) REVERT: K 269 LEU cc_start: 0.6159 (pp) cc_final: 0.5872 (pp) REVERT: K 279 GLU cc_start: 0.8062 (mp0) cc_final: 0.7500 (mp0) REVERT: K 288 VAL cc_start: 0.8979 (m) cc_final: 0.8500 (p) REVERT: K 291 ILE cc_start: 0.8596 (mt) cc_final: 0.8232 (mt) REVERT: K 325 PRO cc_start: 0.8761 (Cg_exo) cc_final: 0.8382 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8923 (pt) cc_final: 0.8169 (tp) REVERT: K 352 LYS cc_start: 0.8759 (tptt) cc_final: 0.8354 (tppt) REVERT: K 386 GLU cc_start: 0.8147 (mp0) cc_final: 0.7816 (mp0) REVERT: L 21 TRP cc_start: 0.7492 (m100) cc_final: 0.6607 (m100) REVERT: L 120 ASP cc_start: 0.7452 (t70) cc_final: 0.6859 (t70) REVERT: L 132 LEU cc_start: 0.7951 (tp) cc_final: 0.7610 (tp) REVERT: L 138 THR cc_start: 0.5073 (p) cc_final: 0.4745 (p) REVERT: L 163 ASP cc_start: 0.7071 (p0) cc_final: 0.6567 (p0) REVERT: L 323 MET cc_start: 0.8447 (mmp) cc_final: 0.8117 (mmm) REVERT: L 327 GLU cc_start: 0.7505 (mp0) cc_final: 0.6176 (tm-30) REVERT: L 425 MET cc_start: 0.7689 (ttt) cc_final: 0.7345 (ttt) REVERT: M 21 TRP cc_start: 0.8425 (m100) cc_final: 0.7636 (m100) REVERT: M 23 LEU cc_start: 0.8102 (tp) cc_final: 0.7769 (tp) REVERT: M 315 CYS cc_start: 0.7318 (t) cc_final: 0.7058 (t) REVERT: M 392 ASP cc_start: 0.6825 (m-30) cc_final: 0.5929 (m-30) REVERT: M 398 MET cc_start: 0.6960 (ptt) cc_final: 0.6726 (ptt) REVERT: M 413 MET cc_start: 0.8931 (mmm) cc_final: 0.8551 (mmm) REVERT: N 154 ILE cc_start: 0.8790 (tp) cc_final: 0.8473 (tp) REVERT: N 163 ASP cc_start: 0.8768 (p0) cc_final: 0.7833 (p0) REVERT: N 259 MET cc_start: 0.7626 (mmm) cc_final: 0.6682 (mmp) REVERT: N 268 PHE cc_start: 0.7244 (m-10) cc_final: 0.6814 (m-80) REVERT: N 391 ILE cc_start: 0.8821 (mm) cc_final: 0.8584 (mm) REVERT: N 413 MET cc_start: 0.6371 (mmt) cc_final: 0.6129 (mmp) REVERT: O 21 TRP cc_start: 0.8355 (m100) cc_final: 0.7600 (m100) REVERT: O 152 LEU cc_start: 0.9133 (tp) cc_final: 0.8919 (tp) REVERT: O 293 ASN cc_start: 0.7459 (m110) cc_final: 0.7135 (m110) REVERT: O 376 CYS cc_start: 0.6958 (t) cc_final: 0.6752 (t) REVERT: P 21 TRP cc_start: 0.8623 (m100) cc_final: 0.7937 (m100) REVERT: P 22 GLU cc_start: 0.6863 (tm-30) cc_final: 0.6590 (tm-30) REVERT: P 62 VAL cc_start: 0.8350 (p) cc_final: 0.7977 (m) REVERT: P 90 ASP cc_start: 0.6927 (m-30) cc_final: 0.6614 (m-30) REVERT: P 113 GLU cc_start: 0.7380 (pm20) cc_final: 0.7144 (pm20) REVERT: P 165 ILE cc_start: 0.7747 (mt) cc_final: 0.7271 (mt) REVERT: P 166 MET cc_start: 0.4557 (ptt) cc_final: 0.3540 (ptt) REVERT: P 259 MET cc_start: 0.7582 (mmm) cc_final: 0.6803 (mmt) REVERT: P 268 PHE cc_start: 0.8415 (m-80) cc_final: 0.7428 (m-80) REVERT: P 292 THR cc_start: 0.8017 (p) cc_final: 0.7560 (p) REVERT: P 333 LEU cc_start: 0.7722 (tt) cc_final: 0.7328 (tp) REVERT: P 415 GLU cc_start: 0.7722 (mt-10) cc_final: 0.6954 (pm20) REVERT: P 425 MET cc_start: 0.7868 (ttt) cc_final: 0.7457 (tpp) REVERT: Q 66 VAL cc_start: 0.8077 (t) cc_final: 0.7836 (t) REVERT: Q 149 PHE cc_start: 0.6324 (t80) cc_final: 0.5833 (t80) REVERT: Q 153 LEU cc_start: 0.8780 (tp) cc_final: 0.8472 (tp) REVERT: Q 239 THR cc_start: 0.6036 (p) cc_final: 0.5815 (p) REVERT: Q 329 ASN cc_start: 0.8071 (m110) cc_final: 0.7865 (m110) REVERT: Q 378 LEU cc_start: 0.6639 (mm) cc_final: 0.6069 (mm) REVERT: Q 398 MET cc_start: 0.7469 (mtp) cc_final: 0.6186 (mmp) REVERT: R 67 LEU cc_start: 0.6697 (mm) cc_final: 0.6443 (mm) REVERT: R 259 MET cc_start: 0.7244 (mmm) cc_final: 0.6574 (mmm) REVERT: R 269 MET cc_start: 0.4531 (tpt) cc_final: 0.3779 (tpt) REVERT: R 314 THR cc_start: 0.8023 (p) cc_final: 0.6688 (p) REVERT: R 398 MET cc_start: 0.6944 (ptt) cc_final: 0.6254 (ptt) REVERT: R 415 GLU cc_start: 0.7400 (pt0) cc_final: 0.6894 (pm20) outliers start: 4 outliers final: 0 residues processed: 1560 average time/residue: 0.6343 time to fit residues: 1670.6103 Evaluate side-chains 1131 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1131 time to evaluate : 5.200 ------------------------------------------------------------------------------- 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: 20.0000 chunk 290 optimal weight: 30.0000 chunk 435 optimal weight: 6.9990 chunk 219 optimal weight: 0.0980 chunk 143 optimal weight: 30.0000 chunk 141 optimal weight: 20.0000 chunk 463 optimal weight: 9.9990 chunk 496 optimal weight: 0.3980 chunk 360 optimal weight: 7.9990 chunk 67 optimal weight: 6.9990 chunk 572 optimal weight: 10.0000 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 356 ASN B 136 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 293 ASN C 309 HIS D 136 GLN ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 HIS E 101 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 HIS F 249 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN H 294 GLN ** 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** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 249 ASN ** K 216 ASN ** 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 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS N 266 HIS P 37 HIS ** Q 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 283 HIS ** R 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.8594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 62262 Z= 0.179 Angle : 0.629 13.187 84582 Z= 0.323 Chirality : 0.045 0.199 9216 Planarity : 0.005 0.076 11043 Dihedral : 10.123 178.271 8595 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.08 % Allowed : 0.95 % Favored : 98.98 % 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: 0.49 (0.10), residues: 7632 helix: 0.39 (0.09), residues: 3528 sheet: 0.87 (0.15), residues: 1233 loop : 0.23 (0.13), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.003 TRP R 21 HIS 0.009 0.001 HIS Q 283 PHE 0.021 0.001 PHE J 92 TYR 0.038 0.001 TYR P 161 ARG 0.013 0.001 ARG R 79 *********************** 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 1522 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1517 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: A 21 TRP cc_start: 0.8700 (m100) cc_final: 0.8189 (m100) REVERT: A 33 ASP cc_start: 0.7453 (p0) cc_final: 0.6547 (t0) REVERT: A 53 PHE cc_start: 0.8065 (m-80) cc_final: 0.7201 (m-80) REVERT: A 75 ILE cc_start: 0.9556 (mm) cc_final: 0.8132 (tt) REVERT: A 291 ILE cc_start: 0.9249 (mt) cc_final: 0.8084 (tp) REVERT: A 300 ASN cc_start: 0.8909 (p0) cc_final: 0.7755 (m-40) REVERT: A 317 LEU cc_start: 0.8402 (mt) cc_final: 0.8122 (mt) REVERT: A 335 ILE cc_start: 0.8123 (tp) cc_final: 0.7637 (tp) REVERT: A 347 CYS cc_start: 0.7316 (p) cc_final: 0.6953 (p) REVERT: A 425 MET cc_start: 0.8500 (ptm) cc_final: 0.8026 (ppp) REVERT: A 435 VAL cc_start: 0.9315 (t) cc_final: 0.9055 (t) REVERT: B 22 GLU cc_start: 0.6865 (tp30) cc_final: 0.5956 (tp30) REVERT: B 51 VAL cc_start: 0.8529 (t) cc_final: 0.8235 (m) REVERT: B 119 LEU cc_start: 0.8028 (mt) cc_final: 0.7543 (mt) REVERT: B 129 CYS cc_start: 0.8150 (p) cc_final: 0.7864 (p) REVERT: B 139 HIS cc_start: 0.7505 (p90) cc_final: 0.6474 (p90) REVERT: B 165 ILE cc_start: 0.8845 (mt) cc_final: 0.8198 (mt) REVERT: B 217 LEU cc_start: 0.8998 (mm) cc_final: 0.8540 (mm) REVERT: B 228 ASN cc_start: 0.8522 (m-40) cc_final: 0.7551 (t0) REVERT: B 267 PHE cc_start: 0.6491 (m-80) cc_final: 0.6084 (m-10) REVERT: B 269 MET cc_start: 0.7774 (ttt) cc_final: 0.6838 (ttm) REVERT: B 398 MET cc_start: 0.7246 (ptt) cc_final: 0.7012 (ptt) REVERT: B 422 GLU cc_start: 0.8816 (pt0) cc_final: 0.8363 (pp20) REVERT: C 75 ILE cc_start: 0.8698 (mm) cc_final: 0.7403 (tt) REVERT: C 217 LEU cc_start: 0.8976 (mm) cc_final: 0.8632 (mm) REVERT: C 295 CYS cc_start: 0.8779 (t) cc_final: 0.8540 (t) REVERT: C 313 MET cc_start: 0.5635 (mpp) cc_final: 0.5404 (tpt) REVERT: D 119 LEU cc_start: 0.8734 (mt) cc_final: 0.8262 (mt) REVERT: D 165 ILE cc_start: 0.7922 (mt) cc_final: 0.7325 (mt) REVERT: D 199 ASP cc_start: 0.8573 (m-30) cc_final: 0.8327 (m-30) REVERT: D 259 MET cc_start: 0.7905 (mmm) cc_final: 0.7093 (mmm) REVERT: D 264 ARG cc_start: 0.6200 (mtt180) cc_final: 0.5395 (mtt180) REVERT: D 302 MET cc_start: 0.8703 (ptp) cc_final: 0.8057 (ptp) REVERT: D 309 HIS cc_start: 0.5027 (OUTLIER) cc_final: 0.4581 (t-90) REVERT: D 369 ARG cc_start: 0.7710 (tmm-80) cc_final: 0.7431 (tmm-80) REVERT: D 378 ILE cc_start: 0.6262 (mp) cc_final: 0.5880 (mp) REVERT: D 405 LEU cc_start: 0.8565 (mt) cc_final: 0.8347 (mt) REVERT: E 21 TRP cc_start: 0.8639 (m100) cc_final: 0.8433 (m100) REVERT: E 53 PHE cc_start: 0.7792 (m-80) cc_final: 0.6861 (m-80) REVERT: E 75 ILE cc_start: 0.9180 (mm) cc_final: 0.8940 (mm) REVERT: E 129 CYS cc_start: 0.7471 (t) cc_final: 0.7175 (t) REVERT: E 154 MET cc_start: 0.6963 (tpp) cc_final: 0.6494 (tpt) REVERT: E 291 ILE cc_start: 0.9004 (mt) cc_final: 0.8056 (tp) REVERT: E 318 LEU cc_start: 0.6842 (pp) cc_final: 0.6282 (pp) REVERT: E 344 VAL cc_start: 0.7674 (m) cc_final: 0.6583 (p) REVERT: E 347 CYS cc_start: 0.7970 (p) cc_final: 0.7355 (p) REVERT: E 425 MET cc_start: 0.8649 (ptm) cc_final: 0.8078 (tmm) REVERT: F 53 TYR cc_start: 0.3956 (m-80) cc_final: 0.3733 (m-80) REVERT: F 66 ILE cc_start: 0.8012 (mm) cc_final: 0.7579 (mm) REVERT: F 116 ASP cc_start: 0.7756 (m-30) cc_final: 0.6901 (m-30) REVERT: F 120 ASP cc_start: 0.7820 (m-30) cc_final: 0.7428 (m-30) REVERT: F 124 LYS cc_start: 0.8452 (tmmt) cc_final: 0.8198 (tmtt) REVERT: F 127 GLU cc_start: 0.7673 (tp30) cc_final: 0.7305 (tp30) REVERT: F 132 LEU cc_start: 0.8569 (mm) cc_final: 0.7148 (mm) REVERT: F 139 HIS cc_start: 0.8059 (p90) cc_final: 0.6793 (p90) REVERT: F 163 ASP cc_start: 0.7423 (p0) cc_final: 0.6305 (p0) REVERT: F 166 MET cc_start: 0.7926 (mmp) cc_final: 0.7486 (mmm) REVERT: F 243 ARG cc_start: 0.8364 (mtm110) cc_final: 0.7985 (mtm110) REVERT: F 369 ARG cc_start: 0.8287 (tmm-80) cc_final: 0.7771 (tmm-80) REVERT: G 156 ARG cc_start: 0.6387 (mmm-85) cc_final: 0.6088 (mmm-85) REVERT: H 19 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8406 (mmmt) REVERT: H 21 TRP cc_start: 0.7525 (m100) cc_final: 0.7028 (m100) REVERT: H 67 LEU cc_start: 0.7929 (mt) cc_final: 0.7207 (mt) REVERT: H 132 LEU cc_start: 0.8926 (tp) cc_final: 0.8418 (tp) REVERT: H 176 LYS cc_start: 0.7513 (mmmt) cc_final: 0.5992 (tmtt) REVERT: H 269 MET cc_start: 0.4928 (ptt) cc_final: 0.4662 (ptt) REVERT: H 288 VAL cc_start: 0.8760 (t) cc_final: 0.8471 (t) REVERT: H 301 MET cc_start: 0.7408 (ppp) cc_final: 0.6669 (ppp) REVERT: I 53 PHE cc_start: 0.7301 (m-80) cc_final: 0.6445 (m-80) REVERT: I 167 LEU cc_start: 0.8327 (tp) cc_final: 0.8022 (tp) REVERT: I 252 LEU cc_start: 0.8499 (mp) cc_final: 0.8248 (mp) REVERT: I 269 LEU cc_start: 0.5926 (mt) cc_final: 0.5608 (mt) REVERT: I 288 VAL cc_start: 0.8607 (m) cc_final: 0.8351 (t) REVERT: I 302 MET cc_start: 0.6382 (mpp) cc_final: 0.5317 (mpp) REVERT: I 335 ILE cc_start: 0.9073 (pt) cc_final: 0.8192 (mm) REVERT: I 376 CYS cc_start: 0.7760 (t) cc_final: 0.7250 (t) REVERT: I 377 MET cc_start: 0.7480 (tmm) cc_final: 0.6511 (tmm) REVERT: J 60 LYS cc_start: 0.8028 (mmtt) cc_final: 0.7476 (mmmt) REVERT: J 103 TRP cc_start: 0.6988 (t-100) cc_final: 0.5490 (t-100) REVERT: J 123 ARG cc_start: 0.7644 (ttp80) cc_final: 0.7430 (ttp80) REVERT: J 132 LEU cc_start: 0.8455 (mm) cc_final: 0.8253 (mm) REVERT: J 138 THR cc_start: 0.6628 (p) cc_final: 0.5539 (p) REVERT: J 165 ILE cc_start: 0.7553 (pt) cc_final: 0.6914 (pt) REVERT: J 239 THR cc_start: 0.9103 (t) cc_final: 0.8788 (t) REVERT: J 349 ASN cc_start: 0.8744 (t0) cc_final: 0.8042 (t0) REVERT: K 23 LEU cc_start: 0.8434 (tp) cc_final: 0.8228 (tp) REVERT: K 33 ASP cc_start: 0.6114 (p0) cc_final: 0.5611 (t70) REVERT: K 78 VAL cc_start: 0.8440 (t) cc_final: 0.7713 (t) REVERT: K 120 ASP cc_start: 0.8034 (m-30) cc_final: 0.7166 (t70) REVERT: K 149 PHE cc_start: 0.6769 (t80) cc_final: 0.5790 (t80) REVERT: K 169 PHE cc_start: 0.6308 (m-80) cc_final: 0.5981 (m-80) REVERT: K 279 GLU cc_start: 0.8115 (mp0) cc_final: 0.7517 (mp0) REVERT: K 288 VAL cc_start: 0.8951 (m) cc_final: 0.8617 (p) REVERT: K 291 ILE cc_start: 0.8684 (mt) cc_final: 0.8434 (mt) REVERT: K 325 PRO cc_start: 0.8811 (Cg_exo) cc_final: 0.8562 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8956 (pt) cc_final: 0.8286 (tp) REVERT: K 386 GLU cc_start: 0.8410 (mp0) cc_final: 0.8094 (mp0) REVERT: L 21 TRP cc_start: 0.7664 (m100) cc_final: 0.6509 (m100) REVERT: L 53 TYR cc_start: 0.4268 (m-10) cc_final: 0.3930 (m-80) REVERT: L 132 LEU cc_start: 0.8233 (tp) cc_final: 0.7814 (tp) REVERT: L 138 THR cc_start: 0.5159 (p) cc_final: 0.4575 (p) REVERT: L 275 LEU cc_start: 0.8019 (pp) cc_final: 0.7800 (pp) REVERT: L 323 MET cc_start: 0.8402 (mmp) cc_final: 0.7996 (mmm) REVERT: L 327 GLU cc_start: 0.7394 (mp0) cc_final: 0.6147 (tm-30) REVERT: M 21 TRP cc_start: 0.8425 (m100) cc_final: 0.7631 (m100) REVERT: M 291 ILE cc_start: 0.7660 (mt) cc_final: 0.7191 (mt) REVERT: M 335 ILE cc_start: 0.8262 (pt) cc_final: 0.7871 (tp) REVERT: M 413 MET cc_start: 0.8975 (mmm) cc_final: 0.8565 (mmm) REVERT: N 132 LEU cc_start: 0.8525 (mm) cc_final: 0.8138 (mt) REVERT: N 163 ASP cc_start: 0.8750 (p0) cc_final: 0.7856 (p0) REVERT: N 259 MET cc_start: 0.7700 (mmm) cc_final: 0.6836 (mmm) REVERT: N 268 PHE cc_start: 0.7552 (m-10) cc_final: 0.7144 (m-80) REVERT: N 355 VAL cc_start: 0.6447 (t) cc_final: 0.6112 (t) REVERT: N 384 ILE cc_start: 0.9076 (mp) cc_final: 0.8742 (mp) REVERT: N 413 MET cc_start: 0.6206 (mmt) cc_final: 0.5853 (mmp) REVERT: N 425 MET cc_start: 0.8175 (tpp) cc_final: 0.7798 (tpp) REVERT: O 21 TRP cc_start: 0.8344 (m100) cc_final: 0.7508 (m100) REVERT: O 23 LEU cc_start: 0.8050 (tp) cc_final: 0.7814 (tp) REVERT: O 36 MET cc_start: 0.2634 (ttp) cc_final: 0.2065 (ttp) REVERT: O 86 LEU cc_start: 0.8662 (tp) cc_final: 0.8382 (tp) REVERT: O 154 MET cc_start: 0.7566 (ttt) cc_final: 0.7366 (ttt) REVERT: O 275 VAL cc_start: 0.8721 (m) cc_final: 0.8444 (m) REVERT: O 295 CYS cc_start: 0.8949 (m) cc_final: 0.8692 (m) REVERT: O 315 CYS cc_start: 0.7694 (t) cc_final: 0.6692 (t) REVERT: O 376 CYS cc_start: 0.6756 (t) cc_final: 0.6496 (t) REVERT: P 21 TRP cc_start: 0.8569 (m100) cc_final: 0.8071 (m100) REVERT: P 22 GLU cc_start: 0.7148 (tm-30) cc_final: 0.6671 (tm-30) REVERT: P 26 ASP cc_start: 0.7127 (m-30) cc_final: 0.6873 (m-30) REVERT: P 62 VAL cc_start: 0.8267 (p) cc_final: 0.7925 (m) REVERT: P 115 VAL cc_start: 0.9271 (t) cc_final: 0.9023 (t) REVERT: P 165 ILE cc_start: 0.7798 (mt) cc_final: 0.7521 (mt) REVERT: P 230 LEU cc_start: 0.8954 (tt) cc_final: 0.8696 (tt) REVERT: P 252 LEU cc_start: 0.7521 (mt) cc_final: 0.7161 (mp) REVERT: P 259 MET cc_start: 0.7324 (mmm) cc_final: 0.6913 (mmt) REVERT: P 268 PHE cc_start: 0.8267 (m-80) cc_final: 0.7438 (m-80) REVERT: P 292 THR cc_start: 0.7848 (p) cc_final: 0.7410 (p) REVERT: P 314 THR cc_start: 0.7769 (p) cc_final: 0.7346 (p) REVERT: P 389 LYS cc_start: 0.8756 (ptpp) cc_final: 0.8454 (ptpp) REVERT: P 391 ILE cc_start: 0.9091 (mm) cc_final: 0.8855 (mm) REVERT: P 425 MET cc_start: 0.7891 (ttt) cc_final: 0.7613 (tpp) REVERT: Q 86 LEU cc_start: 0.8687 (tp) cc_final: 0.8363 (tp) REVERT: Q 152 LEU cc_start: 0.9129 (tp) cc_final: 0.8790 (tp) REVERT: Q 239 THR cc_start: 0.6391 (p) cc_final: 0.6157 (p) REVERT: Q 302 MET cc_start: 0.7131 (ptp) cc_final: 0.6758 (mpp) REVERT: Q 378 LEU cc_start: 0.6880 (mm) cc_final: 0.6474 (mm) REVERT: Q 398 MET cc_start: 0.7643 (mtp) cc_final: 0.6218 (mmp) REVERT: R 259 MET cc_start: 0.7568 (mmm) cc_final: 0.6436 (mmt) REVERT: R 268 PHE cc_start: 0.6832 (m-80) cc_final: 0.4883 (m-80) REVERT: R 269 MET cc_start: 0.4674 (tpt) cc_final: 0.4132 (tpt) REVERT: R 314 THR cc_start: 0.7887 (p) cc_final: 0.7001 (p) REVERT: R 398 MET cc_start: 0.6909 (ptt) cc_final: 0.6394 (ptt) outliers start: 5 outliers final: 0 residues processed: 1518 average time/residue: 0.5791 time to fit residues: 1470.6161 Evaluate side-chains 1123 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1122 time to evaluate : 5.201 ------------------------------------------------------------------------------- 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: 9.9990 chunk 698 optimal weight: 1.9990 chunk 636 optimal weight: 20.0000 chunk 679 optimal weight: 50.0000 chunk 697 optimal weight: 8.9990 chunk 408 optimal weight: 20.0000 chunk 295 optimal weight: 50.0000 chunk 533 optimal weight: 0.0870 chunk 208 optimal weight: 30.0000 chunk 613 optimal weight: 2.9990 chunk 642 optimal weight: 0.7980 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 300 ASN C 309 HIS D 37 HIS D 85 GLN D 249 ASN E 258 ASN ** E 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS E 301 GLN F 37 HIS F 249 ASN F 309 HIS ** F 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 342 GLN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN H 294 GLN ** 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN J 249 ASN ** K 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 372 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN P 406 HIS Q 283 HIS Q 380 ASN R 197 ASN R 249 ASN ** R 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.8867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 62262 Z= 0.169 Angle : 0.627 11.934 84582 Z= 0.321 Chirality : 0.045 0.236 9216 Planarity : 0.005 0.049 11043 Dihedral : 9.716 175.589 8595 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.08 % Allowed : 0.53 % 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: 0.42 (0.10), residues: 7632 helix: 0.40 (0.09), residues: 3501 sheet: 0.75 (0.15), residues: 1242 loop : 0.12 (0.13), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP R 21 HIS 0.011 0.001 HIS F 28 PHE 0.026 0.001 PHE Q 138 TYR 0.032 0.001 TYR P 161 ARG 0.010 0.001 ARG R 79 *********************** 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 1496 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1491 time to evaluate : 5.221 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: A 21 TRP cc_start: 0.8638 (m100) cc_final: 0.8169 (m100) REVERT: A 33 ASP cc_start: 0.7311 (p0) cc_final: 0.6592 (t0) REVERT: A 53 PHE cc_start: 0.7942 (m-80) cc_final: 0.7152 (m-80) REVERT: A 75 ILE cc_start: 0.9453 (mm) cc_final: 0.7802 (tt) REVERT: A 129 CYS cc_start: 0.7607 (t) cc_final: 0.7356 (t) REVERT: A 179 THR cc_start: 0.7844 (m) cc_final: 0.7488 (m) REVERT: A 291 ILE cc_start: 0.9386 (mt) cc_final: 0.8344 (tp) REVERT: A 300 ASN cc_start: 0.8690 (p0) cc_final: 0.8234 (p0) REVERT: A 317 LEU cc_start: 0.8659 (mt) cc_final: 0.8243 (mt) REVERT: A 425 MET cc_start: 0.8504 (ptm) cc_final: 0.7992 (ppp) REVERT: B 14 ASN cc_start: 0.8139 (m-40) cc_final: 0.7766 (m-40) REVERT: B 21 TRP cc_start: 0.8318 (m100) cc_final: 0.7776 (m-10) REVERT: B 51 VAL cc_start: 0.8536 (t) cc_final: 0.8210 (m) REVERT: B 91 ASN cc_start: 0.8222 (m110) cc_final: 0.6819 (m110) REVERT: B 119 LEU cc_start: 0.7933 (mt) cc_final: 0.7558 (mt) REVERT: B 139 HIS cc_start: 0.7528 (p90) cc_final: 0.6692 (p90) REVERT: B 165 ILE cc_start: 0.8506 (mt) cc_final: 0.8100 (mt) REVERT: B 217 LEU cc_start: 0.9092 (mm) cc_final: 0.8699 (mm) REVERT: B 228 ASN cc_start: 0.8497 (m-40) cc_final: 0.7580 (t0) REVERT: B 267 PHE cc_start: 0.6488 (m-80) cc_final: 0.5913 (m-10) REVERT: B 269 MET cc_start: 0.7763 (ttt) cc_final: 0.6693 (ttm) REVERT: B 405 LEU cc_start: 0.8236 (mm) cc_final: 0.7999 (mt) REVERT: B 422 GLU cc_start: 0.8862 (pt0) cc_final: 0.8322 (pp20) REVERT: B 425 MET cc_start: 0.8047 (ttt) cc_final: 0.7824 (ttt) REVERT: B 432 TYR cc_start: 0.6353 (m-80) cc_final: 0.6128 (m-80) REVERT: C 27 GLU cc_start: 0.8103 (tt0) cc_final: 0.7729 (tt0) REVERT: C 217 LEU cc_start: 0.8979 (mm) cc_final: 0.8586 (mm) REVERT: C 317 LEU cc_start: 0.7977 (mm) cc_final: 0.7755 (mm) REVERT: D 53 TYR cc_start: 0.3116 (m-80) cc_final: 0.2817 (m-10) REVERT: D 68 VAL cc_start: 0.8418 (t) cc_final: 0.8118 (t) REVERT: D 119 LEU cc_start: 0.8837 (mt) cc_final: 0.8314 (mt) REVERT: D 165 ILE cc_start: 0.7883 (mt) cc_final: 0.7273 (mt) REVERT: D 199 ASP cc_start: 0.8553 (m-30) cc_final: 0.8187 (m-30) REVERT: D 235 MET cc_start: 0.9169 (mmp) cc_final: 0.8892 (mmt) REVERT: D 264 ARG cc_start: 0.6542 (mtt180) cc_final: 0.5874 (mtt180) REVERT: D 302 MET cc_start: 0.8676 (ptp) cc_final: 0.8056 (ptp) REVERT: D 405 LEU cc_start: 0.8371 (mt) cc_final: 0.8077 (mt) REVERT: E 53 PHE cc_start: 0.7233 (m-80) cc_final: 0.6774 (m-80) REVERT: E 129 CYS cc_start: 0.7483 (t) cc_final: 0.7131 (t) REVERT: E 203 MET cc_start: 0.8449 (tpp) cc_final: 0.8213 (tpp) REVERT: E 228 ASN cc_start: 0.8522 (m-40) cc_final: 0.7711 (p0) REVERT: E 280 LYS cc_start: 0.7552 (mtmt) cc_final: 0.6818 (mmtt) REVERT: E 291 ILE cc_start: 0.9109 (mt) cc_final: 0.7903 (tp) REVERT: E 318 LEU cc_start: 0.6832 (pp) cc_final: 0.6629 (pp) REVERT: E 347 CYS cc_start: 0.8287 (p) cc_final: 0.7588 (p) REVERT: E 425 MET cc_start: 0.8563 (ptm) cc_final: 0.8185 (tmm) REVERT: F 53 TYR cc_start: 0.3865 (m-80) cc_final: 0.3576 (m-80) REVERT: F 66 ILE cc_start: 0.8456 (mm) cc_final: 0.7987 (mm) REVERT: F 108 TYR cc_start: 0.4092 (t80) cc_final: 0.3758 (t80) REVERT: F 116 ASP cc_start: 0.7378 (m-30) cc_final: 0.6936 (m-30) REVERT: F 119 LEU cc_start: 0.8312 (tp) cc_final: 0.7953 (tp) REVERT: F 123 ARG cc_start: 0.7231 (ptp-110) cc_final: 0.6819 (ptp-110) REVERT: F 139 HIS cc_start: 0.7617 (p90) cc_final: 0.6435 (p90) REVERT: F 163 ASP cc_start: 0.7550 (p0) cc_final: 0.6741 (p0) REVERT: F 166 MET cc_start: 0.7762 (mmp) cc_final: 0.7404 (mmm) REVERT: F 181 VAL cc_start: 0.8857 (t) cc_final: 0.8599 (t) REVERT: F 302 MET cc_start: 0.7638 (tpt) cc_final: 0.7360 (tpt) REVERT: F 351 VAL cc_start: 0.8582 (t) cc_final: 0.8172 (t) REVERT: F 355 VAL cc_start: 0.7655 (t) cc_final: 0.7422 (t) REVERT: F 369 ARG cc_start: 0.8333 (tmm-80) cc_final: 0.7814 (tmm-80) REVERT: G 21 TRP cc_start: 0.8403 (m100) cc_final: 0.7499 (m100) REVERT: G 62 VAL cc_start: 0.6892 (p) cc_final: 0.6495 (p) REVERT: G 155 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6190 (tm-30) REVERT: G 376 CYS cc_start: 0.7236 (t) cc_final: 0.6759 (t) REVERT: G 378 LEU cc_start: 0.6991 (mm) cc_final: 0.6564 (mm) REVERT: H 19 LYS cc_start: 0.8901 (mmmt) cc_final: 0.8401 (mmmt) REVERT: H 21 TRP cc_start: 0.7523 (m100) cc_final: 0.7063 (m100) REVERT: H 76 ASP cc_start: 0.6145 (p0) cc_final: 0.5853 (p0) REVERT: H 132 LEU cc_start: 0.9006 (tp) cc_final: 0.8652 (tp) REVERT: H 153 LEU cc_start: 0.9184 (mt) cc_final: 0.8909 (mt) REVERT: H 176 LYS cc_start: 0.7379 (mmmt) cc_final: 0.6009 (tmtt) REVERT: H 269 MET cc_start: 0.4981 (ptt) cc_final: 0.4574 (ptt) REVERT: H 275 LEU cc_start: 0.7857 (pt) cc_final: 0.7602 (pt) REVERT: H 288 VAL cc_start: 0.8871 (t) cc_final: 0.8661 (t) REVERT: H 301 MET cc_start: 0.7504 (ppp) cc_final: 0.6661 (ppp) REVERT: I 27 GLU cc_start: 0.8373 (pt0) cc_final: 0.7625 (tm-30) REVERT: I 53 PHE cc_start: 0.7039 (m-80) cc_final: 0.6092 (m-80) REVERT: I 211 ASP cc_start: 0.5847 (t0) cc_final: 0.5635 (t0) REVERT: I 286 LEU cc_start: 0.7381 (mt) cc_final: 0.6721 (mt) REVERT: I 288 VAL cc_start: 0.8515 (m) cc_final: 0.7816 (t) REVERT: I 302 MET cc_start: 0.6288 (mpp) cc_final: 0.5110 (mpp) REVERT: J 123 ARG cc_start: 0.7532 (ttp80) cc_final: 0.7304 (ttp80) REVERT: J 165 ILE cc_start: 0.7662 (pt) cc_final: 0.6725 (pt) REVERT: J 258 ASN cc_start: 0.8984 (m-40) cc_final: 0.8610 (m-40) REVERT: J 266 HIS cc_start: 0.7502 (p90) cc_final: 0.7023 (p-80) REVERT: J 295 MET cc_start: 0.7865 (tmm) cc_final: 0.7378 (tmm) REVERT: J 393 GLU cc_start: 0.9006 (mp0) cc_final: 0.8781 (mp0) REVERT: K 33 ASP cc_start: 0.5647 (p0) cc_final: 0.5117 (t70) REVERT: K 78 VAL cc_start: 0.8581 (t) cc_final: 0.8070 (t) REVERT: K 120 ASP cc_start: 0.8037 (m-30) cc_final: 0.6639 (t70) REVERT: K 121 ARG cc_start: 0.6517 (mmp80) cc_final: 0.5887 (mmm160) REVERT: K 149 PHE cc_start: 0.6324 (t80) cc_final: 0.6014 (t80) REVERT: K 169 PHE cc_start: 0.6764 (m-80) cc_final: 0.6544 (m-80) REVERT: K 288 VAL cc_start: 0.8787 (m) cc_final: 0.8222 (p) REVERT: K 291 ILE cc_start: 0.8738 (mt) cc_final: 0.8447 (mt) REVERT: K 325 PRO cc_start: 0.8820 (Cg_exo) cc_final: 0.8490 (Cg_endo) REVERT: K 335 ILE cc_start: 0.8949 (pt) cc_final: 0.8097 (tp) REVERT: K 386 GLU cc_start: 0.8580 (mp0) cc_final: 0.8288 (mp0) REVERT: L 21 TRP cc_start: 0.7684 (m100) cc_final: 0.6417 (m100) REVERT: L 87 PHE cc_start: 0.7737 (m-80) cc_final: 0.7376 (m-80) REVERT: L 120 ASP cc_start: 0.7851 (t70) cc_final: 0.7630 (t70) REVERT: L 124 LYS cc_start: 0.7375 (pttm) cc_final: 0.7090 (pttp) REVERT: L 138 THR cc_start: 0.4934 (p) cc_final: 0.4519 (p) REVERT: L 163 ASP cc_start: 0.6549 (p0) cc_final: 0.6067 (m-30) REVERT: L 264 ARG cc_start: 0.3333 (mtt180) cc_final: 0.2692 (ttt180) REVERT: L 327 GLU cc_start: 0.7332 (mp0) cc_final: 0.6077 (tm-30) REVERT: L 330 GLU cc_start: 0.7602 (tp30) cc_final: 0.7064 (tp30) REVERT: M 21 TRP cc_start: 0.8429 (m100) cc_final: 0.7617 (m100) REVERT: M 23 LEU cc_start: 0.8201 (tp) cc_final: 0.7883 (tp) REVERT: M 291 ILE cc_start: 0.7770 (mt) cc_final: 0.7377 (mt) REVERT: M 335 ILE cc_start: 0.8216 (pt) cc_final: 0.7867 (tp) REVERT: M 392 ASP cc_start: 0.7626 (m-30) cc_final: 0.6694 (m-30) REVERT: M 413 MET cc_start: 0.8995 (mmm) cc_final: 0.8639 (mmm) REVERT: N 132 LEU cc_start: 0.8424 (mm) cc_final: 0.8220 (tp) REVERT: N 154 ILE cc_start: 0.8763 (tp) cc_final: 0.8549 (mm) REVERT: N 163 ASP cc_start: 0.8658 (p0) cc_final: 0.7632 (p0) REVERT: N 259 MET cc_start: 0.7645 (mmm) cc_final: 0.6759 (mmp) REVERT: N 268 PHE cc_start: 0.7062 (m-10) cc_final: 0.6666 (m-80) REVERT: N 315 VAL cc_start: 0.7112 (t) cc_final: 0.6804 (t) REVERT: N 333 LEU cc_start: 0.7166 (tp) cc_final: 0.6890 (tp) REVERT: N 351 VAL cc_start: 0.8902 (t) cc_final: 0.8583 (t) REVERT: N 384 ILE cc_start: 0.8755 (mp) cc_final: 0.8142 (mm) REVERT: N 391 ILE cc_start: 0.8761 (mm) cc_final: 0.8497 (mm) REVERT: N 413 MET cc_start: 0.6231 (mmt) cc_final: 0.5806 (mmp) REVERT: O 21 TRP cc_start: 0.8255 (m100) cc_final: 0.7471 (m100) REVERT: O 23 LEU cc_start: 0.8018 (tp) cc_final: 0.7657 (tp) REVERT: O 36 MET cc_start: 0.2316 (ttp) cc_final: 0.0939 (ttp) REVERT: O 86 LEU cc_start: 0.8712 (tp) cc_final: 0.8418 (tp) REVERT: O 152 LEU cc_start: 0.9159 (tp) cc_final: 0.8909 (tp) REVERT: O 154 MET cc_start: 0.7669 (ttt) cc_final: 0.7423 (ttt) REVERT: O 239 THR cc_start: 0.7258 (p) cc_final: 0.7019 (p) REVERT: O 305 CYS cc_start: 0.6210 (p) cc_final: 0.5951 (p) REVERT: O 360 PRO cc_start: 0.9146 (Cg_exo) cc_final: 0.8656 (Cg_endo) REVERT: O 363 VAL cc_start: 0.8621 (t) cc_final: 0.8411 (t) REVERT: O 373 ARG cc_start: 0.8787 (ptp90) cc_final: 0.8151 (mtp180) REVERT: P 21 TRP cc_start: 0.8665 (m100) cc_final: 0.8109 (m100) REVERT: P 22 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6368 (tm-30) REVERT: P 26 ASP cc_start: 0.6959 (m-30) cc_final: 0.6623 (m-30) REVERT: P 47 GLU cc_start: 0.8174 (pm20) cc_final: 0.7771 (pm20) REVERT: P 115 VAL cc_start: 0.9258 (t) cc_final: 0.9024 (t) REVERT: P 230 LEU cc_start: 0.8881 (tt) cc_final: 0.8533 (tt) REVERT: P 252 LEU cc_start: 0.7331 (mt) cc_final: 0.7099 (mp) REVERT: P 259 MET cc_start: 0.7372 (mmm) cc_final: 0.6718 (mmt) REVERT: P 268 PHE cc_start: 0.8113 (m-80) cc_final: 0.7527 (m-80) REVERT: P 314 THR cc_start: 0.7615 (p) cc_final: 0.7404 (p) REVERT: P 332 MET cc_start: 0.7258 (ppp) cc_final: 0.7037 (ppp) REVERT: P 335 VAL cc_start: 0.8067 (t) cc_final: 0.7863 (t) REVERT: P 389 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8368 (ptpp) REVERT: P 425 MET cc_start: 0.7691 (ttt) cc_final: 0.7485 (tpp) REVERT: Q 86 LEU cc_start: 0.8525 (tp) cc_final: 0.8242 (tp) REVERT: Q 214 ARG cc_start: 0.5086 (ptp-110) cc_final: 0.4803 (ptp-110) REVERT: Q 302 MET cc_start: 0.6795 (ptp) cc_final: 0.6533 (mpp) REVERT: Q 378 LEU cc_start: 0.7084 (mm) cc_final: 0.6595 (mm) REVERT: Q 398 MET cc_start: 0.7498 (mtp) cc_final: 0.6323 (mmp) REVERT: R 66 ILE cc_start: 0.7948 (mm) cc_final: 0.7736 (mm) REVERT: R 120 ASP cc_start: 0.7682 (m-30) cc_final: 0.7190 (m-30) REVERT: R 139 HIS cc_start: 0.6702 (p90) cc_final: 0.6097 (p90) REVERT: R 197 ASN cc_start: 0.7187 (m110) cc_final: 0.6650 (t0) REVERT: R 259 MET cc_start: 0.7513 (mmm) cc_final: 0.7062 (mmt) REVERT: R 269 MET cc_start: 0.4700 (tpt) cc_final: 0.4033 (tpt) REVERT: R 314 THR cc_start: 0.7781 (p) cc_final: 0.6787 (p) REVERT: R 325 MET cc_start: 0.6620 (tpp) cc_final: 0.6311 (tpp) REVERT: R 398 MET cc_start: 0.7057 (ptt) cc_final: 0.6390 (ptt) outliers start: 5 outliers final: 1 residues processed: 1491 average time/residue: 0.5797 time to fit residues: 1448.0825 Evaluate side-chains 1140 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1139 time to evaluate : 5.147 ------------------------------------------------------------------------------- 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: 50.0000 chunk 445 optimal weight: 6.9990 chunk 718 optimal weight: 5.9990 chunk 438 optimal weight: 5.9990 chunk 340 optimal weight: 30.0000 chunk 499 optimal weight: 30.0000 chunk 753 optimal weight: 5.9990 chunk 693 optimal weight: 50.0000 chunk 599 optimal weight: 8.9990 chunk 62 optimal weight: 40.0000 chunk 463 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN C 309 HIS D 37 HIS D 249 ASN D 309 HIS ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS F 37 HIS F 249 ASN F 309 HIS G 197 HIS G 329 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 229 HIS 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** ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 186 ASN ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 ASN ** 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 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 91 GLN M 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 176 GLN P 37 HIS ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 HIS R 249 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.9101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62262 Z= 0.195 Angle : 0.650 11.325 84582 Z= 0.334 Chirality : 0.045 0.248 9216 Planarity : 0.005 0.107 11043 Dihedral : 9.558 175.913 8595 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.09 % Allowed : 0.23 % Favored : 99.68 % 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: 0.39 (0.10), residues: 7632 helix: 0.41 (0.09), residues: 3456 sheet: 0.67 (0.15), residues: 1260 loop : 0.12 (0.13), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.003 TRP J 21 HIS 0.011 0.001 HIS E 283 PHE 0.044 0.002 PHE J 169 TYR 0.046 0.002 TYR R 161 ARG 0.009 0.001 ARG R 79 ********************** 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 1432 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1426 time to evaluate : 5.184 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: A 21 TRP cc_start: 0.8650 (m100) cc_final: 0.8201 (m100) REVERT: A 33 ASP cc_start: 0.7600 (p0) cc_final: 0.6645 (t0) REVERT: A 75 ILE cc_start: 0.9406 (mm) cc_final: 0.8000 (tt) REVERT: A 129 CYS cc_start: 0.7505 (t) cc_final: 0.7265 (t) REVERT: A 252 LEU cc_start: 0.8409 (mt) cc_final: 0.7739 (mt) REVERT: A 291 ILE cc_start: 0.9385 (mt) cc_final: 0.8281 (tp) REVERT: A 300 ASN cc_start: 0.8713 (p0) cc_final: 0.8166 (p0) REVERT: A 317 LEU cc_start: 0.8655 (mt) cc_final: 0.8140 (mt) REVERT: A 347 CYS cc_start: 0.7676 (p) cc_final: 0.7211 (p) REVERT: A 425 MET cc_start: 0.8535 (ptm) cc_final: 0.7933 (ppp) REVERT: A 435 VAL cc_start: 0.9289 (t) cc_final: 0.9025 (t) REVERT: B 21 TRP cc_start: 0.7806 (m100) cc_final: 0.7377 (m-10) REVERT: B 22 GLU cc_start: 0.7519 (tp30) cc_final: 0.7010 (tp30) REVERT: B 26 ASP cc_start: 0.8341 (m-30) cc_final: 0.8096 (m-30) REVERT: B 51 VAL cc_start: 0.8550 (t) cc_final: 0.8347 (p) REVERT: B 91 ASN cc_start: 0.8162 (m110) cc_final: 0.6994 (m110) REVERT: B 119 LEU cc_start: 0.8054 (mt) cc_final: 0.7567 (mt) REVERT: B 139 HIS cc_start: 0.7785 (p90) cc_final: 0.6736 (p90) REVERT: B 166 MET cc_start: 0.6079 (ptp) cc_final: 0.5849 (ptp) REVERT: B 228 ASN cc_start: 0.8514 (m-40) cc_final: 0.7627 (t0) REVERT: B 267 PHE cc_start: 0.6501 (m-80) cc_final: 0.6036 (m-10) REVERT: B 269 MET cc_start: 0.7711 (ttt) cc_final: 0.7137 (ttm) REVERT: B 278 ARG cc_start: 0.6821 (mmt180) cc_final: 0.6578 (mmt180) REVERT: B 386 GLU cc_start: 0.8463 (pp20) cc_final: 0.8236 (tm-30) REVERT: B 405 LEU cc_start: 0.8451 (mm) cc_final: 0.8136 (mt) REVERT: B 422 GLU cc_start: 0.8746 (pt0) cc_final: 0.8144 (pp20) REVERT: C 123 ARG cc_start: 0.7449 (tpp80) cc_final: 0.7237 (tpp80) REVERT: C 217 LEU cc_start: 0.8994 (mm) cc_final: 0.8699 (mm) REVERT: C 313 MET cc_start: 0.5999 (mpp) cc_final: 0.5612 (mmt) REVERT: D 68 VAL cc_start: 0.8217 (t) cc_final: 0.7992 (t) REVERT: D 119 LEU cc_start: 0.8629 (mt) cc_final: 0.8363 (mt) REVERT: D 129 CYS cc_start: 0.8423 (m) cc_final: 0.7784 (m) REVERT: D 154 ILE cc_start: 0.9309 (mp) cc_final: 0.8957 (mm) REVERT: D 163 ASP cc_start: 0.8012 (p0) cc_final: 0.7631 (p0) REVERT: D 165 ILE cc_start: 0.7621 (mt) cc_final: 0.6967 (mt) REVERT: D 166 MET cc_start: 0.7153 (mmp) cc_final: 0.6851 (mmm) REVERT: D 235 MET cc_start: 0.9263 (mmp) cc_final: 0.8665 (mmt) REVERT: D 264 ARG cc_start: 0.6162 (mtt180) cc_final: 0.5593 (mtt180) REVERT: D 302 MET cc_start: 0.8653 (ptp) cc_final: 0.8152 (ptp) REVERT: D 309 HIS cc_start: 0.4833 (OUTLIER) cc_final: 0.4427 (t-90) REVERT: D 369 ARG cc_start: 0.7759 (tmm-80) cc_final: 0.7479 (tmm-80) REVERT: D 405 LEU cc_start: 0.8434 (mt) cc_final: 0.8200 (mt) REVERT: E 21 TRP cc_start: 0.8249 (m100) cc_final: 0.8000 (m100) REVERT: E 53 PHE cc_start: 0.7481 (m-80) cc_final: 0.6827 (m-80) REVERT: E 129 CYS cc_start: 0.7652 (t) cc_final: 0.7301 (t) REVERT: E 214 ARG cc_start: 0.6216 (ttm110) cc_final: 0.5785 (ptp-110) REVERT: E 280 LYS cc_start: 0.7614 (mtmt) cc_final: 0.6911 (mmtt) REVERT: E 291 ILE cc_start: 0.9165 (mt) cc_final: 0.8019 (tp) REVERT: E 300 ASN cc_start: 0.7264 (p0) cc_final: 0.6902 (p0) REVERT: E 318 LEU cc_start: 0.6331 (pp) cc_final: 0.6085 (pp) REVERT: E 347 CYS cc_start: 0.8469 (p) cc_final: 0.7838 (p) REVERT: E 425 MET cc_start: 0.8573 (ptm) cc_final: 0.8117 (tmm) REVERT: F 53 TYR cc_start: 0.3715 (m-80) cc_final: 0.3275 (m-80) REVERT: F 108 TYR cc_start: 0.4261 (t80) cc_final: 0.4032 (t80) REVERT: F 116 ASP cc_start: 0.7467 (m-30) cc_final: 0.7068 (m-30) REVERT: F 123 ARG cc_start: 0.7567 (ptp-110) cc_final: 0.7221 (ptm160) REVERT: F 139 HIS cc_start: 0.7502 (p90) cc_final: 0.6458 (p90) REVERT: F 166 MET cc_start: 0.7728 (mmp) cc_final: 0.7446 (mmm) REVERT: F 181 VAL cc_start: 0.8780 (t) cc_final: 0.8441 (t) REVERT: F 243 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8206 (mtm110) REVERT: F 286 LEU cc_start: 0.8830 (mm) cc_final: 0.8575 (mm) REVERT: F 369 ARG cc_start: 0.8141 (tmm-80) cc_final: 0.7544 (tmm-80) REVERT: G 21 TRP cc_start: 0.8636 (m100) cc_final: 0.7817 (m100) REVERT: G 53 PHE cc_start: 0.7224 (m-80) cc_final: 0.6438 (m-80) REVERT: G 135 PHE cc_start: 0.7468 (p90) cc_final: 0.7251 (p90) REVERT: G 435 VAL cc_start: 0.8983 (t) cc_final: 0.8764 (t) REVERT: H 21 TRP cc_start: 0.7430 (m100) cc_final: 0.6965 (m100) REVERT: H 132 LEU cc_start: 0.8962 (tp) cc_final: 0.8631 (tp) REVERT: H 153 LEU cc_start: 0.9148 (mt) cc_final: 0.8881 (mt) REVERT: H 288 VAL cc_start: 0.8845 (t) cc_final: 0.8312 (t) REVERT: H 301 MET cc_start: 0.7650 (ppp) cc_final: 0.6516 (ppp) REVERT: H 333 LEU cc_start: 0.8356 (mt) cc_final: 0.8102 (mt) REVERT: I 53 PHE cc_start: 0.7069 (m-80) cc_final: 0.6160 (m-80) REVERT: I 211 ASP cc_start: 0.5879 (t0) cc_final: 0.5622 (t0) REVERT: I 269 LEU cc_start: 0.5962 (mt) cc_final: 0.5732 (mt) REVERT: I 286 LEU cc_start: 0.6779 (mt) cc_final: 0.6224 (mp) REVERT: I 288 VAL cc_start: 0.8633 (m) cc_final: 0.7824 (t) REVERT: I 302 MET cc_start: 0.6833 (mpp) cc_final: 0.5821 (mpp) REVERT: I 413 MET cc_start: 0.8054 (mmp) cc_final: 0.7762 (mmp) REVERT: J 6 HIS cc_start: 0.7747 (t70) cc_final: 0.7216 (t70) REVERT: J 165 ILE cc_start: 0.7706 (pt) cc_final: 0.6887 (pt) REVERT: J 195 VAL cc_start: 0.6771 (m) cc_final: 0.6283 (p) REVERT: J 239 THR cc_start: 0.9119 (t) cc_final: 0.8830 (t) REVERT: J 259 MET cc_start: 0.6982 (mmp) cc_final: 0.6756 (mmm) REVERT: J 266 HIS cc_start: 0.7485 (p90) cc_final: 0.7066 (p-80) REVERT: J 330 GLU cc_start: 0.7241 (mt-10) cc_final: 0.6973 (mp0) REVERT: K 23 LEU cc_start: 0.8364 (tp) cc_final: 0.8095 (tp) REVERT: K 33 ASP cc_start: 0.5878 (p0) cc_final: 0.5006 (t70) REVERT: K 36 MET cc_start: 0.7134 (mmm) cc_final: 0.6732 (mmm) REVERT: K 78 VAL cc_start: 0.8660 (t) cc_final: 0.8089 (t) REVERT: K 120 ASP cc_start: 0.7700 (m-30) cc_final: 0.6318 (t70) REVERT: K 121 ARG cc_start: 0.6855 (mmp80) cc_final: 0.6129 (mmm160) REVERT: K 132 LEU cc_start: 0.7724 (tp) cc_final: 0.7507 (tp) REVERT: K 149 PHE cc_start: 0.6613 (t80) cc_final: 0.5979 (t80) REVERT: K 167 LEU cc_start: 0.8098 (mm) cc_final: 0.7724 (mm) REVERT: K 169 PHE cc_start: 0.6447 (m-80) cc_final: 0.5952 (m-80) REVERT: K 288 VAL cc_start: 0.8758 (m) cc_final: 0.8401 (p) REVERT: K 335 ILE cc_start: 0.8897 (pt) cc_final: 0.8090 (tp) REVERT: K 386 GLU cc_start: 0.8599 (mp0) cc_final: 0.8256 (mp0) REVERT: L 21 TRP cc_start: 0.7758 (m100) cc_final: 0.6325 (m100) REVERT: L 132 LEU cc_start: 0.8078 (tp) cc_final: 0.7773 (tp) REVERT: L 163 ASP cc_start: 0.6914 (p0) cc_final: 0.6379 (m-30) REVERT: L 327 GLU cc_start: 0.7266 (mp0) cc_final: 0.6082 (tm-30) REVERT: L 330 GLU cc_start: 0.7641 (tp30) cc_final: 0.7291 (tp30) REVERT: L 334 ASN cc_start: 0.8395 (m110) cc_final: 0.7578 (m110) REVERT: M 21 TRP cc_start: 0.8588 (m100) cc_final: 0.7614 (m100) REVERT: M 23 LEU cc_start: 0.8333 (tp) cc_final: 0.7958 (tp) REVERT: M 291 ILE cc_start: 0.7700 (mt) cc_final: 0.7287 (mt) REVERT: M 335 ILE cc_start: 0.8282 (pt) cc_final: 0.7938 (tp) REVERT: M 392 ASP cc_start: 0.7677 (m-30) cc_final: 0.7329 (m-30) REVERT: M 413 MET cc_start: 0.9028 (mmm) cc_final: 0.8653 (mmm) REVERT: N 132 LEU cc_start: 0.8490 (mm) cc_final: 0.8218 (mt) REVERT: N 163 ASP cc_start: 0.8780 (p0) cc_final: 0.7727 (p0) REVERT: N 259 MET cc_start: 0.7340 (mmm) cc_final: 0.6788 (mmp) REVERT: N 266 HIS cc_start: 0.5876 (p-80) cc_final: 0.5214 (p-80) REVERT: N 268 PHE cc_start: 0.6768 (m-10) cc_final: 0.6534 (m-80) REVERT: N 332 MET cc_start: 0.6722 (tmm) cc_final: 0.6472 (tmm) REVERT: N 384 ILE cc_start: 0.8779 (mp) cc_final: 0.8506 (mp) REVERT: N 413 MET cc_start: 0.6231 (mmt) cc_final: 0.5840 (mmp) REVERT: O 21 TRP cc_start: 0.8280 (m100) cc_final: 0.7534 (m100) REVERT: O 23 LEU cc_start: 0.7976 (tp) cc_final: 0.7622 (tp) REVERT: O 66 VAL cc_start: 0.7411 (t) cc_final: 0.7063 (t) REVERT: O 86 LEU cc_start: 0.8686 (tp) cc_final: 0.8429 (tp) REVERT: O 154 MET cc_start: 0.7224 (ttt) cc_final: 0.6899 (ttt) REVERT: O 335 ILE cc_start: 0.8266 (mm) cc_final: 0.7989 (mm) REVERT: O 360 PRO cc_start: 0.9153 (Cg_exo) cc_final: 0.8721 (Cg_endo) REVERT: P 21 TRP cc_start: 0.8619 (m100) cc_final: 0.8010 (m100) REVERT: P 22 GLU cc_start: 0.7179 (tm-30) cc_final: 0.6566 (tm-30) REVERT: P 165 ILE cc_start: 0.7767 (mt) cc_final: 0.7508 (mt) REVERT: P 230 LEU cc_start: 0.8925 (tt) cc_final: 0.8599 (tt) REVERT: P 240 THR cc_start: 0.7860 (t) cc_final: 0.7097 (m) REVERT: P 252 LEU cc_start: 0.7545 (mt) cc_final: 0.7109 (mp) REVERT: P 259 MET cc_start: 0.7265 (mmm) cc_final: 0.6599 (mmt) REVERT: P 314 THR cc_start: 0.7736 (p) cc_final: 0.7480 (p) REVERT: P 384 ILE cc_start: 0.8385 (mt) cc_final: 0.8037 (mt) REVERT: P 386 GLU cc_start: 0.8068 (tm-30) cc_final: 0.7835 (tm-30) REVERT: Q 86 LEU cc_start: 0.8451 (tp) cc_final: 0.8245 (tp) REVERT: Q 214 ARG cc_start: 0.5030 (ptp-110) cc_final: 0.4774 (ptp-110) REVERT: Q 239 THR cc_start: 0.7702 (p) cc_final: 0.7438 (p) REVERT: Q 302 MET cc_start: 0.7008 (ptp) cc_final: 0.6664 (mpp) REVERT: Q 378 LEU cc_start: 0.7259 (mm) cc_final: 0.6769 (mm) REVERT: Q 398 MET cc_start: 0.7609 (mtp) cc_final: 0.6310 (mmp) REVERT: R 7 ILE cc_start: 0.8840 (mp) cc_final: 0.8548 (mp) REVERT: R 120 ASP cc_start: 0.7409 (m-30) cc_final: 0.7205 (m-30) REVERT: R 259 MET cc_start: 0.7657 (mmm) cc_final: 0.7159 (mmt) REVERT: R 266 HIS cc_start: 0.7537 (p90) cc_final: 0.7047 (p90) REVERT: R 269 MET cc_start: 0.4823 (tpt) cc_final: 0.4116 (tpt) REVERT: R 314 THR cc_start: 0.7863 (p) cc_final: 0.6879 (p) REVERT: R 315 VAL cc_start: 0.7865 (t) cc_final: 0.7544 (t) REVERT: R 398 MET cc_start: 0.7115 (ptt) cc_final: 0.6531 (ptt) outliers start: 6 outliers final: 1 residues processed: 1427 average time/residue: 0.5727 time to fit residues: 1374.4289 Evaluate side-chains 1098 residues out of total 6543 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1096 time to evaluate : 5.152 ------------------------------------------------------------------------------- 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: 0.9990 chunk 476 optimal weight: 50.0000 chunk 638 optimal weight: 7.9990 chunk 183 optimal weight: 30.0000 chunk 553 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 600 optimal weight: 7.9990 chunk 251 optimal weight: 20.0000 chunk 616 optimal weight: 50.0000 chunk 76 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN ** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN D 37 HIS D 249 ASN ** E 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 HIS F 37 HIS F 249 ASN F 309 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 249 ASN ** H 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 11 GLN ** 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** ** J 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 394 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 216 ASN ** 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 309 HIS ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 128 GLN P 37 HIS ** P 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 406 HIS R 249 ASN R 309 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.076481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.062315 restraints weight = 209497.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.065129 restraints weight = 126995.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.067217 restraints weight = 84670.994| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.9298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 62262 Z= 0.186 Angle : 0.645 10.549 84582 Z= 0.330 Chirality : 0.045 0.240 9216 Planarity : 0.005 0.082 11043 Dihedral : 9.354 175.363 8595 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.08 % Allowed : 0.24 % Favored : 99.68 % 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: 0.29 (0.10), residues: 7632 helix: 0.32 (0.09), residues: 3501 sheet: 0.65 (0.15), residues: 1260 loop : 0.05 (0.12), residues: 2871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP R 21 HIS 0.012 0.001 HIS I 61 PHE 0.030 0.001 PHE L 395 TYR 0.041 0.002 TYR R 161 ARG 0.009 0.001 ARG R 79 =============================================================================== Job complete usr+sys time: 21137.25 seconds wall clock time: 369 minutes 53.60 seconds (22193.60 seconds total)