Starting phenix.real_space_refine on Sat Mar 16 11:59:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwr_20926/03_2024/6uwr_20926.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwr_20926/03_2024/6uwr_20926.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwr_20926/03_2024/6uwr_20926.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwr_20926/03_2024/6uwr_20926.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwr_20926/03_2024/6uwr_20926.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6uwr_20926/03_2024/6uwr_20926.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 42 9.91 5 S 140 5.16 5 C 45528 2.51 5 N 11816 2.21 5 O 15232 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 218": "OD1" <-> "OD2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 318": "OD1" <-> "OD2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 465": "OD1" <-> "OD2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 520": "OD1" <-> "OD2" Residue "A TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 544": "OE1" <-> "OE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 582": "OD1" <-> "OD2" Residue "A ASP 624": "OD1" <-> "OD2" Residue "A TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 677": "OD1" <-> "OD2" Residue "A GLU 692": "OE1" <-> "OE2" Residue "A TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 715": "OE1" <-> "OE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A ASP 749": "OD1" <-> "OD2" Residue "A GLU 752": "OE1" <-> "OE2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A ASP 763": "OD1" <-> "OD2" Residue "A TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 867": "OD1" <-> "OD2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 318": "OD1" <-> "OD2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 465": "OD1" <-> "OD2" Residue "B PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 520": "OD1" <-> "OD2" Residue "B TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B ASP 561": "OD1" <-> "OD2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B ASP 624": "OD1" <-> "OD2" Residue "B TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 677": "OD1" <-> "OD2" Residue "B GLU 692": "OE1" <-> "OE2" Residue "B TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 715": "OE1" <-> "OE2" Residue "B ASP 717": "OD1" <-> "OD2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B GLU 752": "OE1" <-> "OE2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B ASP 763": "OD1" <-> "OD2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 867": "OD1" <-> "OD2" Residue "C ASP 218": "OD1" <-> "OD2" Residue "C TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 318": "OD1" <-> "OD2" Residue "C ARG 325": "NH1" <-> "NH2" Residue "C PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 465": "OD1" <-> "OD2" Residue "C PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 520": "OD1" <-> "OD2" Residue "C TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 544": "OE1" <-> "OE2" Residue "C ASP 561": "OD1" <-> "OD2" Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 568": "OD1" <-> "OD2" Residue "C ASP 582": "OD1" <-> "OD2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 677": "OD1" <-> "OD2" Residue "C GLU 692": "OE1" <-> "OE2" Residue "C TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 715": "OE1" <-> "OE2" Residue "C ASP 717": "OD1" <-> "OD2" Residue "C ASP 749": "OD1" <-> "OD2" Residue "C GLU 752": "OE1" <-> "OE2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "C ASP 763": "OD1" <-> "OD2" Residue "C TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 867": "OD1" <-> "OD2" Residue "D ASP 218": "OD1" <-> "OD2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 318": "OD1" <-> "OD2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 465": "OD1" <-> "OD2" Residue "D PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 520": "OD1" <-> "OD2" Residue "D TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "D ASP 561": "OD1" <-> "OD2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 568": "OD1" <-> "OD2" Residue "D ASP 582": "OD1" <-> "OD2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 677": "OD1" <-> "OD2" Residue "D GLU 692": "OE1" <-> "OE2" Residue "D TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 715": "OE1" <-> "OE2" Residue "D ASP 717": "OD1" <-> "OD2" Residue "D ASP 749": "OD1" <-> "OD2" Residue "D GLU 752": "OE1" <-> "OE2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D ASP 763": "OD1" <-> "OD2" Residue "D TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 867": "OD1" <-> "OD2" Residue "E ASP 218": "OD1" <-> "OD2" Residue "E TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 318": "OD1" <-> "OD2" Residue "E ARG 325": "NH1" <-> "NH2" Residue "E PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 465": "OD1" <-> "OD2" Residue "E PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 520": "OD1" <-> "OD2" Residue "E TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 544": "OE1" <-> "OE2" Residue "E ASP 561": "OD1" <-> "OD2" Residue "E TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 568": "OD1" <-> "OD2" Residue "E ASP 582": "OD1" <-> "OD2" Residue "E ASP 624": "OD1" <-> "OD2" Residue "E TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 677": "OD1" <-> "OD2" Residue "E GLU 692": "OE1" <-> "OE2" Residue "E TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 715": "OE1" <-> "OE2" Residue "E ASP 717": "OD1" <-> "OD2" Residue "E ASP 749": "OD1" <-> "OD2" Residue "E GLU 752": "OE1" <-> "OE2" Residue "E GLU 760": "OE1" <-> "OE2" Residue "E ASP 763": "OD1" <-> "OD2" Residue "E TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 867": "OD1" <-> "OD2" Residue "F ASP 218": "OD1" <-> "OD2" Residue "F TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 318": "OD1" <-> "OD2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 465": "OD1" <-> "OD2" Residue "F PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 520": "OD1" <-> "OD2" Residue "F TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 544": "OE1" <-> "OE2" Residue "F ASP 561": "OD1" <-> "OD2" Residue "F TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 568": "OD1" <-> "OD2" Residue "F ASP 582": "OD1" <-> "OD2" Residue "F ASP 624": "OD1" <-> "OD2" Residue "F TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 677": "OD1" <-> "OD2" Residue "F GLU 692": "OE1" <-> "OE2" Residue "F TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 715": "OE1" <-> "OE2" Residue "F ASP 717": "OD1" <-> "OD2" Residue "F ASP 749": "OD1" <-> "OD2" Residue "F GLU 752": "OE1" <-> "OE2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F ASP 763": "OD1" <-> "OD2" Residue "F TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 867": "OD1" <-> "OD2" Residue "G ASP 218": "OD1" <-> "OD2" Residue "G TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 318": "OD1" <-> "OD2" Residue "G ARG 325": "NH1" <-> "NH2" Residue "G PHE 349": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 465": "OD1" <-> "OD2" Residue "G PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 520": "OD1" <-> "OD2" Residue "G TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 544": "OE1" <-> "OE2" Residue "G ASP 561": "OD1" <-> "OD2" Residue "G TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 568": "OD1" <-> "OD2" Residue "G ASP 582": "OD1" <-> "OD2" Residue "G ASP 624": "OD1" <-> "OD2" Residue "G TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 677": "OD1" <-> "OD2" Residue "G GLU 692": "OE1" <-> "OE2" Residue "G TYR 704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 715": "OE1" <-> "OE2" Residue "G ASP 717": "OD1" <-> "OD2" Residue "G ASP 749": "OD1" <-> "OD2" Residue "G GLU 752": "OE1" <-> "OE2" Residue "G GLU 760": "OE1" <-> "OE2" Residue "G ASP 763": "OD1" <-> "OD2" Residue "G TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 867": "OD1" <-> "OD2" Residue "H GLU 251": "OE1" <-> "OE2" Residue "H PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 318": "OD1" <-> "OD2" Residue "H GLU 333": "OE1" <-> "OE2" Residue "H TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 362": "OD1" <-> "OD2" Residue "H ASP 369": "OD1" <-> "OD2" Residue "H GLU 373": "OE1" <-> "OE2" Residue "H TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 415": "OD1" <-> "OD2" Residue "H GLU 426": "OE1" <-> "OE2" Residue "H PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 520": "OD1" <-> "OD2" Residue "H TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 544": "OE1" <-> "OE2" Residue "H ASP 561": "OD1" <-> "OD2" Residue "H ASP 568": "OD1" <-> "OD2" Residue "H GLU 573": "OE1" <-> "OE2" Residue "H ASP 582": "OD1" <-> "OD2" Residue "H ASP 597": "OD1" <-> "OD2" Residue "H GLU 653": "OE1" <-> "OE2" Residue "H GLU 662": "OE1" <-> "OE2" Residue "H TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 692": "OE1" <-> "OE2" Residue "H ASP 717": "OD1" <-> "OD2" Residue "H GLU 722": "OE1" <-> "OE2" Residue "H ASP 771": "OD1" <-> "OD2" Residue "H GLU 796": "OE1" <-> "OE2" Residue "H ASP 799": "OD1" <-> "OD2" Residue "H TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 867": "OD1" <-> "OD2" Residue "I GLU 251": "OE1" <-> "OE2" Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 318": "OD1" <-> "OD2" Residue "I GLU 333": "OE1" <-> "OE2" Residue "I TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 362": "OD1" <-> "OD2" Residue "I ASP 369": "OD1" <-> "OD2" Residue "I GLU 373": "OE1" <-> "OE2" Residue "I TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 415": "OD1" <-> "OD2" Residue "I GLU 426": "OE1" <-> "OE2" Residue "I PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 520": "OD1" <-> "OD2" Residue "I TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 544": "OE1" <-> "OE2" Residue "I ASP 561": "OD1" <-> "OD2" Residue "I ASP 568": "OD1" <-> "OD2" Residue "I GLU 573": "OE1" <-> "OE2" Residue "I ASP 582": "OD1" <-> "OD2" Residue "I ASP 597": "OD1" <-> "OD2" Residue "I GLU 653": "OE1" <-> "OE2" Residue "I GLU 662": "OE1" <-> "OE2" Residue "I TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 692": "OE1" <-> "OE2" Residue "I ASP 717": "OD1" <-> "OD2" Residue "I GLU 722": "OE1" <-> "OE2" Residue "I ASP 771": "OD1" <-> "OD2" Residue "I GLU 796": "OE1" <-> "OE2" Residue "I ASP 799": "OD1" <-> "OD2" Residue "I TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 867": "OD1" <-> "OD2" Residue "J GLU 251": "OE1" <-> "OE2" Residue "J PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 318": "OD1" <-> "OD2" Residue "J GLU 333": "OE1" <-> "OE2" Residue "J TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 362": "OD1" <-> "OD2" Residue "J ASP 369": "OD1" <-> "OD2" Residue "J GLU 373": "OE1" <-> "OE2" Residue "J TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 415": "OD1" <-> "OD2" Residue "J GLU 426": "OE1" <-> "OE2" Residue "J PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 520": "OD1" <-> "OD2" Residue "J TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 544": "OE1" <-> "OE2" Residue "J ASP 561": "OD1" <-> "OD2" Residue "J ASP 568": "OD1" <-> "OD2" Residue "J GLU 573": "OE1" <-> "OE2" Residue "J ASP 582": "OD1" <-> "OD2" Residue "J ASP 597": "OD1" <-> "OD2" Residue "J GLU 653": "OE1" <-> "OE2" Residue "J GLU 662": "OE1" <-> "OE2" Residue "J TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 692": "OE1" <-> "OE2" Residue "J ASP 717": "OD1" <-> "OD2" Residue "J GLU 722": "OE1" <-> "OE2" Residue "J ASP 771": "OD1" <-> "OD2" Residue "J GLU 796": "OE1" <-> "OE2" Residue "J ASP 799": "OD1" <-> "OD2" Residue "J TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 867": "OD1" <-> "OD2" Residue "K GLU 251": "OE1" <-> "OE2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 318": "OD1" <-> "OD2" Residue "K GLU 333": "OE1" <-> "OE2" Residue "K TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 362": "OD1" <-> "OD2" Residue "K ASP 369": "OD1" <-> "OD2" Residue "K GLU 373": "OE1" <-> "OE2" Residue "K TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 415": "OD1" <-> "OD2" Residue "K GLU 426": "OE1" <-> "OE2" Residue "K PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 520": "OD1" <-> "OD2" Residue "K TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 544": "OE1" <-> "OE2" Residue "K ASP 561": "OD1" <-> "OD2" Residue "K ASP 568": "OD1" <-> "OD2" Residue "K GLU 573": "OE1" <-> "OE2" Residue "K ASP 582": "OD1" <-> "OD2" Residue "K ASP 597": "OD1" <-> "OD2" Residue "K GLU 653": "OE1" <-> "OE2" Residue "K GLU 662": "OE1" <-> "OE2" Residue "K TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 692": "OE1" <-> "OE2" Residue "K ASP 717": "OD1" <-> "OD2" Residue "K GLU 722": "OE1" <-> "OE2" Residue "K ASP 771": "OD1" <-> "OD2" Residue "K GLU 796": "OE1" <-> "OE2" Residue "K ASP 799": "OD1" <-> "OD2" Residue "K TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 867": "OD1" <-> "OD2" Residue "L GLU 251": "OE1" <-> "OE2" Residue "L PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 318": "OD1" <-> "OD2" Residue "L GLU 333": "OE1" <-> "OE2" Residue "L TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 362": "OD1" <-> "OD2" Residue "L ASP 369": "OD1" <-> "OD2" Residue "L GLU 373": "OE1" <-> "OE2" Residue "L TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 415": "OD1" <-> "OD2" Residue "L GLU 426": "OE1" <-> "OE2" Residue "L PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 520": "OD1" <-> "OD2" Residue "L TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 544": "OE1" <-> "OE2" Residue "L ASP 561": "OD1" <-> "OD2" Residue "L ASP 568": "OD1" <-> "OD2" Residue "L GLU 573": "OE1" <-> "OE2" Residue "L ASP 582": "OD1" <-> "OD2" Residue "L ASP 597": "OD1" <-> "OD2" Residue "L GLU 653": "OE1" <-> "OE2" Residue "L GLU 662": "OE1" <-> "OE2" Residue "L TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 692": "OE1" <-> "OE2" Residue "L ASP 717": "OD1" <-> "OD2" Residue "L GLU 722": "OE1" <-> "OE2" Residue "L ASP 771": "OD1" <-> "OD2" Residue "L GLU 796": "OE1" <-> "OE2" Residue "L ASP 799": "OD1" <-> "OD2" Residue "L TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 867": "OD1" <-> "OD2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 318": "OD1" <-> "OD2" Residue "M GLU 333": "OE1" <-> "OE2" Residue "M TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 362": "OD1" <-> "OD2" Residue "M ASP 369": "OD1" <-> "OD2" Residue "M GLU 373": "OE1" <-> "OE2" Residue "M TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 415": "OD1" <-> "OD2" Residue "M GLU 426": "OE1" <-> "OE2" Residue "M PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 520": "OD1" <-> "OD2" Residue "M TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 544": "OE1" <-> "OE2" Residue "M ASP 561": "OD1" <-> "OD2" Residue "M ASP 568": "OD1" <-> "OD2" Residue "M GLU 573": "OE1" <-> "OE2" Residue "M ASP 582": "OD1" <-> "OD2" Residue "M ASP 597": "OD1" <-> "OD2" Residue "M GLU 653": "OE1" <-> "OE2" Residue "M GLU 662": "OE1" <-> "OE2" Residue "M TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 692": "OE1" <-> "OE2" Residue "M ASP 717": "OD1" <-> "OD2" Residue "M GLU 722": "OE1" <-> "OE2" Residue "M ASP 771": "OD1" <-> "OD2" Residue "M GLU 796": "OE1" <-> "OE2" Residue "M ASP 799": "OD1" <-> "OD2" Residue "M TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 867": "OD1" <-> "OD2" Residue "N GLU 251": "OE1" <-> "OE2" Residue "N PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 318": "OD1" <-> "OD2" Residue "N GLU 333": "OE1" <-> "OE2" Residue "N TYR 357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 362": "OD1" <-> "OD2" Residue "N ASP 369": "OD1" <-> "OD2" Residue "N GLU 373": "OE1" <-> "OE2" Residue "N TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 415": "OD1" <-> "OD2" Residue "N GLU 426": "OE1" <-> "OE2" Residue "N PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 520": "OD1" <-> "OD2" Residue "N TYR 526": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 544": "OE1" <-> "OE2" Residue "N ASP 561": "OD1" <-> "OD2" Residue "N ASP 568": "OD1" <-> "OD2" Residue "N GLU 573": "OE1" <-> "OE2" Residue "N ASP 582": "OD1" <-> "OD2" Residue "N ASP 597": "OD1" <-> "OD2" Residue "N GLU 653": "OE1" <-> "OE2" Residue "N GLU 662": "OE1" <-> "OE2" Residue "N TYR 666": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 669": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 692": "OE1" <-> "OE2" Residue "N ASP 717": "OD1" <-> "OD2" Residue "N GLU 722": "OE1" <-> "OE2" Residue "N ASP 771": "OD1" <-> "OD2" Residue "N GLU 796": "OE1" <-> "OE2" Residue "N ASP 799": "OD1" <-> "OD2" Residue "N TYR 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 855": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 867": "OD1" <-> "OD2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 72758 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "B" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "C" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "D" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "E" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "F" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "G" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "H" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "I" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "J" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "K" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "L" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "M" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "N" Number of atoms: 5194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 660, 5194 Classifications: {'peptide': 660} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 632} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 28.98, per 1000 atoms: 0.40 Number of scatterers: 72758 At special positions: 0 Unit cell: (177.02, 179.14, 245.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 42 19.99 S 140 16.00 O 15232 8.00 N 11816 7.00 C 45528 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 21.03 Conformation dependent library (CDL) restraints added in 9.8 seconds 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17332 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 176 sheets defined 15.5% alpha, 35.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.86 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 250 Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 291 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.729A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.480A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.704A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 757 through 764 Processing helix chain 'A' and resid 794 through 801 removed outlier: 3.653A pdb=" N ILE A 801 " --> pdb=" O ALA A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.729A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.480A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 555 Processing helix chain 'B' and resid 581 through 595 removed outlier: 3.704A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 757 through 764 Processing helix chain 'B' and resid 794 through 801 removed outlier: 3.654A pdb=" N ILE B 801 " --> pdb=" O ALA B 797 " (cutoff:3.500A) Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 250 Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.730A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.480A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 555 Processing helix chain 'C' and resid 581 through 595 removed outlier: 3.704A pdb=" N LYS C 593 " --> pdb=" O LYS C 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR C 594 " --> pdb=" O ASP C 590 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 757 through 764 Processing helix chain 'C' and resid 794 through 801 removed outlier: 3.653A pdb=" N ILE C 801 " --> pdb=" O ALA C 797 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 831 No H-bonds generated for 'chain 'C' and resid 829 through 831' Processing helix chain 'C' and resid 843 through 845 No H-bonds generated for 'chain 'C' and resid 843 through 845' Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.730A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.481A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 555 Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.704A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'D' and resid 757 through 764 Processing helix chain 'D' and resid 794 through 801 removed outlier: 3.653A pdb=" N ILE D 801 " --> pdb=" O ALA D 797 " (cutoff:3.500A) Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'D' and resid 843 through 845 No H-bonds generated for 'chain 'D' and resid 843 through 845' Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 250 Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.729A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.481A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 555 Processing helix chain 'E' and resid 581 through 595 removed outlier: 3.704A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR E 594 " --> pdb=" O ASP E 590 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU E 595 " --> pdb=" O SER E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 757 through 764 Processing helix chain 'E' and resid 794 through 801 removed outlier: 3.654A pdb=" N ILE E 801 " --> pdb=" O ALA E 797 " (cutoff:3.500A) Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 843 through 845 No H-bonds generated for 'chain 'E' and resid 843 through 845' Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 250 removed outlier: 3.500A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.730A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 513 removed outlier: 4.480A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 Processing helix chain 'F' and resid 581 through 595 removed outlier: 3.704A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU F 595 " --> pdb=" O SER F 591 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'F' and resid 757 through 764 Processing helix chain 'F' and resid 794 through 801 removed outlier: 3.653A pdb=" N ILE F 801 " --> pdb=" O ALA F 797 " (cutoff:3.500A) Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'F' and resid 843 through 845 No H-bonds generated for 'chain 'F' and resid 843 through 845' Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.730A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.480A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 555 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.704A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU G 595 " --> pdb=" O SER G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'G' and resid 757 through 764 Processing helix chain 'G' and resid 794 through 801 removed outlier: 3.653A pdb=" N ILE G 801 " --> pdb=" O ALA G 797 " (cutoff:3.500A) Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'G' and resid 843 through 845 No H-bonds generated for 'chain 'G' and resid 843 through 845' Processing helix chain 'H' and resid 227 through 234 Processing helix chain 'H' and resid 272 through 279 Processing helix chain 'H' and resid 286 through 291 Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 463 through 472 removed outlier: 3.501A pdb=" N ASP H 471 " --> pdb=" O LEU H 467 " (cutoff:3.500A) Processing helix chain 'H' and resid 503 through 513 removed outlier: 4.451A pdb=" N SER H 508 " --> pdb=" O SER H 504 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN H 509 " --> pdb=" O ASP H 505 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE H 513 " --> pdb=" O GLN H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 556 Processing helix chain 'H' and resid 582 through 595 removed outlier: 3.628A pdb=" N LYS H 593 " --> pdb=" O LYS H 589 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR H 594 " --> pdb=" O ASP H 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU H 595 " --> pdb=" O SER H 591 " (cutoff:3.500A) Processing helix chain 'H' and resid 599 through 603 Processing helix chain 'H' and resid 757 through 764 Processing helix chain 'H' and resid 794 through 800 Processing helix chain 'H' and resid 829 through 831 No H-bonds generated for 'chain 'H' and resid 829 through 831' Processing helix chain 'H' and resid 843 through 845 No H-bonds generated for 'chain 'H' and resid 843 through 845' Processing helix chain 'I' and resid 227 through 234 Processing helix chain 'I' and resid 272 through 279 Processing helix chain 'I' and resid 286 through 291 Processing helix chain 'I' and resid 332 through 337 Processing helix chain 'I' and resid 463 through 472 Processing helix chain 'I' and resid 503 through 513 removed outlier: 4.451A pdb=" N SER I 508 " --> pdb=" O SER I 504 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N GLN I 509 " --> pdb=" O ASP I 505 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE I 513 " --> pdb=" O GLN I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 546 through 556 Processing helix chain 'I' and resid 582 through 595 removed outlier: 3.629A pdb=" N LYS I 593 " --> pdb=" O LYS I 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR I 594 " --> pdb=" O ASP I 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 595 " --> pdb=" O SER I 591 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 603 Processing helix chain 'I' and resid 757 through 764 Processing helix chain 'I' and resid 794 through 800 Processing helix chain 'I' and resid 829 through 831 No H-bonds generated for 'chain 'I' and resid 829 through 831' Processing helix chain 'I' and resid 843 through 845 No H-bonds generated for 'chain 'I' and resid 843 through 845' Processing helix chain 'J' and resid 227 through 234 Processing helix chain 'J' and resid 272 through 279 Processing helix chain 'J' and resid 286 through 291 Processing helix chain 'J' and resid 332 through 337 Processing helix chain 'J' and resid 463 through 472 removed outlier: 3.501A pdb=" N ASP J 471 " --> pdb=" O LEU J 467 " (cutoff:3.500A) Processing helix chain 'J' and resid 503 through 513 removed outlier: 4.452A pdb=" N SER J 508 " --> pdb=" O SER J 504 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLN J 509 " --> pdb=" O ASP J 505 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE J 513 " --> pdb=" O GLN J 509 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 556 Processing helix chain 'J' and resid 582 through 595 removed outlier: 3.629A pdb=" N LYS J 593 " --> pdb=" O LYS J 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR J 594 " --> pdb=" O ASP J 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU J 595 " --> pdb=" O SER J 591 " (cutoff:3.500A) Processing helix chain 'J' and resid 599 through 603 Processing helix chain 'J' and resid 757 through 764 Processing helix chain 'J' and resid 794 through 800 Processing helix chain 'J' and resid 829 through 831 No H-bonds generated for 'chain 'J' and resid 829 through 831' Processing helix chain 'J' and resid 843 through 845 No H-bonds generated for 'chain 'J' and resid 843 through 845' Processing helix chain 'K' and resid 227 through 234 Processing helix chain 'K' and resid 272 through 279 Processing helix chain 'K' and resid 286 through 291 Processing helix chain 'K' and resid 332 through 337 Processing helix chain 'K' and resid 463 through 472 removed outlier: 3.501A pdb=" N ASP K 471 " --> pdb=" O LEU K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 503 through 513 removed outlier: 4.451A pdb=" N SER K 508 " --> pdb=" O SER K 504 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN K 509 " --> pdb=" O ASP K 505 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE K 513 " --> pdb=" O GLN K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 546 through 556 Processing helix chain 'K' and resid 582 through 595 removed outlier: 3.629A pdb=" N LYS K 593 " --> pdb=" O LYS K 589 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR K 594 " --> pdb=" O ASP K 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU K 595 " --> pdb=" O SER K 591 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 603 Processing helix chain 'K' and resid 757 through 764 Processing helix chain 'K' and resid 794 through 800 Processing helix chain 'K' and resid 829 through 831 No H-bonds generated for 'chain 'K' and resid 829 through 831' Processing helix chain 'K' and resid 843 through 845 No H-bonds generated for 'chain 'K' and resid 843 through 845' Processing helix chain 'L' and resid 227 through 234 Processing helix chain 'L' and resid 272 through 279 Processing helix chain 'L' and resid 286 through 291 Processing helix chain 'L' and resid 332 through 337 Processing helix chain 'L' and resid 463 through 472 removed outlier: 3.501A pdb=" N ASP L 471 " --> pdb=" O LEU L 467 " (cutoff:3.500A) Processing helix chain 'L' and resid 503 through 513 removed outlier: 4.452A pdb=" N SER L 508 " --> pdb=" O SER L 504 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN L 509 " --> pdb=" O ASP L 505 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE L 513 " --> pdb=" O GLN L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 556 Processing helix chain 'L' and resid 582 through 595 removed outlier: 3.629A pdb=" N LYS L 593 " --> pdb=" O LYS L 589 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR L 594 " --> pdb=" O ASP L 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU L 595 " --> pdb=" O SER L 591 " (cutoff:3.500A) Processing helix chain 'L' and resid 599 through 603 Processing helix chain 'L' and resid 757 through 764 Processing helix chain 'L' and resid 794 through 800 Processing helix chain 'L' and resid 829 through 831 No H-bonds generated for 'chain 'L' and resid 829 through 831' Processing helix chain 'L' and resid 843 through 845 No H-bonds generated for 'chain 'L' and resid 843 through 845' Processing helix chain 'M' and resid 227 through 234 Processing helix chain 'M' and resid 272 through 279 Processing helix chain 'M' and resid 286 through 291 Processing helix chain 'M' and resid 332 through 337 Processing helix chain 'M' and resid 463 through 472 removed outlier: 3.500A pdb=" N ASP M 471 " --> pdb=" O LEU M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 503 through 513 removed outlier: 4.451A pdb=" N SER M 508 " --> pdb=" O SER M 504 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N GLN M 509 " --> pdb=" O ASP M 505 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE M 513 " --> pdb=" O GLN M 509 " (cutoff:3.500A) Processing helix chain 'M' and resid 546 through 556 Processing helix chain 'M' and resid 582 through 595 removed outlier: 3.629A pdb=" N LYS M 593 " --> pdb=" O LYS M 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR M 594 " --> pdb=" O ASP M 590 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU M 595 " --> pdb=" O SER M 591 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 603 Processing helix chain 'M' and resid 757 through 764 Processing helix chain 'M' and resid 794 through 800 Processing helix chain 'M' and resid 829 through 831 No H-bonds generated for 'chain 'M' and resid 829 through 831' Processing helix chain 'M' and resid 843 through 845 No H-bonds generated for 'chain 'M' and resid 843 through 845' Processing helix chain 'N' and resid 227 through 234 Processing helix chain 'N' and resid 272 through 279 Processing helix chain 'N' and resid 286 through 291 Processing helix chain 'N' and resid 332 through 337 Processing helix chain 'N' and resid 463 through 472 removed outlier: 3.501A pdb=" N ASP N 471 " --> pdb=" O LEU N 467 " (cutoff:3.500A) Processing helix chain 'N' and resid 503 through 513 removed outlier: 4.452A pdb=" N SER N 508 " --> pdb=" O SER N 504 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLN N 509 " --> pdb=" O ASP N 505 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE N 513 " --> pdb=" O GLN N 509 " (cutoff:3.500A) Processing helix chain 'N' and resid 546 through 556 Processing helix chain 'N' and resid 582 through 595 removed outlier: 3.629A pdb=" N LYS N 593 " --> pdb=" O LYS N 589 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR N 594 " --> pdb=" O ASP N 590 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU N 595 " --> pdb=" O SER N 591 " (cutoff:3.500A) Processing helix chain 'N' and resid 599 through 603 Processing helix chain 'N' and resid 757 through 764 Processing helix chain 'N' and resid 794 through 800 Processing helix chain 'N' and resid 829 through 831 No H-bonds generated for 'chain 'N' and resid 829 through 831' Processing helix chain 'N' and resid 843 through 845 No H-bonds generated for 'chain 'N' and resid 843 through 845' Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 311 removed outlier: 6.780A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.879A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 313 through 345 removed outlier: 3.521A pdb=" N GLY A 344 " --> pdb=" O THR A 350 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY B 344 " --> pdb=" O THR B 350 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 344 " --> pdb=" O THR C 350 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY D 344 " --> pdb=" O THR D 350 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY E 344 " --> pdb=" O THR E 350 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY F 344 " --> pdb=" O THR F 350 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY G 344 " --> pdb=" O THR G 350 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.210A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR A 705 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.600A pdb=" N ASP A 696 " --> pdb=" O VAL A 686 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE A 688 " --> pdb=" O LYS A 694 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 773 removed outlier: 6.285A pdb=" N PHE A 769 " --> pdb=" O MET A 786 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET A 786 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP A 771 " --> pdb=" O ASN A 784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 815 through 821 removed outlier: 6.269A pdb=" N VAL A 806 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR A 820 " --> pdb=" O TYR A 804 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR A 804 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS A 803 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 858 " --> pdb=" O SER A 874 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 874 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE A 860 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AB7, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'B' and resid 300 through 311 removed outlier: 6.781A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.878A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC4, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.209A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC6, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.500A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 705 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.500A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.599A pdb=" N ASP B 696 " --> pdb=" O VAL B 686 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE B 688 " --> pdb=" O LYS B 694 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 768 through 773 removed outlier: 6.284A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 815 through 821 removed outlier: 6.269A pdb=" N VAL B 806 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR B 820 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR B 804 " --> pdb=" O THR B 820 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS B 803 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU B 858 " --> pdb=" O SER B 874 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER B 874 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 860 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AD3, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AD4, first strand: chain 'C' and resid 300 through 311 removed outlier: 6.780A pdb=" N ASN C 392 " --> pdb=" O GLU C 305 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU C 307 " --> pdb=" O ASN C 390 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN C 390 " --> pdb=" O LEU C 307 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE C 309 " --> pdb=" O TYR C 388 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR C 388 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 438 through 439 removed outlier: 3.878A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 489 through 490 Processing sheet with id=AD9, first strand: chain 'C' and resid 526 through 531 removed outlier: 9.209A pdb=" N ILE C 611 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AE2, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.500A pdb=" N LEU C 733 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS C 676 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN C 735 " --> pdb=" O TYR C 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR C 674 " --> pdb=" O ASN C 735 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR C 705 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 618 through 620 removed outlier: 5.500A pdb=" N LEU C 733 " --> pdb=" O LYS C 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS C 676 " --> pdb=" O LEU C 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN C 735 " --> pdb=" O TYR C 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR C 674 " --> pdb=" O ASN C 735 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 655 through 658 removed outlier: 3.599A pdb=" N ASP C 696 " --> pdb=" O VAL C 686 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ILE C 688 " --> pdb=" O LYS C 694 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 768 through 773 removed outlier: 6.285A pdb=" N PHE C 769 " --> pdb=" O MET C 786 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET C 786 " --> pdb=" O PHE C 769 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP C 771 " --> pdb=" O ASN C 784 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 815 through 821 removed outlier: 6.269A pdb=" N VAL C 806 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR C 820 " --> pdb=" O TYR C 804 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR C 804 " --> pdb=" O THR C 820 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS C 803 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU C 858 " --> pdb=" O SER C 874 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER C 874 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE C 860 " --> pdb=" O VAL C 872 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 826 through 827 Processing sheet with id=AE8, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AE9, first strand: chain 'D' and resid 300 through 311 removed outlier: 6.781A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 438 through 439 removed outlier: 3.879A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AF5, first strand: chain 'D' and resid 526 through 531 removed outlier: 9.209A pdb=" N ILE D 611 " --> pdb=" O SER D 514 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER D 516 " --> pdb=" O ILE D 611 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE D 613 " --> pdb=" O SER D 516 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE D 518 " --> pdb=" O ILE D 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AF7, first strand: chain 'D' and resid 618 through 620 removed outlier: 5.500A pdb=" N LEU D 733 " --> pdb=" O LYS D 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS D 676 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN D 735 " --> pdb=" O TYR D 674 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR D 674 " --> pdb=" O ASN D 735 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR D 705 " --> pdb=" O SER D 675 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 618 through 620 removed outlier: 5.500A pdb=" N LEU D 733 " --> pdb=" O LYS D 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS D 676 " --> pdb=" O LEU D 733 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN D 735 " --> pdb=" O TYR D 674 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N TYR D 674 " --> pdb=" O ASN D 735 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 655 through 658 removed outlier: 3.600A pdb=" N ASP D 696 " --> pdb=" O VAL D 686 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE D 688 " --> pdb=" O LYS D 694 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 768 through 773 removed outlier: 6.285A pdb=" N PHE D 769 " --> pdb=" O MET D 786 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET D 786 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 815 through 821 removed outlier: 6.268A pdb=" N VAL D 806 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR D 820 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR D 804 " --> pdb=" O THR D 820 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS D 803 " --> pdb=" O ILE D 863 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU D 858 " --> pdb=" O SER D 874 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER D 874 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE D 860 " --> pdb=" O VAL D 872 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AG4, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AG5, first strand: chain 'E' and resid 300 through 311 removed outlier: 6.781A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 438 through 439 removed outlier: 3.878A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS E 405 " --> pdb=" O GLY E 485 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY E 485 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR E 407 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL E 483 " --> pdb=" O THR E 407 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR E 409 " --> pdb=" O THR E 481 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AH1, first strand: chain 'E' and resid 526 through 531 removed outlier: 9.211A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AH3, first strand: chain 'E' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU E 733 " --> pdb=" O LYS E 676 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS E 676 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN E 735 " --> pdb=" O TYR E 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR E 674 " --> pdb=" O ASN E 735 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR E 705 " --> pdb=" O SER E 675 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU E 733 " --> pdb=" O LYS E 676 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS E 676 " --> pdb=" O LEU E 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN E 735 " --> pdb=" O TYR E 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR E 674 " --> pdb=" O ASN E 735 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 655 through 658 removed outlier: 3.600A pdb=" N ASP E 696 " --> pdb=" O VAL E 686 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE E 688 " --> pdb=" O LYS E 694 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 768 through 773 removed outlier: 6.285A pdb=" N PHE E 769 " --> pdb=" O MET E 786 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET E 786 " --> pdb=" O PHE E 769 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP E 771 " --> pdb=" O ASN E 784 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 815 through 821 removed outlier: 6.269A pdb=" N VAL E 806 " --> pdb=" O ILE E 818 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR E 820 " --> pdb=" O TYR E 804 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR E 804 " --> pdb=" O THR E 820 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS E 803 " --> pdb=" O ILE E 863 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU E 858 " --> pdb=" O SER E 874 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER E 874 " --> pdb=" O LEU E 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE E 860 " --> pdb=" O VAL E 872 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 826 through 827 Processing sheet with id=AH9, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AI1, first strand: chain 'F' and resid 300 through 311 removed outlier: 6.780A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.878A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR F 404 " --> pdb=" O ASN F 432 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASN F 432 " --> pdb=" O TYR F 404 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 489 through 490 Processing sheet with id=AI6, first strand: chain 'F' and resid 526 through 531 removed outlier: 9.210A pdb=" N ILE F 611 " --> pdb=" O SER F 514 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER F 516 " --> pdb=" O ILE F 611 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE F 613 " --> pdb=" O SER F 516 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE F 518 " --> pdb=" O ILE F 613 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AI8, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR F 705 " --> pdb=" O SER F 675 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 655 through 658 removed outlier: 3.599A pdb=" N ASP F 696 " --> pdb=" O VAL F 686 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 688 " --> pdb=" O LYS F 694 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 768 through 773 removed outlier: 6.284A pdb=" N PHE F 769 " --> pdb=" O MET F 786 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET F 786 " --> pdb=" O PHE F 769 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ASP F 771 " --> pdb=" O ASN F 784 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'F' and resid 815 through 821 removed outlier: 6.269A pdb=" N VAL F 806 " --> pdb=" O ILE F 818 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR F 820 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR F 804 " --> pdb=" O THR F 820 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LYS F 803 " --> pdb=" O ILE F 863 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU F 858 " --> pdb=" O SER F 874 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER F 874 " --> pdb=" O LEU F 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE F 860 " --> pdb=" O VAL F 872 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'F' and resid 826 through 827 Processing sheet with id=AJ5, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AJ6, first strand: chain 'G' and resid 300 through 311 removed outlier: 6.781A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.878A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR G 404 " --> pdb=" O ASN G 432 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ASN G 432 " --> pdb=" O TYR G 404 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.654A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N LYS G 405 " --> pdb=" O GLY G 485 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLY G 485 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N THR G 407 " --> pdb=" O VAL G 483 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL G 483 " --> pdb=" O THR G 407 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR G 409 " --> pdb=" O THR G 481 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AK2, first strand: chain 'G' and resid 526 through 531 removed outlier: 9.210A pdb=" N ILE G 611 " --> pdb=" O SER G 514 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AK4, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR G 705 " --> pdb=" O SER G 675 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.499A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 655 through 658 removed outlier: 3.599A pdb=" N ASP G 696 " --> pdb=" O VAL G 686 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE G 688 " --> pdb=" O LYS G 694 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'G' and resid 768 through 773 removed outlier: 6.284A pdb=" N PHE G 769 " --> pdb=" O MET G 786 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET G 786 " --> pdb=" O PHE G 769 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASP G 771 " --> pdb=" O ASN G 784 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'G' and resid 815 through 821 removed outlier: 6.268A pdb=" N VAL G 806 " --> pdb=" O ILE G 818 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N THR G 820 " --> pdb=" O TYR G 804 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR G 804 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS G 803 " --> pdb=" O ILE G 863 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU G 858 " --> pdb=" O SER G 874 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER G 874 " --> pdb=" O LEU G 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE G 860 " --> pdb=" O VAL G 872 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'G' and resid 826 through 827 Processing sheet with id=AL1, first strand: chain 'H' and resid 235 through 237 Processing sheet with id=AL2, first strand: chain 'H' and resid 418 through 423 removed outlier: 3.731A pdb=" N SER H 420 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS H 405 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN H 486 " --> pdb=" O LYS H 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN H 482 " --> pdb=" O THR H 409 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN H 411 " --> pdb=" O THR H 480 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR H 480 " --> pdb=" O ASN H 411 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL H 413 " --> pdb=" O LEU H 478 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU H 478 " --> pdb=" O VAL H 413 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU H 305 " --> pdb=" O THR H 327 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN H 329 " --> pdb=" O GLY H 303 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY H 303 " --> pdb=" O ASN H 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL H 302 " --> pdb=" O TYR H 396 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR H 396 " --> pdb=" O VAL H 302 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N MET H 304 " --> pdb=" O ARG H 394 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG H 394 " --> pdb=" O MET H 304 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'H' and resid 438 through 439 removed outlier: 3.529A pdb=" N ILE H 460 " --> pdb=" O ILE H 389 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'H' and resid 351 through 354 removed outlier: 3.678A pdb=" N GLU H 577 " --> pdb=" O LYS H 614 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP H 581 " --> pdb=" O ASN H 610 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN H 610 " --> pdb=" O ASP H 581 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N ILE H 611 " --> pdb=" O SER H 514 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER H 516 " --> pdb=" O ILE H 611 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE H 613 " --> pdb=" O SER H 516 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE H 518 " --> pdb=" O ILE H 613 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'H' and resid 489 through 490 Processing sheet with id=AL6, first strand: chain 'H' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU H 736 " --> pdb=" O SER H 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER H 672 " --> pdb=" O LEU H 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE H 738 " --> pdb=" O VAL H 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL H 670 " --> pdb=" O ILE H 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU H 740 " --> pdb=" O ARG H 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG H 668 " --> pdb=" O GLU H 740 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'H' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU H 736 " --> pdb=" O SER H 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER H 672 " --> pdb=" O LEU H 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE H 738 " --> pdb=" O VAL H 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL H 670 " --> pdb=" O ILE H 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU H 740 " --> pdb=" O ARG H 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG H 668 " --> pdb=" O GLU H 740 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'H' and resid 657 through 658 Processing sheet with id=AL9, first strand: chain 'H' and resid 768 through 773 removed outlier: 6.137A pdb=" N ASN H 773 " --> pdb=" O ILE H 783 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE H 783 " --> pdb=" O ASN H 773 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'H' and resid 815 through 820 removed outlier: 6.430A pdb=" N VAL H 806 " --> pdb=" O ILE H 818 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR H 820 " --> pdb=" O TYR H 804 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR H 804 " --> pdb=" O THR H 820 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS H 803 " --> pdb=" O ILE H 863 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE H 863 " --> pdb=" O LYS H 803 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE H 860 " --> pdb=" O VAL H 872 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'H' and resid 826 through 827 Processing sheet with id=AM3, first strand: chain 'I' and resid 235 through 237 Processing sheet with id=AM4, first strand: chain 'I' and resid 418 through 423 removed outlier: 3.731A pdb=" N SER I 420 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS I 405 " --> pdb=" O ASN I 486 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN I 486 " --> pdb=" O LYS I 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN I 482 " --> pdb=" O THR I 409 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN I 411 " --> pdb=" O THR I 480 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR I 480 " --> pdb=" O ASN I 411 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL I 413 " --> pdb=" O LEU I 478 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU I 478 " --> pdb=" O VAL I 413 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU I 305 " --> pdb=" O THR I 327 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN I 329 " --> pdb=" O GLY I 303 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY I 303 " --> pdb=" O ASN I 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL I 302 " --> pdb=" O TYR I 396 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N TYR I 396 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N MET I 304 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG I 394 " --> pdb=" O MET I 304 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'I' and resid 438 through 439 removed outlier: 3.529A pdb=" N ILE I 460 " --> pdb=" O ILE I 389 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'I' and resid 351 through 354 removed outlier: 3.678A pdb=" N GLU I 577 " --> pdb=" O LYS I 614 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP I 581 " --> pdb=" O ASN I 610 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN I 610 " --> pdb=" O ASP I 581 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ILE I 611 " --> pdb=" O SER I 514 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER I 516 " --> pdb=" O ILE I 611 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE I 613 " --> pdb=" O SER I 516 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE I 518 " --> pdb=" O ILE I 613 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'I' and resid 489 through 490 Processing sheet with id=AM8, first strand: chain 'I' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU I 736 " --> pdb=" O SER I 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER I 672 " --> pdb=" O LEU I 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE I 738 " --> pdb=" O VAL I 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL I 670 " --> pdb=" O ILE I 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU I 740 " --> pdb=" O ARG I 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG I 668 " --> pdb=" O GLU I 740 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'I' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU I 736 " --> pdb=" O SER I 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER I 672 " --> pdb=" O LEU I 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE I 738 " --> pdb=" O VAL I 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL I 670 " --> pdb=" O ILE I 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU I 740 " --> pdb=" O ARG I 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG I 668 " --> pdb=" O GLU I 740 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'I' and resid 657 through 658 Processing sheet with id=AN2, first strand: chain 'I' and resid 768 through 773 removed outlier: 6.137A pdb=" N ASN I 773 " --> pdb=" O ILE I 783 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE I 783 " --> pdb=" O ASN I 773 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'I' and resid 815 through 820 removed outlier: 6.431A pdb=" N VAL I 806 " --> pdb=" O ILE I 818 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR I 820 " --> pdb=" O TYR I 804 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR I 804 " --> pdb=" O THR I 820 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS I 803 " --> pdb=" O ILE I 863 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE I 863 " --> pdb=" O LYS I 803 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE I 860 " --> pdb=" O VAL I 872 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'I' and resid 826 through 827 Processing sheet with id=AN5, first strand: chain 'J' and resid 235 through 237 Processing sheet with id=AN6, first strand: chain 'J' and resid 418 through 423 removed outlier: 3.731A pdb=" N SER J 420 " --> pdb=" O LEU J 412 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS J 405 " --> pdb=" O ASN J 486 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN J 486 " --> pdb=" O LYS J 405 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN J 482 " --> pdb=" O THR J 409 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN J 411 " --> pdb=" O THR J 480 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR J 480 " --> pdb=" O ASN J 411 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL J 413 " --> pdb=" O LEU J 478 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU J 478 " --> pdb=" O VAL J 413 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU J 305 " --> pdb=" O THR J 327 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN J 329 " --> pdb=" O GLY J 303 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY J 303 " --> pdb=" O ASN J 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL J 302 " --> pdb=" O TYR J 396 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR J 396 " --> pdb=" O VAL J 302 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'J' and resid 438 through 439 removed outlier: 3.529A pdb=" N ILE J 460 " --> pdb=" O ILE J 389 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'J' and resid 351 through 354 removed outlier: 3.678A pdb=" N GLU J 577 " --> pdb=" O LYS J 614 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP J 581 " --> pdb=" O ASN J 610 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN J 610 " --> pdb=" O ASP J 581 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N ILE J 611 " --> pdb=" O SER J 514 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER J 516 " --> pdb=" O ILE J 611 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE J 613 " --> pdb=" O SER J 516 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE J 518 " --> pdb=" O ILE J 613 " (cutoff:3.500A) Processing sheet with id=AN9, first strand: chain 'J' and resid 489 through 490 Processing sheet with id=AO1, first strand: chain 'J' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU J 736 " --> pdb=" O SER J 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER J 672 " --> pdb=" O LEU J 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE J 738 " --> pdb=" O VAL J 670 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL J 670 " --> pdb=" O ILE J 738 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU J 740 " --> pdb=" O ARG J 668 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG J 668 " --> pdb=" O GLU J 740 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'J' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU J 736 " --> pdb=" O SER J 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER J 672 " --> pdb=" O LEU J 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE J 738 " --> pdb=" O VAL J 670 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL J 670 " --> pdb=" O ILE J 738 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU J 740 " --> pdb=" O ARG J 668 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG J 668 " --> pdb=" O GLU J 740 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'J' and resid 657 through 658 Processing sheet with id=AO4, first strand: chain 'J' and resid 768 through 773 removed outlier: 6.136A pdb=" N ASN J 773 " --> pdb=" O ILE J 783 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE J 783 " --> pdb=" O ASN J 773 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'J' and resid 815 through 820 removed outlier: 6.430A pdb=" N VAL J 806 " --> pdb=" O ILE J 818 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR J 820 " --> pdb=" O TYR J 804 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR J 804 " --> pdb=" O THR J 820 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS J 803 " --> pdb=" O ILE J 863 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE J 863 " --> pdb=" O LYS J 803 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE J 860 " --> pdb=" O VAL J 872 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'J' and resid 826 through 827 Processing sheet with id=AO7, first strand: chain 'K' and resid 235 through 237 Processing sheet with id=AO8, first strand: chain 'K' and resid 418 through 423 removed outlier: 3.731A pdb=" N SER K 420 " --> pdb=" O LEU K 412 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS K 405 " --> pdb=" O ASN K 486 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN K 486 " --> pdb=" O LYS K 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN K 482 " --> pdb=" O THR K 409 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN K 411 " --> pdb=" O THR K 480 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR K 480 " --> pdb=" O ASN K 411 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL K 413 " --> pdb=" O LEU K 478 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU K 478 " --> pdb=" O VAL K 413 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU K 305 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN K 329 " --> pdb=" O GLY K 303 " (cutoff:3.500A) removed outlier: 8.827A pdb=" N GLY K 303 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL K 302 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR K 396 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N MET K 304 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG K 394 " --> pdb=" O MET K 304 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'K' and resid 438 through 439 removed outlier: 3.529A pdb=" N ILE K 460 " --> pdb=" O ILE K 389 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'K' and resid 351 through 354 removed outlier: 3.678A pdb=" N GLU K 577 " --> pdb=" O LYS K 614 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP K 581 " --> pdb=" O ASN K 610 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN K 610 " --> pdb=" O ASP K 581 " (cutoff:3.500A) removed outlier: 9.316A pdb=" N ILE K 611 " --> pdb=" O SER K 514 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER K 516 " --> pdb=" O ILE K 611 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE K 613 " --> pdb=" O SER K 516 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE K 518 " --> pdb=" O ILE K 613 " (cutoff:3.500A) Processing sheet with id=AP2, first strand: chain 'K' and resid 489 through 490 Processing sheet with id=AP3, first strand: chain 'K' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU K 736 " --> pdb=" O SER K 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER K 672 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE K 738 " --> pdb=" O VAL K 670 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL K 670 " --> pdb=" O ILE K 738 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU K 740 " --> pdb=" O ARG K 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG K 668 " --> pdb=" O GLU K 740 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'K' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU K 736 " --> pdb=" O SER K 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER K 672 " --> pdb=" O LEU K 736 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE K 738 " --> pdb=" O VAL K 670 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL K 670 " --> pdb=" O ILE K 738 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU K 740 " --> pdb=" O ARG K 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG K 668 " --> pdb=" O GLU K 740 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'K' and resid 657 through 658 Processing sheet with id=AP6, first strand: chain 'K' and resid 768 through 773 removed outlier: 6.137A pdb=" N ASN K 773 " --> pdb=" O ILE K 783 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE K 783 " --> pdb=" O ASN K 773 " (cutoff:3.500A) Processing sheet with id=AP7, first strand: chain 'K' and resid 815 through 820 removed outlier: 6.430A pdb=" N VAL K 806 " --> pdb=" O ILE K 818 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR K 820 " --> pdb=" O TYR K 804 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR K 804 " --> pdb=" O THR K 820 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS K 803 " --> pdb=" O ILE K 863 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE K 863 " --> pdb=" O LYS K 803 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE K 860 " --> pdb=" O VAL K 872 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'K' and resid 826 through 827 Processing sheet with id=AP9, first strand: chain 'L' and resid 235 through 237 Processing sheet with id=AQ1, first strand: chain 'L' and resid 418 through 423 removed outlier: 3.731A pdb=" N SER L 420 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS L 405 " --> pdb=" O ASN L 486 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN L 486 " --> pdb=" O LYS L 405 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN L 482 " --> pdb=" O THR L 409 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN L 411 " --> pdb=" O THR L 480 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR L 480 " --> pdb=" O ASN L 411 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL L 413 " --> pdb=" O LEU L 478 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU L 478 " --> pdb=" O VAL L 413 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N GLU L 305 " --> pdb=" O THR L 327 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN L 329 " --> pdb=" O GLY L 303 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLY L 303 " --> pdb=" O ASN L 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL L 302 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR L 396 " --> pdb=" O VAL L 302 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N MET L 304 " --> pdb=" O ARG L 394 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ARG L 394 " --> pdb=" O MET L 304 " (cutoff:3.500A) Processing sheet with id=AQ2, first strand: chain 'L' and resid 438 through 439 removed outlier: 3.529A pdb=" N ILE L 460 " --> pdb=" O ILE L 389 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'L' and resid 351 through 354 removed outlier: 3.677A pdb=" N GLU L 577 " --> pdb=" O LYS L 614 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP L 581 " --> pdb=" O ASN L 610 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASN L 610 " --> pdb=" O ASP L 581 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ILE L 611 " --> pdb=" O SER L 514 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER L 516 " --> pdb=" O ILE L 611 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE L 613 " --> pdb=" O SER L 516 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ILE L 518 " --> pdb=" O ILE L 613 " (cutoff:3.500A) Processing sheet with id=AQ4, first strand: chain 'L' and resid 489 through 490 Processing sheet with id=AQ5, first strand: chain 'L' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU L 736 " --> pdb=" O SER L 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER L 672 " --> pdb=" O LEU L 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE L 738 " --> pdb=" O VAL L 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL L 670 " --> pdb=" O ILE L 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU L 740 " --> pdb=" O ARG L 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG L 668 " --> pdb=" O GLU L 740 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'L' and resid 618 through 620 removed outlier: 4.290A pdb=" N LEU L 736 " --> pdb=" O SER L 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER L 672 " --> pdb=" O LEU L 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE L 738 " --> pdb=" O VAL L 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL L 670 " --> pdb=" O ILE L 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU L 740 " --> pdb=" O ARG L 668 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG L 668 " --> pdb=" O GLU L 740 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'L' and resid 657 through 658 Processing sheet with id=AQ8, first strand: chain 'L' and resid 768 through 773 removed outlier: 6.137A pdb=" N ASN L 773 " --> pdb=" O ILE L 783 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE L 783 " --> pdb=" O ASN L 773 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'L' and resid 815 through 820 removed outlier: 6.430A pdb=" N VAL L 806 " --> pdb=" O ILE L 818 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR L 820 " --> pdb=" O TYR L 804 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR L 804 " --> pdb=" O THR L 820 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS L 803 " --> pdb=" O ILE L 863 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE L 863 " --> pdb=" O LYS L 803 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE L 860 " --> pdb=" O VAL L 872 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'L' and resid 826 through 827 Processing sheet with id=AR2, first strand: chain 'M' and resid 235 through 237 Processing sheet with id=AR3, first strand: chain 'M' and resid 418 through 423 removed outlier: 3.732A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LYS M 405 " --> pdb=" O ASN M 486 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN M 486 " --> pdb=" O LYS M 405 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN M 482 " --> pdb=" O THR M 409 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN M 411 " --> pdb=" O THR M 480 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N THR M 480 " --> pdb=" O ASN M 411 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL M 413 " --> pdb=" O LEU M 478 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LEU M 478 " --> pdb=" O VAL M 413 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU M 305 " --> pdb=" O THR M 327 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN M 329 " --> pdb=" O GLY M 303 " (cutoff:3.500A) removed outlier: 8.826A pdb=" N GLY M 303 " --> pdb=" O ASN M 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL M 302 " --> pdb=" O TYR M 396 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TYR M 396 " --> pdb=" O VAL M 302 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) Processing sheet with id=AR4, first strand: chain 'M' and resid 438 through 439 removed outlier: 3.529A pdb=" N ILE M 460 " --> pdb=" O ILE M 389 " (cutoff:3.500A) Processing sheet with id=AR5, first strand: chain 'M' and resid 351 through 354 removed outlier: 3.678A pdb=" N GLU M 577 " --> pdb=" O LYS M 614 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP M 581 " --> pdb=" O ASN M 610 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN M 610 " --> pdb=" O ASP M 581 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ILE M 611 " --> pdb=" O SER M 514 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N SER M 516 " --> pdb=" O ILE M 611 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ILE M 613 " --> pdb=" O SER M 516 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE M 518 " --> pdb=" O ILE M 613 " (cutoff:3.500A) Processing sheet with id=AR6, first strand: chain 'M' and resid 489 through 490 Processing sheet with id=AR7, first strand: chain 'M' and resid 618 through 620 removed outlier: 4.291A pdb=" N LEU M 736 " --> pdb=" O SER M 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER M 672 " --> pdb=" O LEU M 736 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE M 738 " --> pdb=" O VAL M 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL M 670 " --> pdb=" O ILE M 738 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU M 740 " --> pdb=" O ARG M 668 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG M 668 " --> pdb=" O GLU M 740 " (cutoff:3.500A) Processing sheet with id=AR8, first strand: chain 'M' and resid 618 through 620 removed outlier: 4.291A pdb=" N LEU M 736 " --> pdb=" O SER M 672 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N SER M 672 " --> pdb=" O LEU M 736 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ILE M 738 " --> pdb=" O VAL M 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL M 670 " --> pdb=" O ILE M 738 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N GLU M 740 " --> pdb=" O ARG M 668 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG M 668 " --> pdb=" O GLU M 740 " (cutoff:3.500A) Processing sheet with id=AR9, first strand: chain 'M' and resid 657 through 658 Processing sheet with id=AS1, first strand: chain 'M' and resid 768 through 773 removed outlier: 6.137A pdb=" N ASN M 773 " --> pdb=" O ILE M 783 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N ILE M 783 " --> pdb=" O ASN M 773 " (cutoff:3.500A) Processing sheet with id=AS2, first strand: chain 'M' and resid 815 through 820 removed outlier: 6.430A pdb=" N VAL M 806 " --> pdb=" O ILE M 818 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR M 820 " --> pdb=" O TYR M 804 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N TYR M 804 " --> pdb=" O THR M 820 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N LYS M 803 " --> pdb=" O ILE M 863 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE M 863 " --> pdb=" O LYS M 803 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE M 860 " --> pdb=" O VAL M 872 " (cutoff:3.500A) Processing sheet with id=AS3, first strand: chain 'M' and resid 826 through 827 Processing sheet with id=AS4, first strand: chain 'N' and resid 235 through 237 Processing sheet with id=AS5, first strand: chain 'N' and resid 418 through 423 removed outlier: 3.731A pdb=" N SER N 420 " --> pdb=" O LEU N 412 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LYS N 405 " --> pdb=" O ASN N 486 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN N 486 " --> pdb=" O LYS N 405 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN N 482 " --> pdb=" O THR N 409 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ASN N 411 " --> pdb=" O THR N 480 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N THR N 480 " --> pdb=" O ASN N 411 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N VAL N 413 " --> pdb=" O LEU N 478 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LEU N 478 " --> pdb=" O VAL N 413 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N GLU N 305 " --> pdb=" O THR N 327 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ASN N 329 " --> pdb=" O GLY N 303 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLY N 303 " --> pdb=" O ASN N 329 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N VAL N 302 " --> pdb=" O TYR N 396 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TYR N 396 " --> pdb=" O VAL N 302 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N MET N 304 " --> pdb=" O ARG N 394 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG N 394 " --> pdb=" O MET N 304 " (cutoff:3.500A) Processing sheet with id=AS6, first strand: chain 'N' and resid 438 through 439 removed outlier: 3.530A pdb=" N ILE N 460 " --> pdb=" O ILE N 389 " (cutoff:3.500A) Processing sheet with id=AS7, first strand: chain 'N' and resid 351 through 354 removed outlier: 3.678A pdb=" N GLU N 577 " --> pdb=" O LYS N 614 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP N 581 " --> pdb=" O ASN N 610 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ASN N 610 " --> pdb=" O ASP N 581 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N ILE N 611 " --> pdb=" O SER N 514 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER N 516 " --> pdb=" O ILE N 611 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ILE N 613 " --> pdb=" O SER N 516 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE N 518 " --> pdb=" O ILE N 613 " (cutoff:3.500A) Processing sheet with id=AS8, first strand: chain 'N' and resid 489 through 490 Processing sheet with id=AS9, first strand: chain 'N' and resid 618 through 620 removed outlier: 4.291A pdb=" N LEU N 736 " --> pdb=" O SER N 672 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER N 672 " --> pdb=" O LEU N 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE N 738 " --> pdb=" O VAL N 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 670 " --> pdb=" O ILE N 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU N 740 " --> pdb=" O ARG N 668 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG N 668 " --> pdb=" O GLU N 740 " (cutoff:3.500A) Processing sheet with id=AT1, first strand: chain 'N' and resid 618 through 620 removed outlier: 4.291A pdb=" N LEU N 736 " --> pdb=" O SER N 672 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N SER N 672 " --> pdb=" O LEU N 736 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ILE N 738 " --> pdb=" O VAL N 670 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL N 670 " --> pdb=" O ILE N 738 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N GLU N 740 " --> pdb=" O ARG N 668 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ARG N 668 " --> pdb=" O GLU N 740 " (cutoff:3.500A) Processing sheet with id=AT2, first strand: chain 'N' and resid 657 through 658 Processing sheet with id=AT3, first strand: chain 'N' and resid 768 through 773 removed outlier: 6.137A pdb=" N ASN N 773 " --> pdb=" O ILE N 783 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE N 783 " --> pdb=" O ASN N 773 " (cutoff:3.500A) Processing sheet with id=AT4, first strand: chain 'N' and resid 815 through 820 removed outlier: 6.431A pdb=" N VAL N 806 " --> pdb=" O ILE N 818 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N THR N 820 " --> pdb=" O TYR N 804 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR N 804 " --> pdb=" O THR N 820 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N LYS N 803 " --> pdb=" O ILE N 863 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N ILE N 863 " --> pdb=" O LYS N 803 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ILE N 860 " --> pdb=" O VAL N 872 " (cutoff:3.500A) Processing sheet with id=AT5, first strand: chain 'N' and resid 826 through 827 2415 hydrogen bonds defined for protein. 6324 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: 33.49 Time building geometry restraints manager: 23.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 23605 1.33 - 1.45: 9830 1.45 - 1.57: 40359 1.57 - 1.69: 0 1.69 - 1.80: 266 Bond restraints: 74060 Sorted by residual: bond pdb=" CA ASN C 636 " pdb=" CB ASN C 636 " ideal model delta sigma weight residual 1.526 1.565 -0.038 1.53e-02 4.27e+03 6.26e+00 bond pdb=" CA ASN F 636 " pdb=" CB ASN F 636 " ideal model delta sigma weight residual 1.526 1.564 -0.038 1.53e-02 4.27e+03 6.17e+00 bond pdb=" CA ASN B 636 " pdb=" CB ASN B 636 " ideal model delta sigma weight residual 1.526 1.564 -0.038 1.53e-02 4.27e+03 6.06e+00 bond pdb=" CA ASN G 636 " pdb=" CB ASN G 636 " ideal model delta sigma weight residual 1.526 1.564 -0.037 1.53e-02 4.27e+03 5.98e+00 bond pdb=" CA ASN D 636 " pdb=" CB ASN D 636 " ideal model delta sigma weight residual 1.526 1.564 -0.037 1.53e-02 4.27e+03 5.95e+00 ... (remaining 74055 not shown) Histogram of bond angle deviations from ideal: 99.58 - 106.48: 1646 106.48 - 113.38: 40809 113.38 - 120.28: 26274 120.28 - 127.18: 31363 127.18 - 134.08: 442 Bond angle restraints: 100534 Sorted by residual: angle pdb=" C THR G 714 " pdb=" N GLU G 715 " pdb=" CA GLU G 715 " ideal model delta sigma weight residual 121.63 111.54 10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C THR E 714 " pdb=" N GLU E 715 " pdb=" CA GLU E 715 " ideal model delta sigma weight residual 121.63 111.54 10.09 1.91e+00 2.74e-01 2.79e+01 angle pdb=" C THR D 714 " pdb=" N GLU D 715 " pdb=" CA GLU D 715 " ideal model delta sigma weight residual 121.63 111.57 10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C THR C 714 " pdb=" N GLU C 715 " pdb=" CA GLU C 715 " ideal model delta sigma weight residual 121.63 111.57 10.06 1.91e+00 2.74e-01 2.77e+01 angle pdb=" C THR F 714 " pdb=" N GLU F 715 " pdb=" CA GLU F 715 " ideal model delta sigma weight residual 121.63 111.58 10.05 1.91e+00 2.74e-01 2.77e+01 ... (remaining 100529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 39120 17.76 - 35.51: 3997 35.51 - 53.27: 1305 53.27 - 71.03: 399 71.03 - 88.79: 133 Dihedral angle restraints: 44954 sinusoidal: 17822 harmonic: 27132 Sorted by residual: dihedral pdb=" CA THR F 521 " pdb=" C THR F 521 " pdb=" N GLU F 522 " pdb=" CA GLU F 522 " ideal model delta harmonic sigma weight residual 180.00 144.38 35.62 0 5.00e+00 4.00e-02 5.08e+01 dihedral pdb=" CA THR G 521 " pdb=" C THR G 521 " pdb=" N GLU G 522 " pdb=" CA GLU G 522 " ideal model delta harmonic sigma weight residual 180.00 144.39 35.61 0 5.00e+00 4.00e-02 5.07e+01 dihedral pdb=" CA THR B 521 " pdb=" C THR B 521 " pdb=" N GLU B 522 " pdb=" CA GLU B 522 " ideal model delta harmonic sigma weight residual 180.00 144.43 35.57 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 44951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 7150 0.042 - 0.084: 2828 0.084 - 0.125: 1115 0.125 - 0.167: 189 0.167 - 0.209: 30 Chirality restraints: 11312 Sorted by residual: chirality pdb=" CA ASN N 342 " pdb=" N ASN N 342 " pdb=" C ASN N 342 " pdb=" CB ASN N 342 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ASN L 342 " pdb=" N ASN L 342 " pdb=" C ASN L 342 " pdb=" CB ASN L 342 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA ASN J 342 " pdb=" N ASN J 342 " pdb=" C ASN J 342 " pdb=" CB ASN J 342 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 11309 not shown) Planarity restraints: 13132 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR D 521 " -0.013 2.00e-02 2.50e+03 2.64e-02 6.97e+00 pdb=" C THR D 521 " 0.046 2.00e-02 2.50e+03 pdb=" O THR D 521 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU D 522 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 521 " -0.013 2.00e-02 2.50e+03 2.62e-02 6.86e+00 pdb=" C THR C 521 " 0.045 2.00e-02 2.50e+03 pdb=" O THR C 521 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU C 522 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 521 " 0.013 2.00e-02 2.50e+03 2.61e-02 6.82e+00 pdb=" C THR A 521 " -0.045 2.00e-02 2.50e+03 pdb=" O THR A 521 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU A 522 " 0.015 2.00e-02 2.50e+03 ... (remaining 13129 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 1195 2.60 - 3.17: 60382 3.17 - 3.75: 106172 3.75 - 4.32: 167088 4.32 - 4.90: 271908 Nonbonded interactions: 606745 Sorted by model distance: nonbonded pdb=" O GLU C 522 " pdb=" ND2 ASN C 523 " model vdw 2.020 2.520 nonbonded pdb=" O GLU E 522 " pdb=" ND2 ASN E 523 " model vdw 2.021 2.520 nonbonded pdb=" O GLU B 522 " pdb=" ND2 ASN B 523 " model vdw 2.021 2.520 nonbonded pdb=" O GLU F 522 " pdb=" ND2 ASN F 523 " model vdw 2.021 2.520 nonbonded pdb=" O GLU D 522 " pdb=" ND2 ASN D 523 " model vdw 2.021 2.520 ... (remaining 606740 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 16.100 Check model and map are aligned: 0.820 Set scattering table: 0.510 Process input model: 153.330 Find NCS groups from input model: 4.040 Set up NCS constraints: 0.560 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:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 190.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 74060 Z= 0.466 Angle : 0.732 11.273 100534 Z= 0.416 Chirality : 0.051 0.209 11312 Planarity : 0.005 0.049 13132 Dihedral : 17.632 88.786 27622 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 9.90 % Favored : 89.87 % Rotamer: Outliers : 11.21 % Allowed : 17.37 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.69 (0.07), residues: 9212 helix: -2.72 (0.11), residues: 1218 sheet: -1.78 (0.09), residues: 2716 loop : -2.84 (0.07), residues: 5278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 503 HIS 0.005 0.001 HIS K 314 PHE 0.025 0.002 PHE G 707 TYR 0.021 0.002 TYR M 297 ARG 0.002 0.000 ARG E 394 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1811 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 920 poor density : 891 time to evaluate : 6.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 464 TYR cc_start: 0.8499 (t80) cc_final: 0.8294 (t80) REVERT: A 694 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7530 (mmtm) REVERT: A 747 ILE cc_start: 0.4588 (OUTLIER) cc_final: 0.4380 (pp) REVERT: A 786 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7952 (tpp) REVERT: A 870 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8656 (mp) REVERT: B 305 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8354 (mt-10) REVERT: B 325 ARG cc_start: 0.8439 (tpt-90) cc_final: 0.8171 (tpt-90) REVERT: B 640 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8086 (mm-40) REVERT: B 660 MET cc_start: 0.8311 (tpt) cc_final: 0.7853 (tpt) REVERT: B 677 ASP cc_start: 0.4742 (OUTLIER) cc_final: 0.4493 (m-30) REVERT: B 689 LYS cc_start: 0.7674 (ttpp) cc_final: 0.7086 (pptt) REVERT: B 717 ASP cc_start: 0.6771 (t70) cc_final: 0.6306 (t0) REVERT: B 747 ILE cc_start: 0.4719 (OUTLIER) cc_final: 0.4469 (pp) REVERT: C 334 SER cc_start: 0.8910 (OUTLIER) cc_final: 0.8708 (t) REVERT: C 614 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8140 (mtpp) REVERT: C 660 MET cc_start: 0.8413 (tpt) cc_final: 0.7944 (tpt) REVERT: C 677 ASP cc_start: 0.4758 (OUTLIER) cc_final: 0.4398 (m-30) REVERT: C 689 LYS cc_start: 0.7619 (ttpp) cc_final: 0.6939 (pptt) REVERT: C 717 ASP cc_start: 0.7025 (t70) cc_final: 0.6438 (t0) REVERT: D 325 ARG cc_start: 0.8470 (tpt-90) cc_final: 0.8254 (tpt-90) REVERT: D 677 ASP cc_start: 0.4771 (OUTLIER) cc_final: 0.4425 (m-30) REVERT: D 689 LYS cc_start: 0.7842 (ttpp) cc_final: 0.7253 (pptt) REVERT: D 747 ILE cc_start: 0.4793 (OUTLIER) cc_final: 0.4497 (pp) REVERT: D 786 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8031 (tpp) REVERT: E 590 ASP cc_start: 0.7182 (OUTLIER) cc_final: 0.6940 (t0) REVERT: E 595 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8178 (mt) REVERT: E 694 LYS cc_start: 0.7230 (OUTLIER) cc_final: 0.7023 (tppp) REVERT: E 747 ILE cc_start: 0.5220 (OUTLIER) cc_final: 0.4813 (pp) REVERT: E 768 TYR cc_start: 0.8750 (p90) cc_final: 0.8312 (p90) REVERT: E 796 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: E 838 ASN cc_start: 0.9329 (OUTLIER) cc_final: 0.9057 (m110) REVERT: F 304 MET cc_start: 0.8933 (ttp) cc_final: 0.8731 (ttm) REVERT: F 499 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7639 (mm-30) REVERT: F 589 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7798 (mtmm) REVERT: F 595 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8074 (mt) REVERT: F 677 ASP cc_start: 0.5579 (OUTLIER) cc_final: 0.5198 (m-30) REVERT: F 689 LYS cc_start: 0.8047 (ttpp) cc_final: 0.7674 (pptt) REVERT: F 714 THR cc_start: 0.7368 (OUTLIER) cc_final: 0.7101 (t) REVERT: F 747 ILE cc_start: 0.4596 (OUTLIER) cc_final: 0.4200 (pp) REVERT: G 589 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.8052 (mtmm) REVERT: G 660 MET cc_start: 0.8249 (tpt) cc_final: 0.7981 (tpt) REVERT: G 689 LYS cc_start: 0.7744 (ttpp) cc_final: 0.7307 (pptt) REVERT: G 714 THR cc_start: 0.7410 (OUTLIER) cc_final: 0.7146 (t) REVERT: H 248 SER cc_start: 0.8227 (OUTLIER) cc_final: 0.7862 (p) REVERT: H 259 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8849 (p) REVERT: H 297 TYR cc_start: 0.8796 (t80) cc_final: 0.8501 (t80) REVERT: H 417 ASP cc_start: 0.7589 (p0) cc_final: 0.7196 (p0) REVERT: H 853 MET cc_start: 0.8772 (mmm) cc_final: 0.8285 (mmm) REVERT: I 248 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7910 (p) REVERT: I 379 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8290 (mt) REVERT: I 414 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7910 (mt) REVERT: I 732 TYR cc_start: 0.6296 (m-80) cc_final: 0.6073 (m-80) REVERT: I 853 MET cc_start: 0.8721 (mmm) cc_final: 0.8366 (mmp) REVERT: J 259 SER cc_start: 0.9065 (OUTLIER) cc_final: 0.8729 (p) REVERT: J 417 ASP cc_start: 0.7501 (p0) cc_final: 0.7156 (p0) REVERT: J 666 TYR cc_start: 0.8585 (m-80) cc_final: 0.8236 (m-80) REVERT: J 759 GLN cc_start: 0.7836 (tp40) cc_final: 0.7610 (tp-100) REVERT: J 763 ASP cc_start: 0.8232 (m-30) cc_final: 0.8002 (m-30) REVERT: K 383 LYS cc_start: 0.8404 (ttmm) cc_final: 0.8145 (mtpt) REVERT: K 666 TYR cc_start: 0.8593 (m-80) cc_final: 0.8333 (m-80) REVERT: K 759 GLN cc_start: 0.7998 (tp40) cc_final: 0.7734 (tp-100) REVERT: K 763 ASP cc_start: 0.8106 (m-30) cc_final: 0.7814 (m-30) REVERT: K 853 MET cc_start: 0.8659 (mmm) cc_final: 0.8444 (mmp) REVERT: L 248 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7936 (p) REVERT: L 666 TYR cc_start: 0.8345 (m-80) cc_final: 0.8045 (m-80) REVERT: L 739 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8719 (m) REVERT: L 786 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7774 (mtp) REVERT: M 248 SER cc_start: 0.8446 (OUTLIER) cc_final: 0.8236 (p) REVERT: M 373 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7569 (tt0) REVERT: M 377 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.7961 (p) REVERT: M 533 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8688 (ttmt) REVERT: M 648 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7124 (t0) REVERT: M 768 TYR cc_start: 0.8705 (p90) cc_final: 0.8452 (p90) REVERT: M 837 THR cc_start: 0.8994 (p) cc_final: 0.8728 (t) REVERT: M 853 MET cc_start: 0.8652 (mmm) cc_final: 0.8144 (mmm) REVERT: M 868 ARG cc_start: 0.7364 (mtp180) cc_final: 0.7027 (ttp-110) REVERT: N 523 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7550 (p0) REVERT: N 786 MET cc_start: 0.8109 (OUTLIER) cc_final: 0.7886 (mtp) REVERT: N 837 THR cc_start: 0.9055 (p) cc_final: 0.8772 (t) outliers start: 920 outliers final: 310 residues processed: 1645 average time/residue: 1.1553 time to fit residues: 2672.0589 Evaluate side-chains 961 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 608 time to evaluate : 6.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 310 SER Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 493 SER Chi-restraints excluded: chain A residue 499 GLU Chi-restraints excluded: chain A residue 589 LYS Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 654 THR Chi-restraints excluded: chain A residue 694 LYS Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 786 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 420 SER Chi-restraints excluded: chain B residue 493 SER Chi-restraints excluded: chain B residue 523 ASN Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 614 LYS Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 654 THR Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 707 PHE Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 310 SER Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 334 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 380 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 493 SER Chi-restraints excluded: chain C residue 574 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 614 LYS Chi-restraints excluded: chain C residue 623 ASP Chi-restraints excluded: chain C residue 654 THR Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 786 MET Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 876 ASP Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 310 SER Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 420 SER Chi-restraints excluded: chain D residue 493 SER Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 614 LYS Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 648 ASN Chi-restraints excluded: chain D residue 654 THR Chi-restraints excluded: chain D residue 677 ASP Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 777 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 786 MET Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain D residue 866 ASP Chi-restraints excluded: chain D residue 876 ASP Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 317 THR Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 493 SER Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 591 SER Chi-restraints excluded: chain E residue 595 LEU Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 648 ASN Chi-restraints excluded: chain E residue 654 THR Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 777 SER Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 786 MET Chi-restraints excluded: chain E residue 796 GLU Chi-restraints excluded: chain E residue 838 ASN Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 866 ASP Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 380 SER Chi-restraints excluded: chain F residue 493 SER Chi-restraints excluded: chain F residue 499 GLU Chi-restraints excluded: chain F residue 589 LYS Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 595 LEU Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 646 SER Chi-restraints excluded: chain F residue 654 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 777 SER Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 322 THR Chi-restraints excluded: chain G residue 364 SER Chi-restraints excluded: chain G residue 380 SER Chi-restraints excluded: chain G residue 493 SER Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 589 LYS Chi-restraints excluded: chain G residue 590 ASP Chi-restraints excluded: chain G residue 591 SER Chi-restraints excluded: chain G residue 614 LYS Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 654 THR Chi-restraints excluded: chain G residue 714 THR Chi-restraints excluded: chain G residue 777 SER Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 786 MET Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 866 ASP Chi-restraints excluded: chain G residue 876 ASP Chi-restraints excluded: chain H residue 229 SER Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 248 SER Chi-restraints excluded: chain H residue 259 SER Chi-restraints excluded: chain H residue 264 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 316 SER Chi-restraints excluded: chain H residue 328 THR Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain H residue 358 SER Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 400 THR Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 456 SER Chi-restraints excluded: chain H residue 462 ILE Chi-restraints excluded: chain H residue 465 ASP Chi-restraints excluded: chain H residue 492 SER Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 504 SER Chi-restraints excluded: chain H residue 516 SER Chi-restraints excluded: chain H residue 568 ASP Chi-restraints excluded: chain H residue 594 THR Chi-restraints excluded: chain H residue 605 LEU Chi-restraints excluded: chain H residue 637 THR Chi-restraints excluded: chain H residue 651 ASN Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 786 MET Chi-restraints excluded: chain H residue 875 VAL Chi-restraints excluded: chain I residue 229 SER Chi-restraints excluded: chain I residue 248 SER Chi-restraints excluded: chain I residue 259 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 316 SER Chi-restraints excluded: chain I residue 328 THR Chi-restraints excluded: chain I residue 334 SER Chi-restraints excluded: chain I residue 358 SER Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 456 SER Chi-restraints excluded: chain I residue 462 ILE Chi-restraints excluded: chain I residue 492 SER Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 504 SER Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 594 THR Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 637 THR Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 753 VAL Chi-restraints excluded: chain I residue 786 MET Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain J residue 229 SER Chi-restraints excluded: chain J residue 259 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 316 SER Chi-restraints excluded: chain J residue 328 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 456 SER Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain J residue 492 SER Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 502 SER Chi-restraints excluded: chain J residue 504 SER Chi-restraints excluded: chain J residue 516 SER Chi-restraints excluded: chain J residue 525 SER Chi-restraints excluded: chain J residue 568 ASP Chi-restraints excluded: chain J residue 594 THR Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 637 THR Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 739 THR Chi-restraints excluded: chain J residue 753 VAL Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain J residue 866 ASP Chi-restraints excluded: chain J residue 875 VAL Chi-restraints excluded: chain K residue 229 SER Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 316 SER Chi-restraints excluded: chain K residue 328 THR Chi-restraints excluded: chain K residue 334 SER Chi-restraints excluded: chain K residue 358 SER Chi-restraints excluded: chain K residue 377 THR Chi-restraints excluded: chain K residue 400 THR Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 456 SER Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 492 SER Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 502 SER Chi-restraints excluded: chain K residue 504 SER Chi-restraints excluded: chain K residue 525 SER Chi-restraints excluded: chain K residue 594 THR Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 637 THR Chi-restraints excluded: chain K residue 651 ASN Chi-restraints excluded: chain K residue 753 VAL Chi-restraints excluded: chain K residue 786 MET Chi-restraints excluded: chain K residue 875 VAL Chi-restraints excluded: chain L residue 229 SER Chi-restraints excluded: chain L residue 236 THR Chi-restraints excluded: chain L residue 248 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 316 SER Chi-restraints excluded: chain L residue 328 THR Chi-restraints excluded: chain L residue 334 SER Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 456 SER Chi-restraints excluded: chain L residue 465 ASP Chi-restraints excluded: chain L residue 492 SER Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 504 SER Chi-restraints excluded: chain L residue 568 ASP Chi-restraints excluded: chain L residue 594 THR Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 651 ASN Chi-restraints excluded: chain L residue 739 THR Chi-restraints excluded: chain L residue 753 VAL Chi-restraints excluded: chain L residue 786 MET Chi-restraints excluded: chain L residue 812 TYR Chi-restraints excluded: chain L residue 822 ASP Chi-restraints excluded: chain L residue 875 VAL Chi-restraints excluded: chain M residue 229 SER Chi-restraints excluded: chain M residue 236 THR Chi-restraints excluded: chain M residue 248 SER Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 316 SER Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 358 SER Chi-restraints excluded: chain M residue 373 GLU Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 456 SER Chi-restraints excluded: chain M residue 492 SER Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 502 SER Chi-restraints excluded: chain M residue 504 SER Chi-restraints excluded: chain M residue 516 SER Chi-restraints excluded: chain M residue 525 SER Chi-restraints excluded: chain M residue 533 LYS Chi-restraints excluded: chain M residue 568 ASP Chi-restraints excluded: chain M residue 594 THR Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 648 ASN Chi-restraints excluded: chain M residue 651 ASN Chi-restraints excluded: chain M residue 739 THR Chi-restraints excluded: chain M residue 753 VAL Chi-restraints excluded: chain M residue 786 MET Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain M residue 874 SER Chi-restraints excluded: chain M residue 875 VAL Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 229 SER Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 280 SER Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 316 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 358 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 456 SER Chi-restraints excluded: chain N residue 492 SER Chi-restraints excluded: chain N residue 497 VAL Chi-restraints excluded: chain N residue 502 SER Chi-restraints excluded: chain N residue 504 SER Chi-restraints excluded: chain N residue 523 ASN Chi-restraints excluded: chain N residue 525 SER Chi-restraints excluded: chain N residue 594 THR Chi-restraints excluded: chain N residue 605 LEU Chi-restraints excluded: chain N residue 637 THR Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 753 VAL Chi-restraints excluded: chain N residue 786 MET Chi-restraints excluded: chain N residue 822 ASP Chi-restraints excluded: chain N residue 874 SER Chi-restraints excluded: chain N residue 875 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 780 optimal weight: 9.9990 chunk 700 optimal weight: 5.9990 chunk 388 optimal weight: 1.9990 chunk 239 optimal weight: 0.8980 chunk 472 optimal weight: 9.9990 chunk 374 optimal weight: 3.9990 chunk 724 optimal weight: 0.9990 chunk 280 optimal weight: 0.8980 chunk 440 optimal weight: 3.9990 chunk 539 optimal weight: 9.9990 chunk 839 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 363 ASN A 382 ASN A 390 ASN A 392 ASN A 397 ASN A 720 ASN A 735 ASN A 773 ASN A 775 ASN A 834 GLN A 838 ASN A 841 ASN B 265 ASN B 382 ASN B 390 ASN B 392 ASN B 397 ASN B 450 ASN B 586 ASN B 627 ASN B 720 ASN B 735 ASN B 775 ASN B 834 GLN B 838 ASN B 841 ASN C 265 ASN C 363 ASN C 382 ASN C 390 ASN C 392 ASN C 397 ASN C 450 ASN C 463 ASN C 536 GLN C 627 ASN C 720 ASN C 735 ASN C 775 ASN C 834 GLN C 841 ASN D 382 ASN D 390 ASN D 392 ASN D 397 ASN D 463 ASN D 627 ASN D 735 ASN D 775 ASN D 834 GLN D 838 ASN D 841 ASN E 265 ASN E 382 ASN E 390 ASN E 392 ASN E 397 ASN E 463 ASN E 735 ASN E 775 ASN E 834 GLN E 838 ASN E 841 ASN F 363 ASN F 382 ASN F 390 ASN F 392 ASN F 397 ASN ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 720 ASN F 775 ASN F 834 GLN F 838 ASN F 841 ASN G 382 ASN G 390 ASN G 392 ASN G 397 ASN G 586 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 735 ASN G 775 ASN G 834 GLN G 838 ASN G 841 ASN H 225 ASN H 314 HIS H 335 ASN H 342 ASN H 425 GLN H 463 ASN H 501 ASN H 509 GLN H 586 ASN H 602 ASN H 610 ASN H 702 GLN H 773 ASN H 775 ASN H 827 ASN H 838 ASN I 225 ASN I 314 HIS I 335 ASN I 342 ASN I 425 GLN I 432 ASN I 463 ASN I 475 GLN I 501 ASN I 509 GLN I 586 ASN I 602 ASN I 610 ASN I 773 ASN I 775 ASN I 838 ASN J 225 ASN J 252 GLN J 314 HIS J 335 ASN J 463 ASN J 475 GLN J 501 ASN J 509 GLN J 586 ASN J 602 ASN J 610 ASN ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 773 ASN J 775 ASN J 827 ASN J 838 ASN K 225 ASN K 314 HIS K 335 ASN K 342 ASN K 432 ASN K 463 ASN K 475 GLN K 501 ASN K 509 GLN K 586 ASN K 602 ASN K 610 ASN K 773 ASN K 775 ASN K 838 ASN L 225 ASN L 314 HIS L 335 ASN L 432 ASN L 475 GLN L 501 ASN L 509 GLN L 586 ASN L 602 ASN L 610 ASN L 773 ASN L 775 ASN L 838 ASN M 225 ASN M 314 HIS M 335 ASN M 342 ASN M 432 ASN M 463 ASN M 475 GLN M 501 ASN M 509 GLN M 586 ASN M 602 ASN M 610 ASN M 759 GLN M 773 ASN M 775 ASN M 838 ASN N 225 ASN N 314 HIS N 335 ASN N 342 ASN N 425 GLN N 475 GLN N 501 ASN N 509 GLN N 586 ASN N 602 ASN N 610 ASN N 773 ASN N 775 ASN N 838 ASN Total number of N/Q/H flips: 189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 74060 Z= 0.216 Angle : 0.607 16.104 100534 Z= 0.328 Chirality : 0.047 0.184 11312 Planarity : 0.005 0.047 13132 Dihedral : 8.400 74.952 10519 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.27 % Favored : 91.64 % Rotamer: Outliers : 6.23 % Allowed : 20.26 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -2.62 (0.08), residues: 9212 helix: -1.10 (0.14), residues: 1225 sheet: -0.84 (0.10), residues: 2450 loop : -2.42 (0.07), residues: 5537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 503 HIS 0.003 0.001 HIS A 765 PHE 0.018 0.001 PHE D 707 TYR 0.023 0.001 TYR N 297 ARG 0.002 0.000 ARG F 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1281 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 511 poor density : 770 time to evaluate : 6.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 452 MET cc_start: 0.9133 (ptm) cc_final: 0.8879 (ptp) REVERT: A 464 TYR cc_start: 0.8353 (t80) cc_final: 0.8129 (t80) REVERT: A 623 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: B 305 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8218 (mt-10) REVERT: B 414 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8393 (tp) REVERT: B 660 MET cc_start: 0.8187 (tpt) cc_final: 0.7821 (tpt) REVERT: B 677 ASP cc_start: 0.5075 (OUTLIER) cc_final: 0.4832 (m-30) REVERT: B 689 LYS cc_start: 0.7779 (ttpp) cc_final: 0.7152 (pptt) REVERT: B 717 ASP cc_start: 0.7019 (t70) cc_final: 0.6553 (t0) REVERT: B 747 ILE cc_start: 0.4662 (OUTLIER) cc_final: 0.4456 (pp) REVERT: C 325 ARG cc_start: 0.8285 (tpt-90) cc_final: 0.8049 (tpt-90) REVERT: C 499 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: C 623 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: C 660 MET cc_start: 0.8289 (tpt) cc_final: 0.8004 (tpt) REVERT: C 689 LYS cc_start: 0.7776 (ttpp) cc_final: 0.7135 (pptt) REVERT: C 717 ASP cc_start: 0.7414 (t70) cc_final: 0.6967 (t70) REVERT: C 762 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7492 (mpp) REVERT: D 589 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8232 (mtmm) REVERT: D 677 ASP cc_start: 0.5300 (OUTLIER) cc_final: 0.4806 (m-30) REVERT: D 689 LYS cc_start: 0.7983 (ttpp) cc_final: 0.7633 (pptt) REVERT: E 451 THR cc_start: 0.8861 (p) cc_final: 0.8622 (p) REVERT: E 499 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: E 589 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (mtmm) REVERT: E 614 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8057 (tmtt) REVERT: E 868 ARG cc_start: 0.8000 (ttp-110) cc_final: 0.7723 (mtm110) REVERT: F 590 ASP cc_start: 0.7239 (OUTLIER) cc_final: 0.6937 (t0) REVERT: F 677 ASP cc_start: 0.6021 (OUTLIER) cc_final: 0.5583 (m-30) REVERT: F 689 LYS cc_start: 0.7939 (ttpp) cc_final: 0.7533 (pptt) REVERT: F 708 SER cc_start: 0.7671 (OUTLIER) cc_final: 0.7448 (t) REVERT: F 853 MET cc_start: 0.8541 (mmm) cc_final: 0.7886 (mmp) REVERT: G 305 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: G 499 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7576 (tp30) REVERT: G 655 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7617 (ttpp) REVERT: H 687 LYS cc_start: 0.8096 (OUTLIER) cc_final: 0.7702 (tttm) REVERT: H 726 ILE cc_start: 0.5564 (OUTLIER) cc_final: 0.5309 (mp) REVERT: H 748 LEU cc_start: 0.7399 (OUTLIER) cc_final: 0.7054 (mt) REVERT: H 853 MET cc_start: 0.8759 (mmm) cc_final: 0.8357 (mmm) REVERT: I 259 SER cc_start: 0.9056 (OUTLIER) cc_final: 0.8669 (p) REVERT: I 309 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8868 (mt) REVERT: I 377 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7844 (p) REVERT: I 379 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8250 (mt) REVERT: I 414 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7814 (mt) REVERT: I 747 ILE cc_start: 0.7751 (mm) cc_final: 0.7530 (mm) REVERT: I 853 MET cc_start: 0.8766 (mmm) cc_final: 0.8443 (mmp) REVERT: I 866 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: J 417 ASP cc_start: 0.7428 (p0) cc_final: 0.7023 (p0) REVERT: J 437 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7758 (m-30) REVERT: J 666 TYR cc_start: 0.8542 (m-80) cc_final: 0.8190 (m-80) REVERT: J 757 THR cc_start: 0.8213 (OUTLIER) cc_final: 0.7918 (p) REVERT: J 759 GLN cc_start: 0.7922 (tp40) cc_final: 0.7592 (tp-100) REVERT: J 763 ASP cc_start: 0.8119 (m-30) cc_final: 0.7778 (m-30) REVERT: K 379 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8259 (mt) REVERT: K 666 TYR cc_start: 0.8494 (m-80) cc_final: 0.8237 (m-80) REVERT: K 694 LYS cc_start: 0.7813 (tppp) cc_final: 0.7379 (mmmt) REVERT: K 748 LEU cc_start: 0.7440 (OUTLIER) cc_final: 0.7058 (mt) REVERT: K 759 GLN cc_start: 0.8008 (tp40) cc_final: 0.7720 (tp-100) REVERT: K 763 ASP cc_start: 0.8075 (m-30) cc_final: 0.7732 (m-30) REVERT: K 853 MET cc_start: 0.8733 (mmm) cc_final: 0.8502 (mmp) REVERT: L 297 TYR cc_start: 0.8501 (t80) cc_final: 0.8226 (t80) REVERT: L 821 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8377 (mtpt) REVERT: M 377 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7792 (p) REVERT: M 426 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7698 (tt0) REVERT: M 694 LYS cc_start: 0.7598 (mttm) cc_final: 0.7384 (tptp) REVERT: M 748 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7269 (mt) REVERT: M 825 MET cc_start: 0.7623 (mmm) cc_final: 0.7209 (mmt) REVERT: M 853 MET cc_start: 0.8710 (mmm) cc_final: 0.8227 (mmm) REVERT: M 876 ASP cc_start: 0.6116 (p0) cc_final: 0.5915 (p0) REVERT: N 377 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.7772 (p) REVERT: N 379 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7933 (mp) REVERT: N 732 TYR cc_start: 0.6252 (m-80) cc_final: 0.5903 (m-80) REVERT: N 748 LEU cc_start: 0.7506 (OUTLIER) cc_final: 0.7082 (mt) outliers start: 511 outliers final: 232 residues processed: 1208 average time/residue: 1.2131 time to fit residues: 2046.7569 Evaluate side-chains 911 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 640 time to evaluate : 6.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 646 SER Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 714 THR Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 793 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 677 ASP Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 623 ASP Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain C residue 876 ASP Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 591 SER Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 677 ASP Chi-restraints excluded: chain D residue 777 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain D residue 876 ASP Chi-restraints excluded: chain E residue 248 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 561 ASP Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 623 ASP Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 646 SER Chi-restraints excluded: chain E residue 695 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 777 SER Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 866 ASP Chi-restraints excluded: chain E residue 874 SER Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 248 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 708 SER Chi-restraints excluded: chain F residue 777 SER Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 499 GLU Chi-restraints excluded: chain G residue 590 ASP Chi-restraints excluded: chain G residue 591 SER Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 655 LYS Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 762 MET Chi-restraints excluded: chain G residue 777 SER Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 866 ASP Chi-restraints excluded: chain G residue 874 SER Chi-restraints excluded: chain G residue 876 ASP Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 400 THR Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 437 ASP Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 597 ASP Chi-restraints excluded: chain H residue 605 LEU Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 644 GLN Chi-restraints excluded: chain H residue 654 THR Chi-restraints excluded: chain H residue 687 LYS Chi-restraints excluded: chain H residue 726 ILE Chi-restraints excluded: chain H residue 748 LEU Chi-restraints excluded: chain H residue 757 THR Chi-restraints excluded: chain H residue 866 ASP Chi-restraints excluded: chain H residue 875 VAL Chi-restraints excluded: chain I residue 259 SER Chi-restraints excluded: chain I residue 280 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 377 THR Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 437 ASP Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 573 GLU Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 821 LYS Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 866 ASP Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 635 VAL Chi-restraints excluded: chain J residue 654 THR Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 875 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 368 GLN Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 377 THR Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 400 THR Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 433 LEU Chi-restraints excluded: chain K residue 437 ASP Chi-restraints excluded: chain K residue 465 ASP Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 568 ASP Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 824 GLU Chi-restraints excluded: chain K residue 866 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 875 VAL Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 654 THR Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 866 ASP Chi-restraints excluded: chain L residue 868 ARG Chi-restraints excluded: chain L residue 875 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 377 THR Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 426 GLU Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 568 ASP Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 644 GLN Chi-restraints excluded: chain M residue 654 THR Chi-restraints excluded: chain M residue 748 LEU Chi-restraints excluded: chain M residue 757 THR Chi-restraints excluded: chain M residue 875 VAL Chi-restraints excluded: chain N residue 251 GLU Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 264 SER Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 368 GLN Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 437 ASP Chi-restraints excluded: chain N residue 465 ASP Chi-restraints excluded: chain N residue 497 VAL Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 605 LEU Chi-restraints excluded: chain N residue 634 ASN Chi-restraints excluded: chain N residue 643 LEU Chi-restraints excluded: chain N residue 644 GLN Chi-restraints excluded: chain N residue 748 LEU Chi-restraints excluded: chain N residue 749 ASP Chi-restraints excluded: chain N residue 757 THR Chi-restraints excluded: chain N residue 824 GLU Chi-restraints excluded: chain N residue 868 ARG Chi-restraints excluded: chain N residue 874 SER Chi-restraints excluded: chain N residue 875 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 466 optimal weight: 0.0070 chunk 260 optimal weight: 6.9990 chunk 698 optimal weight: 0.6980 chunk 571 optimal weight: 7.9990 chunk 231 optimal weight: 5.9990 chunk 840 optimal weight: 4.9990 chunk 908 optimal weight: 4.9990 chunk 748 optimal weight: 3.9990 chunk 833 optimal weight: 9.9990 chunk 286 optimal weight: 0.7980 chunk 674 optimal weight: 8.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN A 509 GLN A 720 ASN A 773 ASN B 463 ASN B 586 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN C 509 GLN D 463 ASN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 ASN E 509 GLN ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 ASN F 509 GLN ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 586 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 425 GLN J 342 ASN ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 463 ASN K 780 ASN L 342 ASN L 780 ASN M 463 ASN M 759 GLN M 780 ASN N 425 GLN N 523 ASN N 780 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 74060 Z= 0.246 Angle : 0.607 15.409 100534 Z= 0.325 Chirality : 0.047 0.189 11312 Planarity : 0.004 0.044 13132 Dihedral : 7.310 59.864 10196 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.26 % Favored : 91.67 % Rotamer: Outliers : 6.22 % Allowed : 20.75 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.08), residues: 9212 helix: -0.46 (0.15), residues: 1232 sheet: -0.21 (0.10), residues: 2660 loop : -2.21 (0.08), residues: 5320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 503 HIS 0.009 0.001 HIS H 314 PHE 0.017 0.001 PHE C 707 TYR 0.028 0.001 TYR C 357 ARG 0.006 0.000 ARG B 868 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 510 poor density : 684 time to evaluate : 6.659 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 545 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8725 (tp) REVERT: A 623 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7706 (m-30) REVERT: A 762 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7464 (mpp) REVERT: B 305 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: B 414 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8417 (tp) REVERT: B 452 MET cc_start: 0.9123 (ptm) cc_final: 0.8917 (ptp) REVERT: B 499 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7705 (mm-30) REVERT: B 623 ASP cc_start: 0.8021 (OUTLIER) cc_final: 0.7804 (m-30) REVERT: B 660 MET cc_start: 0.8180 (tpt) cc_final: 0.7870 (tpt) REVERT: B 689 LYS cc_start: 0.7856 (ttpp) cc_final: 0.7248 (pptt) REVERT: B 717 ASP cc_start: 0.6937 (t70) cc_final: 0.6516 (t0) REVERT: B 868 ARG cc_start: 0.7894 (ttp-110) cc_final: 0.7624 (mtm110) REVERT: C 499 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7776 (tp30) REVERT: C 660 MET cc_start: 0.8288 (tpt) cc_final: 0.7943 (tpt) REVERT: C 677 ASP cc_start: 0.5132 (OUTLIER) cc_final: 0.4838 (m-30) REVERT: C 689 LYS cc_start: 0.7849 (ttpp) cc_final: 0.7130 (pptt) REVERT: C 717 ASP cc_start: 0.7467 (t70) cc_final: 0.7115 (t70) REVERT: C 762 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.7572 (mpp) REVERT: D 677 ASP cc_start: 0.5274 (OUTLIER) cc_final: 0.4852 (m-30) REVERT: E 451 THR cc_start: 0.8815 (p) cc_final: 0.8561 (p) REVERT: E 499 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7700 (tp30) REVERT: E 589 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.8150 (mtmm) REVERT: E 655 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7797 (ttpp) REVERT: E 868 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7704 (mtm110) REVERT: F 305 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: F 590 ASP cc_start: 0.7275 (OUTLIER) cc_final: 0.6984 (t70) REVERT: F 660 MET cc_start: 0.8358 (tpt) cc_final: 0.7730 (tpt) REVERT: F 677 ASP cc_start: 0.5592 (OUTLIER) cc_final: 0.5178 (m-30) REVERT: F 689 LYS cc_start: 0.7867 (ttpp) cc_final: 0.7466 (pptt) REVERT: F 747 ILE cc_start: 0.5045 (OUTLIER) cc_final: 0.4556 (pp) REVERT: F 762 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7375 (mpp) REVERT: G 305 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: G 499 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7669 (tp30) REVERT: G 623 ASP cc_start: 0.8016 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: H 426 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: H 429 ILE cc_start: 0.9151 (mt) cc_final: 0.8927 (mm) REVERT: H 536 GLN cc_start: 0.7755 (mm110) cc_final: 0.7479 (mt0) REVERT: H 604 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7871 (tttt) REVERT: H 748 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7053 (mt) REVERT: H 759 GLN cc_start: 0.7983 (tp-100) cc_final: 0.7655 (tp-100) REVERT: H 763 ASP cc_start: 0.8141 (m-30) cc_final: 0.7740 (m-30) REVERT: H 853 MET cc_start: 0.8731 (mmm) cc_final: 0.8334 (mmm) REVERT: I 379 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7864 (mp) REVERT: I 414 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7821 (mt) REVERT: I 425 GLN cc_start: 0.7812 (mm110) cc_final: 0.7251 (pt0) REVERT: I 426 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7706 (tt0) REVERT: I 666 TYR cc_start: 0.8464 (m-80) cc_final: 0.8022 (m-80) REVERT: I 747 ILE cc_start: 0.7800 (mm) cc_final: 0.7600 (mm) REVERT: I 853 MET cc_start: 0.8755 (mmm) cc_final: 0.8485 (mmp) REVERT: I 866 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7761 (m-30) REVERT: J 417 ASP cc_start: 0.7475 (p0) cc_final: 0.7018 (p0) REVERT: J 437 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: J 606 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7758 (mt-10) REVERT: J 666 TYR cc_start: 0.8515 (m-80) cc_final: 0.8148 (m-80) REVERT: J 687 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7435 (tttt) REVERT: J 757 THR cc_start: 0.8217 (OUTLIER) cc_final: 0.7940 (p) REVERT: J 759 GLN cc_start: 0.7955 (tp40) cc_final: 0.7565 (tp-100) REVERT: J 763 ASP cc_start: 0.8090 (m-30) cc_final: 0.7677 (m-30) REVERT: K 309 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8962 (mt) REVERT: K 452 MET cc_start: 0.8118 (mtm) cc_final: 0.7754 (mtm) REVERT: K 666 TYR cc_start: 0.8510 (m-80) cc_final: 0.8239 (m-80) REVERT: K 694 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7596 (tppt) REVERT: K 748 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7060 (mt) REVERT: K 759 GLN cc_start: 0.7987 (tp40) cc_final: 0.7635 (tp-100) REVERT: K 762 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.7651 (mmm) REVERT: K 763 ASP cc_start: 0.8050 (m-30) cc_final: 0.7656 (m-30) REVERT: K 853 MET cc_start: 0.8755 (mmm) cc_final: 0.8510 (mmp) REVERT: L 426 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7691 (tt0) REVERT: L 821 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8335 (mtpt) REVERT: L 852 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8893 (mp) REVERT: M 246 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6707 (mm-30) REVERT: M 426 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: M 564 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8434 (mp) REVERT: M 748 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7256 (mt) REVERT: M 825 MET cc_start: 0.7737 (mmm) cc_final: 0.7448 (mmt) REVERT: M 853 MET cc_start: 0.8767 (mmm) cc_final: 0.8253 (mmm) REVERT: M 876 ASP cc_start: 0.6022 (p0) cc_final: 0.5799 (p0) REVERT: N 246 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7272 (mm-30) REVERT: N 377 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7850 (p) REVERT: N 379 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7684 (mp) REVERT: N 626 ASN cc_start: 0.8058 (t0) cc_final: 0.7776 (t0) REVERT: N 638 THR cc_start: 0.7670 (p) cc_final: 0.7406 (p) REVERT: N 694 LYS cc_start: 0.7594 (mttm) cc_final: 0.7388 (tptm) REVERT: N 732 TYR cc_start: 0.6301 (m-80) cc_final: 0.6014 (m-80) REVERT: N 748 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7028 (mt) outliers start: 510 outliers final: 282 residues processed: 1113 average time/residue: 1.1887 time to fit residues: 1860.6496 Evaluate side-chains 942 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 612 time to evaluate : 6.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain C residue 876 ASP Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 623 ASP Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 677 ASP Chi-restraints excluded: chain D residue 680 THR Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 715 GLU Chi-restraints excluded: chain D residue 777 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain D residue 866 ASP Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain D residue 876 ASP Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 646 SER Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 755 ILE Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 777 SER Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 866 ASP Chi-restraints excluded: chain E residue 874 SER Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain F residue 219 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 648 ASN Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 777 SER Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 499 GLU Chi-restraints excluded: chain G residue 590 ASP Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 708 SER Chi-restraints excluded: chain G residue 777 SER Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 874 SER Chi-restraints excluded: chain G residue 876 ASP Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 309 ILE Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 400 THR Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 437 ASP Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 568 ASP Chi-restraints excluded: chain H residue 604 LYS Chi-restraints excluded: chain H residue 605 LEU Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 643 LEU Chi-restraints excluded: chain H residue 644 GLN Chi-restraints excluded: chain H residue 748 LEU Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain H residue 757 THR Chi-restraints excluded: chain H residue 875 VAL Chi-restraints excluded: chain I residue 280 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 405 LYS Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 426 GLU Chi-restraints excluded: chain I residue 437 ASP Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 573 GLU Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 643 LEU Chi-restraints excluded: chain I residue 670 VAL Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 821 LYS Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 866 ASP Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain J residue 476 ILE Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 568 ASP Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 643 LEU Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 866 ASP Chi-restraints excluded: chain J residue 875 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 368 GLN Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 377 THR Chi-restraints excluded: chain K residue 400 THR Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 433 LEU Chi-restraints excluded: chain K residue 437 ASP Chi-restraints excluded: chain K residue 465 ASP Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 568 ASP Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 694 LYS Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain K residue 762 MET Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 824 GLU Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 875 VAL Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 341 VAL Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 426 GLU Chi-restraints excluded: chain L residue 437 ASP Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 525 SER Chi-restraints excluded: chain L residue 533 LYS Chi-restraints excluded: chain L residue 568 ASP Chi-restraints excluded: chain L residue 573 GLU Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 634 ASN Chi-restraints excluded: chain L residue 643 LEU Chi-restraints excluded: chain L residue 726 ILE Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 822 ASP Chi-restraints excluded: chain L residue 852 ILE Chi-restraints excluded: chain L residue 866 ASP Chi-restraints excluded: chain L residue 875 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 246 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 426 GLU Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 542 THR Chi-restraints excluded: chain M residue 564 LEU Chi-restraints excluded: chain M residue 568 ASP Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 634 ASN Chi-restraints excluded: chain M residue 643 LEU Chi-restraints excluded: chain M residue 644 GLN Chi-restraints excluded: chain M residue 699 VAL Chi-restraints excluded: chain M residue 748 LEU Chi-restraints excluded: chain M residue 749 ASP Chi-restraints excluded: chain M residue 753 VAL Chi-restraints excluded: chain M residue 757 THR Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 875 VAL Chi-restraints excluded: chain N residue 246 GLU Chi-restraints excluded: chain N residue 251 GLU Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 280 SER Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 355 THR Chi-restraints excluded: chain N residue 368 GLN Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 377 THR Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 497 VAL Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 535 LEU Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 605 LEU Chi-restraints excluded: chain N residue 634 ASN Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 748 LEU Chi-restraints excluded: chain N residue 749 ASP Chi-restraints excluded: chain N residue 757 THR Chi-restraints excluded: chain N residue 822 ASP Chi-restraints excluded: chain N residue 824 GLU Chi-restraints excluded: chain N residue 868 ARG Chi-restraints excluded: chain N residue 875 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 830 optimal weight: 5.9990 chunk 632 optimal weight: 7.9990 chunk 436 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 401 optimal weight: 3.9990 chunk 564 optimal weight: 5.9990 chunk 843 optimal weight: 6.9990 chunk 893 optimal weight: 0.4980 chunk 440 optimal weight: 8.9990 chunk 799 optimal weight: 0.9990 chunk 240 optimal weight: 10.0000 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN B 509 GLN B 586 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN B 780 ASN C 371 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 509 GLN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 773 ASN ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 780 ASN F 411 ASN ** F 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 265 ASN G 411 ASN ** G 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 463 ASN ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 463 ASN M 759 GLN N 425 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 74060 Z= 0.258 Angle : 0.608 15.526 100534 Z= 0.325 Chirality : 0.047 0.204 11312 Planarity : 0.004 0.044 13132 Dihedral : 7.133 59.576 10167 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.30 % Favored : 91.63 % Rotamer: Outliers : 6.69 % Allowed : 20.83 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.08), residues: 9212 helix: -0.20 (0.15), residues: 1225 sheet: 0.02 (0.10), residues: 2660 loop : -2.09 (0.08), residues: 5327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 503 HIS 0.005 0.001 HIS H 314 PHE 0.019 0.002 PHE C 707 TYR 0.028 0.001 TYR C 357 ARG 0.004 0.000 ARG B 868 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1186 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 549 poor density : 637 time to evaluate : 6.642 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8267 (tp) REVERT: A 545 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8745 (tp) REVERT: A 623 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7623 (m-30) REVERT: A 656 ILE cc_start: 0.7963 (OUTLIER) cc_final: 0.7679 (tp) REVERT: A 747 ILE cc_start: 0.4971 (OUTLIER) cc_final: 0.4763 (pp) REVERT: A 762 MET cc_start: 0.8413 (OUTLIER) cc_final: 0.7428 (mpp) REVERT: A 870 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8484 (mt) REVERT: B 305 GLU cc_start: 0.8836 (OUTLIER) cc_final: 0.8237 (mt-10) REVERT: B 414 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8386 (tp) REVERT: B 623 ASP cc_start: 0.8072 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: B 660 MET cc_start: 0.8215 (tpt) cc_final: 0.7929 (tpt) REVERT: B 689 LYS cc_start: 0.7874 (ttpp) cc_final: 0.7364 (pptt) REVERT: B 717 ASP cc_start: 0.6924 (t70) cc_final: 0.6541 (t0) REVERT: B 747 ILE cc_start: 0.4841 (OUTLIER) cc_final: 0.4619 (pp) REVERT: C 499 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: C 623 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7701 (m-30) REVERT: C 677 ASP cc_start: 0.5127 (OUTLIER) cc_final: 0.4840 (m-30) REVERT: C 689 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7587 (ttpt) REVERT: C 717 ASP cc_start: 0.7485 (t70) cc_final: 0.7148 (t70) REVERT: C 762 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7551 (mpp) REVERT: D 305 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7934 (mt-10) REVERT: D 589 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8302 (mtmm) REVERT: D 677 ASP cc_start: 0.5387 (OUTLIER) cc_final: 0.4959 (m-30) REVERT: D 747 ILE cc_start: 0.5082 (OUTLIER) cc_final: 0.4617 (pp) REVERT: D 802 GLN cc_start: 0.6815 (OUTLIER) cc_final: 0.6500 (mt0) REVERT: E 499 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7659 (tp30) REVERT: E 589 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8173 (mtmm) REVERT: E 614 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8040 (tmtt) REVERT: E 655 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7813 (ttpp) REVERT: E 741 LEU cc_start: 0.7594 (mt) cc_final: 0.7294 (mt) REVERT: E 747 ILE cc_start: 0.5479 (OUTLIER) cc_final: 0.4977 (pp) REVERT: F 305 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8355 (mt-10) REVERT: F 660 MET cc_start: 0.8282 (tpt) cc_final: 0.7708 (tpt) REVERT: F 677 ASP cc_start: 0.5631 (OUTLIER) cc_final: 0.5258 (m-30) REVERT: F 689 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7666 (tmtt) REVERT: F 762 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: F 853 MET cc_start: 0.8656 (mmp) cc_final: 0.8245 (mmm) REVERT: G 305 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: G 499 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7598 (tp30) REVERT: G 524 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7049 (tt0) REVERT: G 623 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7776 (m-30) REVERT: G 868 ARG cc_start: 0.7929 (ttp-110) cc_final: 0.7605 (mtm110) REVERT: H 429 ILE cc_start: 0.9145 (mt) cc_final: 0.8937 (mm) REVERT: H 524 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.6919 (tt0) REVERT: H 533 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8421 (ttmt) REVERT: H 748 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7057 (mt) REVERT: H 757 THR cc_start: 0.8161 (OUTLIER) cc_final: 0.7957 (p) REVERT: H 759 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7606 (tp-100) REVERT: H 763 ASP cc_start: 0.8057 (m-30) cc_final: 0.7603 (m-30) REVERT: H 853 MET cc_start: 0.8746 (mmm) cc_final: 0.8318 (mmm) REVERT: I 309 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8899 (mt) REVERT: I 414 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7879 (mt) REVERT: I 425 GLN cc_start: 0.7855 (mm110) cc_final: 0.7258 (pt0) REVERT: I 536 GLN cc_start: 0.7568 (mm110) cc_final: 0.7337 (mt0) REVERT: I 666 TYR cc_start: 0.8434 (m-80) cc_final: 0.8017 (m-80) REVERT: I 747 ILE cc_start: 0.7734 (mm) cc_final: 0.7517 (mm) REVERT: I 866 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7833 (m-30) REVERT: J 417 ASP cc_start: 0.7444 (p0) cc_final: 0.6979 (p0) REVERT: J 437 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: J 606 GLU cc_start: 0.7899 (mt-10) cc_final: 0.7685 (mt-10) REVERT: J 660 MET cc_start: 0.8589 (tpp) cc_final: 0.8315 (tpp) REVERT: J 666 TYR cc_start: 0.8496 (m-80) cc_final: 0.8143 (m-80) REVERT: J 687 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7436 (tttt) REVERT: J 757 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7952 (p) REVERT: J 759 GLN cc_start: 0.7981 (tp40) cc_final: 0.7635 (tp-100) REVERT: J 763 ASP cc_start: 0.8068 (m-30) cc_final: 0.7638 (m-30) REVERT: K 309 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8940 (mt) REVERT: K 379 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8227 (mt) REVERT: K 660 MET cc_start: 0.8517 (tpt) cc_final: 0.8255 (tpt) REVERT: K 666 TYR cc_start: 0.8495 (m-80) cc_final: 0.8213 (m-80) REVERT: K 694 LYS cc_start: 0.7917 (tppp) cc_final: 0.7588 (tppt) REVERT: K 748 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7131 (mt) REVERT: K 759 GLN cc_start: 0.7939 (tp40) cc_final: 0.7557 (tp-100) REVERT: K 763 ASP cc_start: 0.8048 (m-30) cc_final: 0.7619 (m-30) REVERT: K 853 MET cc_start: 0.8771 (mmm) cc_final: 0.8525 (mmp) REVERT: L 297 TYR cc_start: 0.8513 (t80) cc_final: 0.8300 (t80) REVERT: L 426 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: L 821 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8455 (mtpt) REVERT: L 852 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8913 (mp) REVERT: M 246 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: M 426 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: M 564 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8408 (mp) REVERT: M 694 LYS cc_start: 0.7328 (OUTLIER) cc_final: 0.7107 (tptp) REVERT: M 748 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.7224 (mt) REVERT: M 757 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.7983 (p) REVERT: M 825 MET cc_start: 0.7730 (mmm) cc_final: 0.7358 (mmt) REVERT: M 853 MET cc_start: 0.8778 (mmm) cc_final: 0.8206 (mmm) REVERT: N 246 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7287 (mm-30) REVERT: N 379 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7732 (mp) REVERT: N 437 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: N 638 THR cc_start: 0.7686 (p) cc_final: 0.7410 (p) REVERT: N 748 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.6998 (mt) outliers start: 549 outliers final: 325 residues processed: 1103 average time/residue: 1.2009 time to fit residues: 1850.3799 Evaluate side-chains 995 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 612 time to evaluate : 6.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 561 ASP Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 623 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 747 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 876 ASP Chi-restraints excluded: chain B residue 229 SER Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 414 LEU Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 561 ASP Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 623 ASP Chi-restraints excluded: chain B residue 648 ASN Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 777 SER Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain B residue 876 ASP Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 330 SER Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 420 SER Chi-restraints excluded: chain C residue 438 THR Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 623 ASP Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain C residue 876 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 677 ASP Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 777 SER Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 802 GLN Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain D residue 866 ASP Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain D residue 876 ASP Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 328 THR Chi-restraints excluded: chain E residue 330 SER Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 420 SER Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 447 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain E residue 590 ASP Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 715 GLU Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 755 ILE Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 777 SER Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 866 ASP Chi-restraints excluded: chain E residue 874 SER Chi-restraints excluded: chain E residue 876 ASP Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 317 THR Chi-restraints excluded: chain F residue 328 THR Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 623 ASP Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 648 ASN Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 706 LYS Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 777 SER Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain F residue 876 ASP Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 420 SER Chi-restraints excluded: chain G residue 438 THR Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 499 GLU Chi-restraints excluded: chain G residue 524 GLU Chi-restraints excluded: chain G residue 590 ASP Chi-restraints excluded: chain G residue 623 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 777 SER Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 866 ASP Chi-restraints excluded: chain G residue 874 SER Chi-restraints excluded: chain G residue 876 ASP Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 377 THR Chi-restraints excluded: chain H residue 400 THR Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 437 ASP Chi-restraints excluded: chain H residue 465 ASP Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 524 GLU Chi-restraints excluded: chain H residue 533 LYS Chi-restraints excluded: chain H residue 568 ASP Chi-restraints excluded: chain H residue 605 LEU Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 643 LEU Chi-restraints excluded: chain H residue 644 GLN Chi-restraints excluded: chain H residue 699 VAL Chi-restraints excluded: chain H residue 748 LEU Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain H residue 753 VAL Chi-restraints excluded: chain H residue 757 THR Chi-restraints excluded: chain H residue 875 VAL Chi-restraints excluded: chain I residue 280 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 354 THR Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 379 LEU Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 405 LYS Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 414 LEU Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 437 ASP Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 563 LEU Chi-restraints excluded: chain I residue 568 ASP Chi-restraints excluded: chain I residue 573 GLU Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 643 LEU Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 654 THR Chi-restraints excluded: chain I residue 693 GLU Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 753 VAL Chi-restraints excluded: chain I residue 821 LYS Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 858 LEU Chi-restraints excluded: chain I residue 866 ASP Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain J residue 264 SER Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 317 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 368 GLN Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 437 ASP Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain J residue 476 ILE Chi-restraints excluded: chain J residue 497 VAL Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 568 ASP Chi-restraints excluded: chain J residue 573 GLU Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 635 VAL Chi-restraints excluded: chain J residue 643 LEU Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 699 VAL Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain J residue 866 ASP Chi-restraints excluded: chain J residue 875 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 259 SER Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 317 THR Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 368 GLN Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 377 THR Chi-restraints excluded: chain K residue 379 LEU Chi-restraints excluded: chain K residue 400 THR Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 433 LEU Chi-restraints excluded: chain K residue 437 ASP Chi-restraints excluded: chain K residue 465 ASP Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 568 ASP Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 643 LEU Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 748 LEU Chi-restraints excluded: chain K residue 749 ASP Chi-restraints excluded: chain K residue 753 VAL Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 824 GLU Chi-restraints excluded: chain K residue 866 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 875 VAL Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain L residue 334 SER Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 377 THR Chi-restraints excluded: chain L residue 379 LEU Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 422 ILE Chi-restraints excluded: chain L residue 426 GLU Chi-restraints excluded: chain L residue 437 ASP Chi-restraints excluded: chain L residue 465 ASP Chi-restraints excluded: chain L residue 497 VAL Chi-restraints excluded: chain L residue 525 SER Chi-restraints excluded: chain L residue 533 LYS Chi-restraints excluded: chain L residue 568 ASP Chi-restraints excluded: chain L residue 573 GLU Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 634 ASN Chi-restraints excluded: chain L residue 643 LEU Chi-restraints excluded: chain L residue 699 VAL Chi-restraints excluded: chain L residue 707 PHE Chi-restraints excluded: chain L residue 726 ILE Chi-restraints excluded: chain L residue 747 ILE Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 852 ILE Chi-restraints excluded: chain L residue 866 ASP Chi-restraints excluded: chain L residue 875 VAL Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 246 GLU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 414 LEU Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 426 GLU Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 542 THR Chi-restraints excluded: chain M residue 563 LEU Chi-restraints excluded: chain M residue 564 LEU Chi-restraints excluded: chain M residue 568 ASP Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 634 ASN Chi-restraints excluded: chain M residue 643 LEU Chi-restraints excluded: chain M residue 644 GLN Chi-restraints excluded: chain M residue 694 LYS Chi-restraints excluded: chain M residue 707 PHE Chi-restraints excluded: chain M residue 748 LEU Chi-restraints excluded: chain M residue 749 ASP Chi-restraints excluded: chain M residue 757 THR Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 875 VAL Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 246 GLU Chi-restraints excluded: chain N residue 251 GLU Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 THR Chi-restraints excluded: chain N residue 368 GLN Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 379 LEU Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ILE Chi-restraints excluded: chain N residue 437 ASP Chi-restraints excluded: chain N residue 497 VAL Chi-restraints excluded: chain N residue 516 SER Chi-restraints excluded: chain N residue 535 LEU Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 605 LEU Chi-restraints excluded: chain N residue 634 ASN Chi-restraints excluded: chain N residue 643 LEU Chi-restraints excluded: chain N residue 644 GLN Chi-restraints excluded: chain N residue 661 SER Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 748 LEU Chi-restraints excluded: chain N residue 749 ASP Chi-restraints excluded: chain N residue 757 THR Chi-restraints excluded: chain N residue 822 ASP Chi-restraints excluded: chain N residue 824 GLU Chi-restraints excluded: chain N residue 868 ARG Chi-restraints excluded: chain N residue 875 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 743 optimal weight: 2.9990 chunk 506 optimal weight: 0.0170 chunk 12 optimal weight: 10.0000 chunk 665 optimal weight: 2.9990 chunk 368 optimal weight: 1.9990 chunk 762 optimal weight: 0.9980 chunk 617 optimal weight: 0.0270 chunk 1 optimal weight: 0.7980 chunk 456 optimal weight: 7.9990 chunk 801 optimal weight: 10.0000 chunk 225 optimal weight: 0.0010 overall best weight: 0.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 773 ASN A 802 GLN B 636 ASN B 720 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN D 463 ASN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 773 ASN ** E 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 636 ASN F 735 ASN G 636 ASN H 780 ASN I 392 ASN ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 780 ASN J 392 ASN ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 780 ASN M 463 ASN M 567 ASN N 425 GLN N 827 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 74060 Z= 0.125 Angle : 0.529 12.975 100534 Z= 0.282 Chirality : 0.044 0.204 11312 Planarity : 0.004 0.039 13132 Dihedral : 6.131 59.048 10163 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.01 % Allowed : 23.55 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.09), residues: 9212 helix: 0.23 (0.15), residues: 1225 sheet: 0.26 (0.10), residues: 2702 loop : -1.87 (0.08), residues: 5285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 632 HIS 0.001 0.000 HIS H 314 PHE 0.007 0.001 PHE J 580 TYR 0.032 0.001 TYR C 357 ARG 0.005 0.000 ARG C 868 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1136 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 329 poor density : 807 time to evaluate : 6.640 Fit side-chains revert: symmetry clash REVERT: A 305 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7487 (mt-10) REVERT: A 545 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8604 (tp) REVERT: A 590 ASP cc_start: 0.7016 (OUTLIER) cc_final: 0.6643 (t70) REVERT: A 762 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.7452 (mpp) REVERT: A 854 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8295 (p) REVERT: A 870 LEU cc_start: 0.8620 (mt) cc_final: 0.8356 (mp) REVERT: B 660 MET cc_start: 0.8182 (tpt) cc_final: 0.7837 (tpt) REVERT: B 689 LYS cc_start: 0.7809 (ttpp) cc_final: 0.7208 (pptt) REVERT: B 747 ILE cc_start: 0.4971 (OUTLIER) cc_final: 0.4726 (pp) REVERT: C 589 LYS cc_start: 0.8506 (ttpt) cc_final: 0.8296 (mtmm) REVERT: C 689 LYS cc_start: 0.7765 (ttpp) cc_final: 0.7555 (ttpt) REVERT: C 762 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7635 (mpp) REVERT: C 868 ARG cc_start: 0.7916 (ttp-110) cc_final: 0.7614 (mtm110) REVERT: D 524 GLU cc_start: 0.7438 (tp30) cc_final: 0.6684 (tt0) REVERT: D 689 LYS cc_start: 0.8002 (ttpp) cc_final: 0.7611 (pptt) REVERT: D 717 ASP cc_start: 0.7644 (t70) cc_final: 0.7229 (t0) REVERT: D 747 ILE cc_start: 0.4959 (OUTLIER) cc_final: 0.4489 (pp) REVERT: D 868 ARG cc_start: 0.7861 (ttp-110) cc_final: 0.7629 (mtm110) REVERT: E 452 MET cc_start: 0.9012 (ptm) cc_final: 0.8730 (ptm) REVERT: E 614 LYS cc_start: 0.8355 (OUTLIER) cc_final: 0.7935 (tmtt) REVERT: E 717 ASP cc_start: 0.7271 (t70) cc_final: 0.6820 (t0) REVERT: E 741 LEU cc_start: 0.7353 (mt) cc_final: 0.7018 (mt) REVERT: E 747 ILE cc_start: 0.5319 (OUTLIER) cc_final: 0.4844 (pp) REVERT: F 660 MET cc_start: 0.8095 (tpt) cc_final: 0.7537 (tpt) REVERT: F 677 ASP cc_start: 0.5504 (OUTLIER) cc_final: 0.5153 (m-30) REVERT: F 689 LYS cc_start: 0.7821 (ttpp) cc_final: 0.7473 (pptt) REVERT: F 717 ASP cc_start: 0.7342 (t70) cc_final: 0.6643 (t0) REVERT: F 747 ILE cc_start: 0.5049 (OUTLIER) cc_final: 0.4561 (pp) REVERT: F 762 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7427 (mpp) REVERT: G 305 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7988 (mt-10) REVERT: G 868 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7670 (mtm110) REVERT: H 426 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7619 (tt0) REVERT: H 429 ILE cc_start: 0.9059 (mt) cc_final: 0.8857 (mm) REVERT: H 463 ASN cc_start: 0.7508 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: H 568 ASP cc_start: 0.7145 (p0) cc_final: 0.6838 (p0) REVERT: H 759 GLN cc_start: 0.7986 (tp-100) cc_final: 0.7265 (mm110) REVERT: H 763 ASP cc_start: 0.8073 (m-30) cc_final: 0.7618 (m-30) REVERT: H 853 MET cc_start: 0.8707 (mmm) cc_final: 0.8403 (mmm) REVERT: I 666 TYR cc_start: 0.8306 (m-80) cc_final: 0.7987 (m-80) REVERT: I 762 MET cc_start: 0.7703 (OUTLIER) cc_final: 0.7033 (mpp) REVERT: J 417 ASP cc_start: 0.7036 (p0) cc_final: 0.6580 (p0) REVERT: J 463 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.7220 (m-40) REVERT: J 568 ASP cc_start: 0.7040 (p0) cc_final: 0.6767 (p0) REVERT: J 666 TYR cc_start: 0.8421 (m-80) cc_final: 0.8076 (m-80) REVERT: J 687 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7297 (tttt) REVERT: J 759 GLN cc_start: 0.8023 (tp40) cc_final: 0.7613 (tp-100) REVERT: J 763 ASP cc_start: 0.8075 (m-30) cc_final: 0.7637 (m-30) REVERT: K 452 MET cc_start: 0.8130 (mtm) cc_final: 0.7700 (mtm) REVERT: K 573 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7509 (pt0) REVERT: K 666 TYR cc_start: 0.8384 (m-80) cc_final: 0.8140 (m-80) REVERT: K 694 LYS cc_start: 0.7987 (tppp) cc_final: 0.7200 (tptm) REVERT: K 759 GLN cc_start: 0.7985 (tp40) cc_final: 0.7571 (tp-100) REVERT: K 763 ASP cc_start: 0.8051 (m-30) cc_final: 0.7624 (m-30) REVERT: K 853 MET cc_start: 0.8726 (mmm) cc_final: 0.8490 (mmp) REVERT: L 568 ASP cc_start: 0.6889 (p0) cc_final: 0.6555 (p0) REVERT: L 821 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8331 (mtpt) REVERT: M 825 MET cc_start: 0.7447 (mmm) cc_final: 0.7076 (mmt) REVERT: M 853 MET cc_start: 0.8765 (mmm) cc_final: 0.8254 (mmm) REVERT: N 732 TYR cc_start: 0.6167 (m-80) cc_final: 0.5950 (m-80) outliers start: 329 outliers final: 161 residues processed: 1073 average time/residue: 1.1796 time to fit residues: 1777.8344 Evaluate side-chains 856 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 674 time to evaluate : 6.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 288 GLU Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 777 SER Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 755 ILE Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 704 TYR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 590 ASP Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 463 ASN Chi-restraints excluded: chain H residue 497 VAL Chi-restraints excluded: chain H residue 605 LEU Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 699 VAL Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain H residue 866 ASP Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 354 THR Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 762 MET Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 858 LEU Chi-restraints excluded: chain I residue 876 ASP Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 463 ASN Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain J residue 866 ASP Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 573 GLU Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 866 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 876 ASP Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 317 THR Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 422 ILE Chi-restraints excluded: chain L residue 563 LEU Chi-restraints excluded: chain L residue 573 GLU Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 699 VAL Chi-restraints excluded: chain L residue 726 ILE Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 858 LEU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 644 GLN Chi-restraints excluded: chain M residue 699 VAL Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain N residue 280 SER Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 405 LYS Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ILE Chi-restraints excluded: chain N residue 463 ASN Chi-restraints excluded: chain N residue 497 VAL Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 661 SER Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 876 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 300 optimal weight: 1.9990 chunk 804 optimal weight: 10.0000 chunk 176 optimal weight: 5.9990 chunk 524 optimal weight: 8.9990 chunk 220 optimal weight: 0.7980 chunk 894 optimal weight: 5.9990 chunk 742 optimal weight: 0.0050 chunk 413 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 469 optimal weight: 0.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 773 ASN ** B 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 773 ASN D 371 ASN ** D 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 773 ASN E 463 ASN E 636 ASN ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 411 ASN G 509 GLN ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 463 ASN N 425 GLN N 523 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 74060 Z= 0.198 Angle : 0.568 14.430 100534 Z= 0.303 Chirality : 0.045 0.194 11312 Planarity : 0.004 0.041 13132 Dihedral : 5.902 55.647 10087 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer: Outliers : 4.29 % Allowed : 24.20 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.09), residues: 9212 helix: 0.28 (0.15), residues: 1218 sheet: 0.40 (0.10), residues: 2681 loop : -1.81 (0.08), residues: 5313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 503 HIS 0.005 0.001 HIS H 314 PHE 0.012 0.001 PHE C 707 TYR 0.030 0.001 TYR C 357 ARG 0.005 0.000 ARG A 868 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 352 poor density : 689 time to evaluate : 7.588 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8271 (tp) REVERT: A 656 ILE cc_start: 0.7861 (OUTLIER) cc_final: 0.7655 (tp) REVERT: A 762 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.7457 (mpp) REVERT: A 870 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8402 (mt) REVERT: B 499 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7748 (mm-30) REVERT: B 581 ASP cc_start: 0.8115 (p0) cc_final: 0.7910 (p0) REVERT: B 660 MET cc_start: 0.8171 (tpt) cc_final: 0.7945 (tpt) REVERT: B 689 LYS cc_start: 0.7864 (ttpp) cc_final: 0.7236 (pptt) REVERT: B 747 ILE cc_start: 0.5150 (OUTLIER) cc_final: 0.4922 (pp) REVERT: B 853 MET cc_start: 0.8302 (mmm) cc_final: 0.7658 (mmt) REVERT: C 325 ARG cc_start: 0.8260 (tpt-90) cc_final: 0.7889 (tmt90) REVERT: C 499 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: C 677 ASP cc_start: 0.4979 (OUTLIER) cc_final: 0.4686 (m-30) REVERT: C 762 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7601 (mpp) REVERT: D 589 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8199 (mtmm) REVERT: D 717 ASP cc_start: 0.7303 (t70) cc_final: 0.6941 (t0) REVERT: D 747 ILE cc_start: 0.5045 (OUTLIER) cc_final: 0.4638 (pp) REVERT: D 868 ARG cc_start: 0.7928 (ttp-110) cc_final: 0.7649 (mtm110) REVERT: E 451 THR cc_start: 0.8724 (p) cc_final: 0.8461 (p) REVERT: E 452 MET cc_start: 0.9013 (ptm) cc_final: 0.8705 (ptm) REVERT: E 536 GLN cc_start: 0.7990 (mm110) cc_final: 0.7738 (mm110) REVERT: E 589 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8186 (mtmm) REVERT: E 660 MET cc_start: 0.8183 (tpt) cc_final: 0.7947 (tpt) REVERT: E 717 ASP cc_start: 0.7156 (t70) cc_final: 0.6718 (t0) REVERT: E 741 LEU cc_start: 0.7502 (mt) cc_final: 0.7136 (mt) REVERT: E 747 ILE cc_start: 0.5287 (OUTLIER) cc_final: 0.4774 (pp) REVERT: E 762 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7703 (mpp) REVERT: F 627 ASN cc_start: 0.7933 (t0) cc_final: 0.7561 (t0) REVERT: F 660 MET cc_start: 0.8136 (tpt) cc_final: 0.7617 (tpt) REVERT: F 677 ASP cc_start: 0.5804 (OUTLIER) cc_final: 0.5583 (m-30) REVERT: F 689 LYS cc_start: 0.7912 (ttpp) cc_final: 0.7450 (pptt) REVERT: F 717 ASP cc_start: 0.7402 (t70) cc_final: 0.6612 (t0) REVERT: F 747 ILE cc_start: 0.5129 (OUTLIER) cc_final: 0.4650 (pp) REVERT: F 762 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7389 (mpp) REVERT: G 305 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8106 (mt-10) REVERT: G 868 ARG cc_start: 0.7942 (ttp-110) cc_final: 0.7646 (mtm110) REVERT: H 426 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: H 429 ILE cc_start: 0.9126 (mt) cc_final: 0.8909 (mm) REVERT: H 463 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7298 (m-40) REVERT: H 759 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7288 (mm110) REVERT: H 763 ASP cc_start: 0.8049 (m-30) cc_final: 0.7603 (m-30) REVERT: H 837 THR cc_start: 0.8948 (p) cc_final: 0.8626 (t) REVERT: H 853 MET cc_start: 0.8729 (mmm) cc_final: 0.8332 (mmm) REVERT: I 309 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8806 (mt) REVERT: I 524 GLU cc_start: 0.7255 (tp30) cc_final: 0.7039 (tp30) REVERT: I 666 TYR cc_start: 0.8362 (m-80) cc_final: 0.8022 (m-80) REVERT: I 748 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7242 (mt) REVERT: I 762 MET cc_start: 0.7775 (OUTLIER) cc_final: 0.7064 (mpp) REVERT: J 417 ASP cc_start: 0.7128 (p0) cc_final: 0.6569 (p0) REVERT: J 463 ASN cc_start: 0.7561 (OUTLIER) cc_final: 0.7339 (m-40) REVERT: J 568 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6983 (p0) REVERT: J 666 TYR cc_start: 0.8457 (m-80) cc_final: 0.8088 (m-80) REVERT: J 687 LYS cc_start: 0.7586 (OUTLIER) cc_final: 0.7339 (tttt) REVERT: J 759 GLN cc_start: 0.8045 (tp40) cc_final: 0.7669 (tp-100) REVERT: J 763 ASP cc_start: 0.8098 (m-30) cc_final: 0.7685 (m-30) REVERT: K 309 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8871 (mt) REVERT: K 452 MET cc_start: 0.8151 (mtm) cc_final: 0.7730 (mtm) REVERT: K 660 MET cc_start: 0.8518 (tpt) cc_final: 0.8266 (tpt) REVERT: K 666 TYR cc_start: 0.8426 (m-80) cc_final: 0.8159 (m-80) REVERT: K 694 LYS cc_start: 0.7973 (tppp) cc_final: 0.7187 (tptm) REVERT: K 759 GLN cc_start: 0.7995 (tp40) cc_final: 0.7598 (tp-100) REVERT: K 763 ASP cc_start: 0.8071 (m-30) cc_final: 0.7628 (m-30) REVERT: K 853 MET cc_start: 0.8669 (mmm) cc_final: 0.8433 (mmp) REVERT: L 693 GLU cc_start: 0.5732 (mp0) cc_final: 0.5488 (pm20) REVERT: L 716 LYS cc_start: 0.6537 (OUTLIER) cc_final: 0.5841 (tptp) REVERT: L 821 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8384 (mtpt) REVERT: L 852 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8920 (mp) REVERT: M 716 LYS cc_start: 0.6639 (OUTLIER) cc_final: 0.5927 (tptp) REVERT: M 753 VAL cc_start: 0.7233 (OUTLIER) cc_final: 0.7030 (p) REVERT: M 757 THR cc_start: 0.8112 (OUTLIER) cc_final: 0.7839 (p) REVERT: M 825 MET cc_start: 0.7698 (mmm) cc_final: 0.7345 (mmt) REVERT: M 853 MET cc_start: 0.8754 (mmm) cc_final: 0.8208 (mmm) outliers start: 352 outliers final: 224 residues processed: 975 average time/residue: 1.2356 time to fit residues: 1694.0839 Evaluate side-chains 900 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 643 time to evaluate : 6.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 866 ASP Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 317 THR Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 499 GLU Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 590 ASP Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 590 ASP Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain D residue 866 ASP Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 755 ILE Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 874 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 590 ASP Chi-restraints excluded: chain F residue 596 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 866 ASP Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 590 ASP Chi-restraints excluded: chain G residue 596 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 866 ASP Chi-restraints excluded: chain G residue 874 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 463 ASN Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 605 LEU Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 651 ASN Chi-restraints excluded: chain H residue 699 VAL Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain H residue 866 ASP Chi-restraints excluded: chain I residue 280 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 354 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 437 ASP Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 713 THR Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 748 LEU Chi-restraints excluded: chain I residue 762 MET Chi-restraints excluded: chain I residue 821 LYS Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 858 LEU Chi-restraints excluded: chain I residue 876 ASP Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 377 THR Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 463 ASN Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 568 ASP Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 726 ILE Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain J residue 866 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 309 ILE Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 373 GLU Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 377 THR Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 433 LEU Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 568 ASP Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 866 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain L residue 368 GLN Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 422 ILE Chi-restraints excluded: chain L residue 525 SER Chi-restraints excluded: chain L residue 563 LEU Chi-restraints excluded: chain L residue 573 GLU Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 634 ASN Chi-restraints excluded: chain L residue 644 GLN Chi-restraints excluded: chain L residue 651 ASN Chi-restraints excluded: chain L residue 699 VAL Chi-restraints excluded: chain L residue 716 LYS Chi-restraints excluded: chain L residue 726 ILE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 852 ILE Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 542 THR Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 634 ASN Chi-restraints excluded: chain M residue 644 GLN Chi-restraints excluded: chain M residue 651 ASN Chi-restraints excluded: chain M residue 699 VAL Chi-restraints excluded: chain M residue 713 THR Chi-restraints excluded: chain M residue 716 LYS Chi-restraints excluded: chain M residue 753 VAL Chi-restraints excluded: chain M residue 757 THR Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 368 GLN Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 405 LYS Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ILE Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 569 ILE Chi-restraints excluded: chain N residue 644 GLN Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 661 SER Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 866 ASP Chi-restraints excluded: chain N residue 868 ARG Chi-restraints excluded: chain N residue 876 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 861 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 509 optimal weight: 5.9990 chunk 652 optimal weight: 5.9990 chunk 505 optimal weight: 0.0470 chunk 752 optimal weight: 5.9990 chunk 499 optimal weight: 0.1980 chunk 890 optimal weight: 0.0470 chunk 557 optimal weight: 0.7980 chunk 542 optimal weight: 9.9990 chunk 411 optimal weight: 3.9990 overall best weight: 0.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 773 ASN B 363 ASN ** B 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN C 773 ASN D 371 ASN D 636 ASN D 648 ASN D 773 ASN E 648 ASN ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 463 ASN M 639 ASN ** M 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 GLN N 523 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 74060 Z= 0.147 Angle : 0.544 14.042 100534 Z= 0.289 Chirality : 0.044 0.224 11312 Planarity : 0.004 0.038 13132 Dihedral : 5.629 58.194 10083 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 4.06 % Allowed : 24.65 % Favored : 71.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.09), residues: 9212 helix: 0.42 (0.16), residues: 1218 sheet: 0.49 (0.10), residues: 2688 loop : -1.72 (0.08), residues: 5306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP J 503 HIS 0.003 0.001 HIS N 314 PHE 0.011 0.001 PHE G 707 TYR 0.028 0.001 TYR F 357 ARG 0.005 0.000 ARG C 868 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1015 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 682 time to evaluate : 6.638 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8234 (tp) REVERT: A 590 ASP cc_start: 0.6914 (OUTLIER) cc_final: 0.6580 (t70) REVERT: A 656 ILE cc_start: 0.7832 (OUTLIER) cc_final: 0.7618 (tp) REVERT: A 762 MET cc_start: 0.8386 (OUTLIER) cc_final: 0.7493 (mpp) REVERT: A 870 LEU cc_start: 0.8646 (mt) cc_final: 0.8374 (mp) REVERT: B 660 MET cc_start: 0.8154 (tpt) cc_final: 0.7903 (tpt) REVERT: B 689 LYS cc_start: 0.7832 (ttpp) cc_final: 0.7222 (pptt) REVERT: B 704 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.6899 (m-80) REVERT: B 747 ILE cc_start: 0.5197 (OUTLIER) cc_final: 0.4950 (pp) REVERT: C 325 ARG cc_start: 0.8248 (tpt-90) cc_final: 0.8019 (tmt90) REVERT: C 589 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8295 (mtmm) REVERT: C 668 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7565 (ttp-170) REVERT: C 677 ASP cc_start: 0.4948 (OUTLIER) cc_final: 0.4666 (m-30) REVERT: C 762 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.7606 (mpp) REVERT: C 868 ARG cc_start: 0.7876 (ttp-110) cc_final: 0.7533 (mtm110) REVERT: D 589 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8152 (mtmm) REVERT: D 747 ILE cc_start: 0.5098 (OUTLIER) cc_final: 0.4661 (pp) REVERT: D 868 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7641 (mtm110) REVERT: E 451 THR cc_start: 0.8651 (p) cc_final: 0.8394 (p) REVERT: E 536 GLN cc_start: 0.7997 (mm110) cc_final: 0.7744 (mm110) REVERT: E 589 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8181 (mtmm) REVERT: E 614 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7957 (tmtt) REVERT: E 655 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7782 (ttpp) REVERT: E 660 MET cc_start: 0.8173 (tpt) cc_final: 0.7931 (tpt) REVERT: E 717 ASP cc_start: 0.7058 (t70) cc_final: 0.6762 (t0) REVERT: E 741 LEU cc_start: 0.7386 (mt) cc_final: 0.7025 (mt) REVERT: E 747 ILE cc_start: 0.5287 (OUTLIER) cc_final: 0.4772 (pp) REVERT: E 762 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.7734 (mpp) REVERT: F 660 MET cc_start: 0.8024 (tpt) cc_final: 0.7484 (tpt) REVERT: F 677 ASP cc_start: 0.5800 (OUTLIER) cc_final: 0.5463 (m-30) REVERT: F 689 LYS cc_start: 0.7845 (ttpp) cc_final: 0.7361 (pptt) REVERT: F 747 ILE cc_start: 0.5127 (OUTLIER) cc_final: 0.4654 (pp) REVERT: F 762 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7384 (mpp) REVERT: G 305 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: G 696 ASP cc_start: 0.6770 (t0) cc_final: 0.6537 (t0) REVERT: G 754 LYS cc_start: 0.7582 (mmmm) cc_final: 0.7012 (mmtt) REVERT: G 868 ARG cc_start: 0.7967 (ttp-110) cc_final: 0.7672 (mtm110) REVERT: H 426 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7671 (tt0) REVERT: H 429 ILE cc_start: 0.9105 (mt) cc_final: 0.8896 (mm) REVERT: H 463 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7238 (m-40) REVERT: H 759 GLN cc_start: 0.7933 (tp-100) cc_final: 0.7262 (mm110) REVERT: H 763 ASP cc_start: 0.8075 (m-30) cc_final: 0.7605 (m-30) REVERT: H 837 THR cc_start: 0.8846 (p) cc_final: 0.8532 (t) REVERT: H 853 MET cc_start: 0.8733 (mmm) cc_final: 0.8323 (mmm) REVERT: I 309 ILE cc_start: 0.8954 (OUTLIER) cc_final: 0.8735 (mt) REVERT: I 666 TYR cc_start: 0.8305 (m-80) cc_final: 0.7957 (m-80) REVERT: I 716 LYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5763 (tptp) REVERT: I 762 MET cc_start: 0.7765 (OUTLIER) cc_final: 0.7083 (mpp) REVERT: J 463 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7256 (m-40) REVERT: J 666 TYR cc_start: 0.8413 (m-80) cc_final: 0.8052 (m-80) REVERT: J 687 LYS cc_start: 0.7542 (OUTLIER) cc_final: 0.7290 (tttt) REVERT: J 757 THR cc_start: 0.8107 (OUTLIER) cc_final: 0.7899 (p) REVERT: J 759 GLN cc_start: 0.8078 (tp40) cc_final: 0.7782 (tp-100) REVERT: J 763 ASP cc_start: 0.8073 (m-30) cc_final: 0.7634 (m-30) REVERT: K 666 TYR cc_start: 0.8373 (m-80) cc_final: 0.8117 (m-80) REVERT: K 694 LYS cc_start: 0.7973 (tppp) cc_final: 0.7185 (tptm) REVERT: K 759 GLN cc_start: 0.8016 (tp40) cc_final: 0.7622 (tp-100) REVERT: K 763 ASP cc_start: 0.8058 (m-30) cc_final: 0.7617 (m-30) REVERT: K 853 MET cc_start: 0.8656 (mmm) cc_final: 0.8434 (mmp) REVERT: L 568 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6657 (p0) REVERT: L 821 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8353 (mtpt) REVERT: L 852 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8900 (mp) REVERT: M 694 LYS cc_start: 0.7511 (OUTLIER) cc_final: 0.7304 (tptp) REVERT: M 825 MET cc_start: 0.7482 (mmm) cc_final: 0.7123 (mmt) REVERT: M 853 MET cc_start: 0.8745 (mmm) cc_final: 0.8176 (mmm) REVERT: N 437 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7734 (m-30) REVERT: N 563 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6644 (mt) outliers start: 333 outliers final: 203 residues processed: 953 average time/residue: 1.2015 time to fit residues: 1603.9255 Evaluate side-chains 875 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 638 time to evaluate : 6.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 704 TYR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 589 LYS Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 677 ASP Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 417 ASP Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 755 ILE Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 802 GLN Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 497 VAL Chi-restraints excluded: chain F residue 596 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 704 TYR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 317 THR Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 463 ASN Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 651 ASN Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 699 VAL Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain H residue 822 ASP Chi-restraints excluded: chain H residue 866 ASP Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 354 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 405 LYS Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 713 THR Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 762 MET Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 858 LEU Chi-restraints excluded: chain I residue 876 ASP Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 322 THR Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 463 ASN Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain J residue 476 ILE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 377 THR Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 433 LEU Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 866 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 876 ASP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain L residue 373 GLU Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 422 ILE Chi-restraints excluded: chain L residue 525 SER Chi-restraints excluded: chain L residue 568 ASP Chi-restraints excluded: chain L residue 573 GLU Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 634 ASN Chi-restraints excluded: chain L residue 644 GLN Chi-restraints excluded: chain L residue 651 ASN Chi-restraints excluded: chain L residue 699 VAL Chi-restraints excluded: chain L residue 726 ILE Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 822 ASP Chi-restraints excluded: chain L residue 852 ILE Chi-restraints excluded: chain L residue 868 ARG Chi-restraints excluded: chain L residue 876 ASP Chi-restraints excluded: chain M residue 219 LEU Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 563 LEU Chi-restraints excluded: chain M residue 568 ASP Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 634 ASN Chi-restraints excluded: chain M residue 644 GLN Chi-restraints excluded: chain M residue 651 ASN Chi-restraints excluded: chain M residue 693 GLU Chi-restraints excluded: chain M residue 694 LYS Chi-restraints excluded: chain M residue 699 VAL Chi-restraints excluded: chain M residue 713 THR Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain N residue 219 LEU Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 405 LYS Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ILE Chi-restraints excluded: chain N residue 437 ASP Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 563 LEU Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 569 ILE Chi-restraints excluded: chain N residue 644 GLN Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 713 THR Chi-restraints excluded: chain N residue 822 ASP Chi-restraints excluded: chain N residue 866 ASP Chi-restraints excluded: chain N residue 876 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 550 optimal weight: 7.9990 chunk 355 optimal weight: 0.6980 chunk 531 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 172 optimal weight: 5.9990 chunk 566 optimal weight: 2.9990 chunk 606 optimal weight: 7.9990 chunk 440 optimal weight: 2.9990 chunk 82 optimal weight: 9.9990 chunk 700 optimal weight: 10.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN A 780 ASN B 720 ASN ** C 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN C 773 ASN D 319 GLN D 371 ASN D 773 ASN D 780 ASN F 780 ASN G 411 ASN G 780 ASN ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 GLN N 463 ASN N 523 ASN ** N 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 74060 Z= 0.318 Angle : 0.637 15.613 100534 Z= 0.339 Chirality : 0.048 0.239 11312 Planarity : 0.004 0.043 13132 Dihedral : 6.231 59.852 10073 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.58 % Favored : 91.35 % Rotamer: Outliers : 4.68 % Allowed : 24.28 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.09), residues: 9212 helix: 0.13 (0.15), residues: 1211 sheet: 0.37 (0.10), residues: 2723 loop : -1.80 (0.08), residues: 5278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 503 HIS 0.007 0.001 HIS K 314 PHE 0.021 0.002 PHE F 707 TYR 0.029 0.002 TYR D 357 ARG 0.005 0.000 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 642 time to evaluate : 6.641 Fit side-chains revert: symmetry clash REVERT: A 305 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: A 414 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8329 (tp) REVERT: A 590 ASP cc_start: 0.7097 (OUTLIER) cc_final: 0.6595 (t70) REVERT: A 656 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7708 (tp) REVERT: A 762 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7468 (mpp) REVERT: A 870 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 499 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: B 660 MET cc_start: 0.8203 (tpt) cc_final: 0.7953 (tpt) REVERT: B 689 LYS cc_start: 0.7920 (ttpp) cc_final: 0.7389 (pptt) REVERT: B 747 ILE cc_start: 0.5059 (OUTLIER) cc_final: 0.4803 (pp) REVERT: B 853 MET cc_start: 0.8426 (mmm) cc_final: 0.7773 (mmt) REVERT: C 325 ARG cc_start: 0.8306 (tpt-90) cc_final: 0.8080 (tmt90) REVERT: C 668 ARG cc_start: 0.7844 (ttp80) cc_final: 0.7484 (ttp-170) REVERT: C 722 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6847 (mt-10) REVERT: C 762 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7581 (mpp) REVERT: D 589 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8274 (mtmm) REVERT: D 747 ILE cc_start: 0.5047 (OUTLIER) cc_final: 0.4638 (pp) REVERT: D 868 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7667 (mtm110) REVERT: E 499 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7585 (tp30) REVERT: E 614 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8046 (tmtt) REVERT: E 655 LYS cc_start: 0.8059 (OUTLIER) cc_final: 0.7809 (ttpp) REVERT: E 660 MET cc_start: 0.8275 (tpt) cc_final: 0.8026 (tpt) REVERT: E 692 GLU cc_start: 0.7259 (mt-10) cc_final: 0.6745 (tm-30) REVERT: E 717 ASP cc_start: 0.7073 (t70) cc_final: 0.6652 (t0) REVERT: E 741 LEU cc_start: 0.7639 (mt) cc_final: 0.7364 (mt) REVERT: E 747 ILE cc_start: 0.5310 (OUTLIER) cc_final: 0.4793 (pp) REVERT: F 660 MET cc_start: 0.8225 (tpt) cc_final: 0.7691 (tpt) REVERT: F 689 LYS cc_start: 0.7850 (ttpp) cc_final: 0.7579 (tmtt) REVERT: F 717 ASP cc_start: 0.7434 (t70) cc_final: 0.6648 (t0) REVERT: F 747 ILE cc_start: 0.5086 (OUTLIER) cc_final: 0.4602 (pp) REVERT: F 762 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7385 (mpp) REVERT: F 796 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7236 (pp20) REVERT: G 305 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: G 325 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7921 (tpt-90) REVERT: G 524 GLU cc_start: 0.7702 (tp30) cc_final: 0.6740 (tt0) REVERT: G 704 TYR cc_start: 0.8184 (OUTLIER) cc_final: 0.6991 (m-80) REVERT: G 868 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7611 (mtm110) REVERT: H 382 ASN cc_start: 0.8029 (m-40) cc_final: 0.7825 (m-40) REVERT: H 426 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7662 (tt0) REVERT: H 429 ILE cc_start: 0.9170 (mt) cc_final: 0.8951 (mm) REVERT: H 748 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7123 (mt) REVERT: H 759 GLN cc_start: 0.7984 (tp-100) cc_final: 0.7293 (mm110) REVERT: H 763 ASP cc_start: 0.8074 (m-30) cc_final: 0.7602 (m-30) REVERT: H 837 THR cc_start: 0.8984 (p) cc_final: 0.8693 (t) REVERT: H 853 MET cc_start: 0.8763 (mmm) cc_final: 0.8360 (mmm) REVERT: I 309 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8888 (mt) REVERT: I 425 GLN cc_start: 0.7870 (mm110) cc_final: 0.7288 (pt0) REVERT: I 535 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7561 (mm) REVERT: I 666 TYR cc_start: 0.8447 (m-80) cc_final: 0.8123 (m-80) REVERT: I 716 LYS cc_start: 0.6812 (OUTLIER) cc_final: 0.6032 (tptp) REVERT: J 666 TYR cc_start: 0.8527 (m-80) cc_final: 0.8149 (m-80) REVERT: J 687 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7382 (tttt) REVERT: J 757 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7959 (p) REVERT: J 759 GLN cc_start: 0.8022 (tp40) cc_final: 0.7685 (tp-100) REVERT: J 763 ASP cc_start: 0.8068 (m-30) cc_final: 0.7668 (m-30) REVERT: K 437 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: K 666 TYR cc_start: 0.8476 (m-80) cc_final: 0.8212 (m-80) REVERT: K 694 LYS cc_start: 0.7904 (tppp) cc_final: 0.7602 (tppt) REVERT: K 759 GLN cc_start: 0.7981 (tp40) cc_final: 0.7596 (tp-100) REVERT: K 763 ASP cc_start: 0.8025 (m-30) cc_final: 0.7577 (m-30) REVERT: K 853 MET cc_start: 0.8686 (mmm) cc_final: 0.8442 (mmp) REVERT: L 821 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8456 (mtpt) REVERT: L 852 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (mp) REVERT: M 716 LYS cc_start: 0.6717 (OUTLIER) cc_final: 0.6046 (tptp) REVERT: M 748 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7205 (mt) REVERT: M 757 THR cc_start: 0.8096 (OUTLIER) cc_final: 0.7868 (p) REVERT: M 853 MET cc_start: 0.8794 (mmm) cc_final: 0.8245 (mmm) REVERT: N 563 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6763 (mt) REVERT: N 748 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7076 (mt) REVERT: N 837 THR cc_start: 0.9014 (p) cc_final: 0.8777 (t) outliers start: 384 outliers final: 255 residues processed: 964 average time/residue: 1.2120 time to fit residues: 1630.7515 Evaluate side-chains 916 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 292 poor density : 624 time to evaluate : 6.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 305 GLU Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 452 MET Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 330 SER Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 452 MET Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 499 GLU Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 414 LEU Chi-restraints excluded: chain C residue 452 MET Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 777 SER Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 589 LYS Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 778 THR Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 837 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 499 GLU Chi-restraints excluded: chain E residue 589 LYS Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 655 LYS Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 793 THR Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 874 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 330 SER Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 438 THR Chi-restraints excluded: chain F residue 447 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 591 SER Chi-restraints excluded: chain F residue 596 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 695 THR Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 704 TYR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 796 GLU Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 596 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 695 THR Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 778 THR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 874 SER Chi-restraints excluded: chain H residue 236 THR Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 422 ILE Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 465 ASP Chi-restraints excluded: chain H residue 569 ILE Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 651 ASN Chi-restraints excluded: chain H residue 661 SER Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 699 VAL Chi-restraints excluded: chain H residue 739 THR Chi-restraints excluded: chain H residue 748 LEU Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain H residue 866 ASP Chi-restraints excluded: chain H residue 875 VAL Chi-restraints excluded: chain I residue 280 SER Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 354 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 405 LYS Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 437 ASP Chi-restraints excluded: chain I residue 497 VAL Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 661 SER Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 713 THR Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 747 ILE Chi-restraints excluded: chain I residue 821 LYS Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 858 LEU Chi-restraints excluded: chain I residue 875 VAL Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 465 ASP Chi-restraints excluded: chain J residue 476 ILE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 563 LEU Chi-restraints excluded: chain J residue 568 ASP Chi-restraints excluded: chain J residue 605 LEU Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 640 GLN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 693 GLU Chi-restraints excluded: chain J residue 713 THR Chi-restraints excluded: chain J residue 757 THR Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain J residue 875 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 236 THR Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 341 VAL Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 433 LEU Chi-restraints excluded: chain K residue 437 ASP Chi-restraints excluded: chain K residue 465 ASP Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 568 ASP Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 876 ASP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 410 THR Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 437 ASP Chi-restraints excluded: chain L residue 465 ASP Chi-restraints excluded: chain L residue 525 SER Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 644 GLN Chi-restraints excluded: chain L residue 651 ASN Chi-restraints excluded: chain L residue 699 VAL Chi-restraints excluded: chain L residue 726 ILE Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 747 ILE Chi-restraints excluded: chain L residue 749 ASP Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 822 ASP Chi-restraints excluded: chain L residue 852 ILE Chi-restraints excluded: chain L residue 875 VAL Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 400 THR Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 422 ILE Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 497 VAL Chi-restraints excluded: chain M residue 542 THR Chi-restraints excluded: chain M residue 605 LEU Chi-restraints excluded: chain M residue 634 ASN Chi-restraints excluded: chain M residue 644 GLN Chi-restraints excluded: chain M residue 661 SER Chi-restraints excluded: chain M residue 693 GLU Chi-restraints excluded: chain M residue 699 VAL Chi-restraints excluded: chain M residue 707 PHE Chi-restraints excluded: chain M residue 716 LYS Chi-restraints excluded: chain M residue 741 LEU Chi-restraints excluded: chain M residue 748 LEU Chi-restraints excluded: chain M residue 757 THR Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain N residue 259 SER Chi-restraints excluded: chain N residue 280 SER Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 368 GLN Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 405 LYS Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ILE Chi-restraints excluded: chain N residue 437 ASP Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 563 LEU Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 661 SER Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 747 ILE Chi-restraints excluded: chain N residue 748 LEU Chi-restraints excluded: chain N residue 749 ASP Chi-restraints excluded: chain N residue 757 THR Chi-restraints excluded: chain N residue 809 THR Chi-restraints excluded: chain N residue 822 ASP Chi-restraints excluded: chain N residue 876 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 810 optimal weight: 0.8980 chunk 853 optimal weight: 0.0270 chunk 778 optimal weight: 2.9990 chunk 829 optimal weight: 0.0980 chunk 852 optimal weight: 1.9990 chunk 499 optimal weight: 10.0000 chunk 361 optimal weight: 3.9990 chunk 651 optimal weight: 0.6980 chunk 254 optimal weight: 0.9990 chunk 749 optimal weight: 8.9990 chunk 784 optimal weight: 6.9990 overall best weight: 0.5440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 720 ASN A 773 ASN B 463 ASN ** B 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 720 ASN C 636 ASN ** C 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 720 ASN C 773 ASN D 335 ASN D 371 ASN D 773 ASN ** F 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 773 ASN ** H 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 759 GLN N 363 ASN N 425 GLN N 432 ASN N 523 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 74060 Z= 0.138 Angle : 0.548 14.031 100534 Z= 0.290 Chirality : 0.044 0.230 11312 Planarity : 0.004 0.039 13132 Dihedral : 5.569 58.809 10071 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.19 % Favored : 92.80 % Rotamer: Outliers : 2.96 % Allowed : 26.06 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.09), residues: 9212 helix: 0.44 (0.16), residues: 1218 sheet: 0.44 (0.10), residues: 2625 loop : -1.60 (0.08), residues: 5369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 245 HIS 0.002 0.000 HIS N 314 PHE 0.015 0.001 PHE D 707 TYR 0.027 0.001 TYR C 357 ARG 0.006 0.000 ARG C 668 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 927 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 684 time to evaluate : 6.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 590 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6509 (t70) REVERT: A 656 ILE cc_start: 0.7787 (OUTLIER) cc_final: 0.7579 (tp) REVERT: A 762 MET cc_start: 0.8393 (OUTLIER) cc_final: 0.7511 (mpp) REVERT: A 854 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8341 (p) REVERT: B 660 MET cc_start: 0.8117 (tpt) cc_final: 0.7878 (tpt) REVERT: B 689 LYS cc_start: 0.7823 (ttpp) cc_final: 0.7217 (pptt) REVERT: B 704 TYR cc_start: 0.7853 (OUTLIER) cc_final: 0.6918 (m-80) REVERT: B 747 ILE cc_start: 0.5079 (OUTLIER) cc_final: 0.4813 (pp) REVERT: C 325 ARG cc_start: 0.8212 (tpt-90) cc_final: 0.8003 (tmt90) REVERT: C 668 ARG cc_start: 0.7800 (ttp80) cc_final: 0.7537 (ttp-170) REVERT: C 762 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7639 (mpp) REVERT: C 868 ARG cc_start: 0.7883 (ttp-110) cc_final: 0.7557 (mtm110) REVERT: D 545 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8607 (tp) REVERT: D 689 LYS cc_start: 0.8046 (ttpp) cc_final: 0.7590 (pptt) REVERT: D 747 ILE cc_start: 0.5222 (OUTLIER) cc_final: 0.4785 (pp) REVERT: D 754 LYS cc_start: 0.7583 (mmmm) cc_final: 0.7068 (mmtt) REVERT: D 868 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7638 (mtm110) REVERT: E 536 GLN cc_start: 0.7995 (mm110) cc_final: 0.7713 (mm110) REVERT: E 614 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7979 (tmtt) REVERT: E 717 ASP cc_start: 0.6962 (t70) cc_final: 0.6674 (t0) REVERT: E 741 LEU cc_start: 0.7373 (mt) cc_final: 0.7006 (mt) REVERT: E 747 ILE cc_start: 0.5211 (OUTLIER) cc_final: 0.4737 (pp) REVERT: F 660 MET cc_start: 0.8018 (tpt) cc_final: 0.7491 (tpt) REVERT: F 677 ASP cc_start: 0.5917 (OUTLIER) cc_final: 0.5613 (m-30) REVERT: F 689 LYS cc_start: 0.7696 (ttpp) cc_final: 0.7393 (pptt) REVERT: F 717 ASP cc_start: 0.7057 (t70) cc_final: 0.6413 (t0) REVERT: F 747 ILE cc_start: 0.4957 (OUTLIER) cc_final: 0.4537 (pp) REVERT: F 762 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7376 (mpp) REVERT: G 305 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: G 704 TYR cc_start: 0.7963 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: G 709 TYR cc_start: 0.7609 (m-80) cc_final: 0.7360 (m-80) REVERT: G 868 ARG cc_start: 0.7926 (ttp-110) cc_final: 0.7649 (mtm110) REVERT: H 382 ASN cc_start: 0.7744 (m-40) cc_final: 0.7467 (m110) REVERT: H 426 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: H 759 GLN cc_start: 0.7951 (tp-100) cc_final: 0.7263 (mm110) REVERT: H 763 ASP cc_start: 0.8074 (m-30) cc_final: 0.7617 (m-30) REVERT: H 837 THR cc_start: 0.8802 (p) cc_final: 0.8510 (t) REVERT: H 853 MET cc_start: 0.8753 (mmm) cc_final: 0.8300 (mmm) REVERT: I 309 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8711 (mt) REVERT: I 535 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7492 (mm) REVERT: I 666 TYR cc_start: 0.8292 (m-80) cc_final: 0.8021 (m-80) REVERT: I 716 LYS cc_start: 0.6645 (OUTLIER) cc_final: 0.5896 (tptp) REVERT: J 463 ASN cc_start: 0.7466 (OUTLIER) cc_final: 0.7156 (m-40) REVERT: J 666 TYR cc_start: 0.8411 (m-80) cc_final: 0.8054 (m-80) REVERT: J 687 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7245 (tttt) REVERT: K 660 MET cc_start: 0.8327 (tpp) cc_final: 0.8078 (tpt) REVERT: K 666 TYR cc_start: 0.8431 (m-80) cc_final: 0.8158 (m-80) REVERT: K 694 LYS cc_start: 0.7944 (tppp) cc_final: 0.7652 (tppt) REVERT: K 759 GLN cc_start: 0.8018 (tp40) cc_final: 0.7662 (tp-100) REVERT: K 763 ASP cc_start: 0.8002 (m-30) cc_final: 0.7585 (m-30) REVERT: K 853 MET cc_start: 0.8673 (mmm) cc_final: 0.8422 (mmp) REVERT: L 815 PHE cc_start: 0.8422 (t80) cc_final: 0.8138 (t80) REVERT: L 821 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.8342 (mtpt) REVERT: L 852 ILE cc_start: 0.9164 (OUTLIER) cc_final: 0.8898 (mp) REVERT: M 716 LYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5991 (tptp) REVERT: M 757 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7790 (p) REVERT: M 825 MET cc_start: 0.7542 (mmm) cc_final: 0.7110 (mmt) REVERT: M 853 MET cc_start: 0.8762 (mmm) cc_final: 0.8198 (mmm) REVERT: N 692 GLU cc_start: 0.6477 (mm-30) cc_final: 0.6111 (tp30) outliers start: 243 outliers final: 164 residues processed: 897 average time/residue: 1.2222 time to fit residues: 1530.2236 Evaluate side-chains 830 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 640 time to evaluate : 6.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 590 ASP Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 762 MET Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 704 TYR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 229 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 720 ASN Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain C residue 874 SER Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 755 ILE Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 874 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 704 TYR Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 646 SER Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 874 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 426 GLU Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 651 ASN Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 699 VAL Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain H residue 866 ASP Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 354 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 405 LYS Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 713 THR Chi-restraints excluded: chain I residue 715 GLU Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 858 LEU Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 463 ASN Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 876 ASP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 573 GLU Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 661 SER Chi-restraints excluded: chain L residue 699 VAL Chi-restraints excluded: chain L residue 726 ILE Chi-restraints excluded: chain L residue 749 ASP Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 822 ASP Chi-restraints excluded: chain L residue 852 ILE Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 634 ASN Chi-restraints excluded: chain M residue 699 VAL Chi-restraints excluded: chain M residue 707 PHE Chi-restraints excluded: chain M residue 716 LYS Chi-restraints excluded: chain M residue 757 THR Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 368 GLN Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ILE Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 757 THR Chi-restraints excluded: chain N residue 822 ASP Chi-restraints excluded: chain N residue 875 VAL Chi-restraints excluded: chain N residue 876 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 827 optimal weight: 3.9990 chunk 544 optimal weight: 8.9990 chunk 877 optimal weight: 1.9990 chunk 535 optimal weight: 4.9990 chunk 416 optimal weight: 6.9990 chunk 610 optimal weight: 10.0000 chunk 920 optimal weight: 6.9990 chunk 847 optimal weight: 2.9990 chunk 733 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 566 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN B 463 ASN C 720 ASN C 773 ASN D 319 GLN D 371 ASN D 773 ASN E 702 GLN ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 759 GLN ** L 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 GLN N 523 ASN ** N 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 74060 Z= 0.324 Angle : 0.644 16.282 100534 Z= 0.342 Chirality : 0.048 0.249 11312 Planarity : 0.004 0.043 13132 Dihedral : 6.072 59.491 10060 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.34 % Favored : 91.61 % Rotamer: Outliers : 3.06 % Allowed : 26.15 % Favored : 70.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.09), residues: 9212 helix: 0.17 (0.15), residues: 1211 sheet: 0.43 (0.10), residues: 2772 loop : -1.73 (0.08), residues: 5229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 503 HIS 0.007 0.002 HIS K 314 PHE 0.024 0.002 PHE D 707 TYR 0.031 0.002 TYR A 297 ARG 0.005 0.000 ARG C 868 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18424 Ramachandran restraints generated. 9212 Oldfield, 0 Emsley, 9212 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 867 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 616 time to evaluate : 6.611 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8339 (tp) REVERT: A 656 ILE cc_start: 0.7908 (OUTLIER) cc_final: 0.7705 (tp) REVERT: B 660 MET cc_start: 0.8207 (tpt) cc_final: 0.7941 (tpt) REVERT: B 689 LYS cc_start: 0.7932 (ttpp) cc_final: 0.7406 (pptt) REVERT: B 704 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.6994 (m-80) REVERT: B 747 ILE cc_start: 0.4939 (OUTLIER) cc_final: 0.4685 (pp) REVERT: C 325 ARG cc_start: 0.8302 (tpt-90) cc_final: 0.8077 (tmt90) REVERT: C 668 ARG cc_start: 0.7841 (ttp80) cc_final: 0.7445 (ttp-170) REVERT: C 762 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7576 (mpp) REVERT: D 305 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: D 697 TYR cc_start: 0.6656 (OUTLIER) cc_final: 0.5789 (m-80) REVERT: D 747 ILE cc_start: 0.5419 (OUTLIER) cc_final: 0.5017 (pp) REVERT: D 868 ARG cc_start: 0.7959 (ttp-110) cc_final: 0.7682 (mtm110) REVERT: E 536 GLN cc_start: 0.8024 (mm110) cc_final: 0.7802 (mm110) REVERT: E 614 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8048 (tmtt) REVERT: E 717 ASP cc_start: 0.7066 (t70) cc_final: 0.6676 (t0) REVERT: E 747 ILE cc_start: 0.5128 (OUTLIER) cc_final: 0.4688 (pp) REVERT: F 452 MET cc_start: 0.9182 (OUTLIER) cc_final: 0.8970 (ptt) REVERT: F 660 MET cc_start: 0.8210 (tpt) cc_final: 0.7664 (tpt) REVERT: F 677 ASP cc_start: 0.5734 (OUTLIER) cc_final: 0.5485 (m-30) REVERT: F 689 LYS cc_start: 0.7872 (ttpp) cc_final: 0.7396 (pptt) REVERT: F 717 ASP cc_start: 0.7435 (t70) cc_final: 0.6639 (t0) REVERT: F 747 ILE cc_start: 0.4794 (OUTLIER) cc_final: 0.4370 (pp) REVERT: F 762 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7358 (mpp) REVERT: F 796 GLU cc_start: 0.7557 (OUTLIER) cc_final: 0.7248 (pp20) REVERT: G 305 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: G 325 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7958 (tpt-90) REVERT: G 524 GLU cc_start: 0.7627 (tp30) cc_final: 0.6703 (tt0) REVERT: G 704 TYR cc_start: 0.8222 (OUTLIER) cc_final: 0.7036 (m-80) REVERT: G 868 ARG cc_start: 0.7927 (ttp-110) cc_final: 0.7606 (mtm110) REVERT: H 382 ASN cc_start: 0.8033 (m-40) cc_final: 0.7802 (m-40) REVERT: H 429 ILE cc_start: 0.9169 (mt) cc_final: 0.8946 (mm) REVERT: H 759 GLN cc_start: 0.8011 (tp-100) cc_final: 0.7715 (mm110) REVERT: H 837 THR cc_start: 0.9003 (p) cc_final: 0.8719 (t) REVERT: H 853 MET cc_start: 0.8771 (mmm) cc_final: 0.8346 (mmm) REVERT: I 309 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8895 (mt) REVERT: I 425 GLN cc_start: 0.7856 (mm110) cc_final: 0.7294 (pt0) REVERT: I 535 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7555 (mm) REVERT: I 666 TYR cc_start: 0.8403 (m-80) cc_final: 0.8143 (m-80) REVERT: I 716 LYS cc_start: 0.6797 (OUTLIER) cc_final: 0.5943 (tptp) REVERT: J 463 ASN cc_start: 0.7922 (OUTLIER) cc_final: 0.7607 (m-40) REVERT: J 666 TYR cc_start: 0.8538 (m-80) cc_final: 0.8162 (m-80) REVERT: J 687 LYS cc_start: 0.7571 (OUTLIER) cc_final: 0.7334 (tttt) REVERT: K 437 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: K 463 ASN cc_start: 0.7631 (OUTLIER) cc_final: 0.7421 (m-40) REVERT: K 666 TYR cc_start: 0.8461 (m-80) cc_final: 0.8215 (m-80) REVERT: K 694 LYS cc_start: 0.7870 (tppp) cc_final: 0.7558 (tppt) REVERT: L 821 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8479 (mtpt) REVERT: L 852 ILE cc_start: 0.9174 (OUTLIER) cc_final: 0.8931 (mp) REVERT: M 716 LYS cc_start: 0.6730 (OUTLIER) cc_final: 0.6091 (tptp) REVERT: M 757 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7865 (p) REVERT: M 825 MET cc_start: 0.7913 (mmm) cc_final: 0.7565 (mmt) REVERT: M 853 MET cc_start: 0.8807 (mmm) cc_final: 0.8252 (mmm) REVERT: N 536 GLN cc_start: 0.7806 (mm110) cc_final: 0.7340 (mt0) REVERT: N 660 MET cc_start: 0.8303 (tpp) cc_final: 0.8019 (tpt) REVERT: N 837 THR cc_start: 0.9022 (p) cc_final: 0.8794 (t) outliers start: 251 outliers final: 180 residues processed: 836 average time/residue: 1.2552 time to fit residues: 1475.1671 Evaluate side-chains 808 residues out of total 8204 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 599 time to evaluate : 6.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 364 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 648 ASN Chi-restraints excluded: chain A residue 656 ILE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain B residue 251 GLU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 364 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 417 ASP Chi-restraints excluded: chain B residue 480 THR Chi-restraints excluded: chain B residue 497 VAL Chi-restraints excluded: chain B residue 589 LYS Chi-restraints excluded: chain B residue 590 ASP Chi-restraints excluded: chain B residue 704 TYR Chi-restraints excluded: chain B residue 714 THR Chi-restraints excluded: chain B residue 747 ILE Chi-restraints excluded: chain B residue 778 THR Chi-restraints excluded: chain B residue 793 THR Chi-restraints excluded: chain B residue 854 THR Chi-restraints excluded: chain B residue 866 ASP Chi-restraints excluded: chain B residue 874 SER Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 364 SER Chi-restraints excluded: chain C residue 370 SER Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 707 PHE Chi-restraints excluded: chain C residue 714 THR Chi-restraints excluded: chain C residue 762 MET Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 854 THR Chi-restraints excluded: chain C residue 866 ASP Chi-restraints excluded: chain D residue 229 SER Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 305 GLU Chi-restraints excluded: chain D residue 330 SER Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 596 SER Chi-restraints excluded: chain D residue 638 THR Chi-restraints excluded: chain D residue 697 TYR Chi-restraints excluded: chain D residue 714 THR Chi-restraints excluded: chain D residue 747 ILE Chi-restraints excluded: chain D residue 793 THR Chi-restraints excluded: chain D residue 854 THR Chi-restraints excluded: chain D residue 874 SER Chi-restraints excluded: chain E residue 229 SER Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 305 GLU Chi-restraints excluded: chain E residue 354 THR Chi-restraints excluded: chain E residue 370 SER Chi-restraints excluded: chain E residue 414 LEU Chi-restraints excluded: chain E residue 438 THR Chi-restraints excluded: chain E residue 480 THR Chi-restraints excluded: chain E residue 596 SER Chi-restraints excluded: chain E residue 614 LYS Chi-restraints excluded: chain E residue 638 THR Chi-restraints excluded: chain E residue 707 PHE Chi-restraints excluded: chain E residue 714 THR Chi-restraints excluded: chain E residue 747 ILE Chi-restraints excluded: chain E residue 778 THR Chi-restraints excluded: chain E residue 854 THR Chi-restraints excluded: chain E residue 874 SER Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 364 SER Chi-restraints excluded: chain F residue 370 SER Chi-restraints excluded: chain F residue 414 LEU Chi-restraints excluded: chain F residue 452 MET Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 596 SER Chi-restraints excluded: chain F residue 638 THR Chi-restraints excluded: chain F residue 677 ASP Chi-restraints excluded: chain F residue 698 LEU Chi-restraints excluded: chain F residue 707 PHE Chi-restraints excluded: chain F residue 747 ILE Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 778 THR Chi-restraints excluded: chain F residue 796 GLU Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain F residue 874 SER Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 305 GLU Chi-restraints excluded: chain G residue 325 ARG Chi-restraints excluded: chain G residue 328 THR Chi-restraints excluded: chain G residue 330 SER Chi-restraints excluded: chain G residue 365 THR Chi-restraints excluded: chain G residue 370 SER Chi-restraints excluded: chain G residue 414 LEU Chi-restraints excluded: chain G residue 497 VAL Chi-restraints excluded: chain G residue 596 SER Chi-restraints excluded: chain G residue 638 THR Chi-restraints excluded: chain G residue 648 ASN Chi-restraints excluded: chain G residue 704 TYR Chi-restraints excluded: chain G residue 854 THR Chi-restraints excluded: chain G residue 874 SER Chi-restraints excluded: chain H residue 281 PHE Chi-restraints excluded: chain H residue 354 THR Chi-restraints excluded: chain H residue 374 SER Chi-restraints excluded: chain H residue 379 LEU Chi-restraints excluded: chain H residue 410 THR Chi-restraints excluded: chain H residue 414 LEU Chi-restraints excluded: chain H residue 634 ASN Chi-restraints excluded: chain H residue 651 ASN Chi-restraints excluded: chain H residue 670 VAL Chi-restraints excluded: chain H residue 699 VAL Chi-restraints excluded: chain H residue 749 ASP Chi-restraints excluded: chain I residue 281 PHE Chi-restraints excluded: chain I residue 309 ILE Chi-restraints excluded: chain I residue 354 THR Chi-restraints excluded: chain I residue 373 GLU Chi-restraints excluded: chain I residue 374 SER Chi-restraints excluded: chain I residue 400 THR Chi-restraints excluded: chain I residue 405 LYS Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 422 ILE Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 605 LEU Chi-restraints excluded: chain I residue 634 ASN Chi-restraints excluded: chain I residue 651 ASN Chi-restraints excluded: chain I residue 699 VAL Chi-restraints excluded: chain I residue 713 THR Chi-restraints excluded: chain I residue 716 LYS Chi-restraints excluded: chain I residue 739 THR Chi-restraints excluded: chain I residue 753 VAL Chi-restraints excluded: chain I residue 821 LYS Chi-restraints excluded: chain I residue 822 ASP Chi-restraints excluded: chain I residue 858 LEU Chi-restraints excluded: chain J residue 280 SER Chi-restraints excluded: chain J residue 281 PHE Chi-restraints excluded: chain J residue 354 THR Chi-restraints excluded: chain J residue 374 SER Chi-restraints excluded: chain J residue 400 THR Chi-restraints excluded: chain J residue 410 THR Chi-restraints excluded: chain J residue 414 LEU Chi-restraints excluded: chain J residue 422 ILE Chi-restraints excluded: chain J residue 463 ASN Chi-restraints excluded: chain J residue 476 ILE Chi-restraints excluded: chain J residue 542 THR Chi-restraints excluded: chain J residue 634 ASN Chi-restraints excluded: chain J residue 651 ASN Chi-restraints excluded: chain J residue 687 LYS Chi-restraints excluded: chain J residue 822 ASP Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain K residue 281 PHE Chi-restraints excluded: chain K residue 354 THR Chi-restraints excluded: chain K residue 374 SER Chi-restraints excluded: chain K residue 410 THR Chi-restraints excluded: chain K residue 414 LEU Chi-restraints excluded: chain K residue 422 ILE Chi-restraints excluded: chain K residue 437 ASP Chi-restraints excluded: chain K residue 463 ASN Chi-restraints excluded: chain K residue 497 VAL Chi-restraints excluded: chain K residue 542 THR Chi-restraints excluded: chain K residue 634 ASN Chi-restraints excluded: chain K residue 699 VAL Chi-restraints excluded: chain K residue 739 THR Chi-restraints excluded: chain K residue 822 ASP Chi-restraints excluded: chain K residue 868 ARG Chi-restraints excluded: chain K residue 876 ASP Chi-restraints excluded: chain L residue 219 LEU Chi-restraints excluded: chain L residue 280 SER Chi-restraints excluded: chain L residue 281 PHE Chi-restraints excluded: chain L residue 322 THR Chi-restraints excluded: chain L residue 374 SER Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 605 LEU Chi-restraints excluded: chain L residue 661 SER Chi-restraints excluded: chain L residue 699 VAL Chi-restraints excluded: chain L residue 741 LEU Chi-restraints excluded: chain L residue 749 ASP Chi-restraints excluded: chain L residue 821 LYS Chi-restraints excluded: chain L residue 822 ASP Chi-restraints excluded: chain L residue 852 ILE Chi-restraints excluded: chain M residue 281 PHE Chi-restraints excluded: chain M residue 354 THR Chi-restraints excluded: chain M residue 374 SER Chi-restraints excluded: chain M residue 410 THR Chi-restraints excluded: chain M residue 437 ASP Chi-restraints excluded: chain M residue 542 THR Chi-restraints excluded: chain M residue 634 ASN Chi-restraints excluded: chain M residue 699 VAL Chi-restraints excluded: chain M residue 716 LYS Chi-restraints excluded: chain M residue 757 THR Chi-restraints excluded: chain M residue 822 ASP Chi-restraints excluded: chain M residue 866 ASP Chi-restraints excluded: chain N residue 280 SER Chi-restraints excluded: chain N residue 281 PHE Chi-restraints excluded: chain N residue 374 SER Chi-restraints excluded: chain N residue 400 THR Chi-restraints excluded: chain N residue 410 THR Chi-restraints excluded: chain N residue 414 LEU Chi-restraints excluded: chain N residue 422 ILE Chi-restraints excluded: chain N residue 542 THR Chi-restraints excluded: chain N residue 568 ASP Chi-restraints excluded: chain N residue 634 ASN Chi-restraints excluded: chain N residue 651 ASN Chi-restraints excluded: chain N residue 699 VAL Chi-restraints excluded: chain N residue 757 THR Chi-restraints excluded: chain N residue 822 ASP Chi-restraints excluded: chain N residue 875 VAL Chi-restraints excluded: chain N residue 876 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 924 random chunks: chunk 449 optimal weight: 20.0000 chunk 582 optimal weight: 9.9990 chunk 780 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 675 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 203 optimal weight: 2.9990 chunk 734 optimal weight: 0.8980 chunk 307 optimal weight: 4.9990 chunk 753 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 ASN C 720 ASN C 773 ASN D 371 ASN D 773 ASN I 392 ASN ** I 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 759 GLN ** L 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 425 GLN N 523 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.130638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101785 restraints weight = 95101.722| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 1.60 r_work: 0.2999 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 74060 Z= 0.318 Angle : 0.644 16.032 100534 Z= 0.343 Chirality : 0.049 0.238 11312 Planarity : 0.004 0.043 13132 Dihedral : 6.200 59.230 10058 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.98 % Favored : 91.98 % Rotamer: Outliers : 3.27 % Allowed : 25.88 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.09), residues: 9212 helix: 0.08 (0.15), residues: 1204 sheet: 0.47 (0.10), residues: 2681 loop : -1.76 (0.08), residues: 5327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 503 HIS 0.006 0.001 HIS K 314 PHE 0.023 0.002 PHE D 707 TYR 0.030 0.002 TYR C 297 ARG 0.012 0.000 ARG C 868 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25364.02 seconds wall clock time: 443 minutes 0.93 seconds (26580.93 seconds total)