Starting phenix.real_space_refine (version: dev) on Wed Dec 14 18:38:46 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/12_2022/6o2n_0609.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/12_2022/6o2n_0609.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/12_2022/6o2n_0609.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/12_2022/6o2n_0609.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/12_2022/6o2n_0609.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o2n_0609/12_2022/6o2n_0609.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.008 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ASP 228": "OD1" <-> "OD2" Residue "A ARG 232": "NH1" <-> "NH2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A ARG 325": "NH1" <-> "NH2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 415": "OD1" <-> "OD2" Residue "A TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 522": "OE1" <-> "OE2" Residue "A ASP 540": "OD1" <-> "OD2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 607": "NH1" <-> "NH2" Residue "A PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 868": "NH1" <-> "NH2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 290": "NH1" <-> "NH2" Residue "B GLU 313": "OE1" <-> "OE2" Residue "B ARG 325": "NH1" <-> "NH2" Residue "B ASP 362": "OD1" <-> "OD2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 415": "OD1" <-> "OD2" Residue "B ASP 417": "OD1" <-> "OD2" Residue "B GLU 499": "OE1" <-> "OE2" Residue "B GLU 522": "OE1" <-> "OE2" Residue "B TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 568": "OD1" <-> "OD2" Residue "B ASP 582": "OD1" <-> "OD2" Residue "B ARG 607": "NH1" <-> "NH2" Residue "B TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 722": "OE1" <-> "OE2" Residue "B ASP 749": "OD1" <-> "OD2" Residue "B TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 799": "OD1" <-> "OD2" Residue "B TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 868": "NH1" <-> "NH2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C ARG 232": "NH1" <-> "NH2" Residue "C TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 239": "OD1" <-> "OD2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 290": "NH1" <-> "NH2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 458": "NH1" <-> "NH2" Residue "C TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 581": "OD1" <-> "OD2" Residue "C TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 868": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 263": "OE1" <-> "OE2" Residue "D ARG 290": "NH1" <-> "NH2" Residue "D GLU 313": "OE1" <-> "OE2" Residue "D ARG 325": "NH1" <-> "NH2" Residue "D ASP 369": "OD1" <-> "OD2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 415": "OD1" <-> "OD2" Residue "D ASP 417": "OD1" <-> "OD2" Residue "D ASP 471": "OD1" <-> "OD2" Residue "D GLU 499": "OE1" <-> "OE2" Residue "D ASP 540": "OD1" <-> "OD2" Residue "D GLU 544": "OE1" <-> "OE2" Residue "D TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 568": "OD1" <-> "OD2" Residue "D ARG 607": "NH1" <-> "NH2" Residue "D ASP 624": "OD1" <-> "OD2" Residue "D PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 722": "OE1" <-> "OE2" Residue "D GLU 740": "OE1" <-> "OE2" Residue "D ASP 758": "OD1" <-> "OD2" Residue "D TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 866": "OD1" <-> "OD2" Residue "D ARG 868": "NH1" <-> "NH2" Residue "E ARG 232": "NH1" <-> "NH2" Residue "E PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 290": "NH1" <-> "NH2" Residue "E PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 458": "NH1" <-> "NH2" Residue "E TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 623": "OD1" <-> "OD2" Residue "E GLU 662": "OE1" <-> "OE2" Residue "E TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 868": "NH1" <-> "NH2" Residue "F ARG 232": "NH1" <-> "NH2" Residue "F GLU 246": "OE1" <-> "OE2" Residue "F TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 290": "NH1" <-> "NH2" Residue "F ARG 325": "NH1" <-> "NH2" Residue "F ASP 362": "OD1" <-> "OD2" Residue "F TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 415": "OD1" <-> "OD2" Residue "F GLU 499": "OE1" <-> "OE2" Residue "F TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 522": "OE1" <-> "OE2" Residue "F TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 568": "OD1" <-> "OD2" Residue "F ARG 607": "NH1" <-> "NH2" Residue "F TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 722": "OE1" <-> "OE2" Residue "F GLU 746": "OE1" <-> "OE2" Residue "F GLU 752": "OE1" <-> "OE2" Residue "F TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 799": "OD1" <-> "OD2" Residue "F PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 868": "NH1" <-> "NH2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G ARG 232": "NH1" <-> "NH2" Residue "G PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 263": "OE1" <-> "OE2" Residue "G PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 290": "NH1" <-> "NH2" Residue "G GLU 426": "OE1" <-> "OE2" Residue "G PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 458": "NH1" <-> "NH2" Residue "G ASP 520": "OD1" <-> "OD2" Residue "G ASP 537": "OD1" <-> "OD2" Residue "G TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 581": "OD1" <-> "OD2" Residue "G TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 692": "OE1" <-> "OE2" Residue "G GLU 715": "OE1" <-> "OE2" Residue "G TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 868": "NH1" <-> "NH2" Residue "H ASP 228": "OD1" <-> "OD2" Residue "H ARG 232": "NH1" <-> "NH2" Residue "H GLU 251": "OE1" <-> "OE2" Residue "H TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 290": "NH1" <-> "NH2" Residue "H ASP 291": "OD1" <-> "OD2" Residue "H GLU 313": "OE1" <-> "OE2" Residue "H ARG 325": "NH1" <-> "NH2" Residue "H TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 417": "OD1" <-> "OD2" Residue "H ASP 471": "OD1" <-> "OD2" Residue "H GLU 499": "OE1" <-> "OE2" Residue "H TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 544": "OE1" <-> "OE2" Residue "H TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 582": "OD1" <-> "OD2" Residue "H ARG 607": "NH1" <-> "NH2" Residue "H TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 641": "OD1" <-> "OD2" Residue "H PHE 711": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 752": "OE1" <-> "OE2" Residue "H TYR 768": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 866": "OD1" <-> "OD2" Residue "H ARG 868": "NH1" <-> "NH2" Residue "I ARG 232": "NH1" <-> "NH2" Residue "I ASP 239": "OD1" <-> "OD2" Residue "I ASP 247": "OD1" <-> "OD2" Residue "I PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 263": "OE1" <-> "OE2" Residue "I PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 290": "NH1" <-> "NH2" Residue "I ASP 291": "OD1" <-> "OD2" Residue "I ASP 362": "OD1" <-> "OD2" Residue "I ASP 415": "OD1" <-> "OD2" Residue "I PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 458": "NH1" <-> "NH2" Residue "I TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 522": "OE1" <-> "OE2" Residue "I TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 573": "OE1" <-> "OE2" Residue "I ASP 581": "OD1" <-> "OD2" Residue "I GLU 662": "OE1" <-> "OE2" Residue "I TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 758": "OD1" <-> "OD2" Residue "I PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 796": "OE1" <-> "OE2" Residue "I TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 868": "NH1" <-> "NH2" Residue "J ARG 232": "NH1" <-> "NH2" Residue "J TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 290": "NH1" <-> "NH2" Residue "J GLU 313": "OE1" <-> "OE2" Residue "J ARG 325": "NH1" <-> "NH2" Residue "J ASP 362": "OD1" <-> "OD2" Residue "J TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 522": "OE1" <-> "OE2" Residue "J TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 607": "NH1" <-> "NH2" Residue "J ASP 624": "OD1" <-> "OD2" Residue "J TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 746": "OE1" <-> "OE2" Residue "J ASP 799": "OD1" <-> "OD2" Residue "J TYR 839": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 868": "NH1" <-> "NH2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K ARG 232": "NH1" <-> "NH2" Residue "K GLU 263": "OE1" <-> "OE2" Residue "K PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 290": "NH1" <-> "NH2" Residue "K GLU 426": "OE1" <-> "OE2" Residue "K PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 458": "NH1" <-> "NH2" Residue "K ASP 465": "OD1" <-> "OD2" Residue "K GLU 479": "OE1" <-> "OE2" Residue "K GLU 499": "OE1" <-> "OE2" Residue "K TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 581": "OD1" <-> "OD2" Residue "K ASP 623": "OD1" <-> "OD2" Residue "K TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 868": "NH1" <-> "NH2" Residue "L ARG 232": "NH1" <-> "NH2" Residue "L TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 263": "OE1" <-> "OE2" Residue "L ARG 290": "NH1" <-> "NH2" Residue "L ARG 325": "NH1" <-> "NH2" Residue "L TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 415": "OD1" <-> "OD2" Residue "L ASP 417": "OD1" <-> "OD2" Residue "L ASP 453": "OD1" <-> "OD2" Residue "L GLU 499": "OE1" <-> "OE2" Residue "L TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 522": "OE1" <-> "OE2" Residue "L ASP 540": "OD1" <-> "OD2" Residue "L GLU 544": "OE1" <-> "OE2" Residue "L TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 582": "OD1" <-> "OD2" Residue "L ARG 607": "NH1" <-> "NH2" Residue "L TYR 628": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 722": "OE1" <-> "OE2" Residue "L GLU 746": "OE1" <-> "OE2" Residue "L ASP 758": "OD1" <-> "OD2" Residue "L PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 799": "OD1" <-> "OD2" Residue "L TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 868": "NH1" <-> "NH2" Residue "M ASP 218": "OD1" <-> "OD2" Residue "M ARG 232": "NH1" <-> "NH2" Residue "M ASP 239": "OD1" <-> "OD2" Residue "M ASP 247": "OD1" <-> "OD2" Residue "M PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 290": "NH1" <-> "NH2" Residue "M PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 458": "NH1" <-> "NH2" Residue "M GLU 499": "OE1" <-> "OE2" Residue "M GLU 522": "OE1" <-> "OE2" Residue "M TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 572": "OD1" <-> "OD2" Residue "M ASP 581": "OD1" <-> "OD2" Residue "M TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 868": "NH1" <-> "NH2" Residue "Z ARG 232": "NH1" <-> "NH2" Residue "Z ASP 239": "OD1" <-> "OD2" Residue "Z GLU 263": "OE1" <-> "OE2" Residue "Z PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 290": "NH1" <-> "NH2" Residue "Z PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 458": "NH1" <-> "NH2" Residue "Z ASP 537": "OD1" <-> "OD2" Residue "Z GLU 544": "OE1" <-> "OE2" Residue "Z TYR 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 581": "OD1" <-> "OD2" Residue "Z ASP 582": "OD1" <-> "OD2" Residue "Z TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 715": "OE1" <-> "OE2" Residue "Z ASP 749": "OD1" <-> "OD2" Residue "Z PHE 788": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 868": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 72637 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "B" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "C" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "D" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "E" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "F" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "G" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "H" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "I" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "J" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "K" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "L" Number of atoms: 5196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5196 Classifications: {'peptide': 659} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 631} Chain: "M" Number of atoms: 5182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 658, 5182 Classifications: {'peptide': 658} Link IDs: {'PTRANS': 27, 'TRANS': 630} Chain: "Z" Number of atoms: 5173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 657, 5173 Classifications: {'peptide': 657} Link IDs: {'PTRANS': 27, 'TRANS': 629} Time building chain proxies: 32.31, per 1000 atoms: 0.44 Number of scatterers: 72637 At special positions: 0 Unit cell: (184.15, 181.25, 269.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 140 16.00 O 15222 8.00 N 11801 7.00 C 45474 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: 22.33 Conformation dependent library (CDL) restraints added in 9.0 seconds 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17288 Finding SS restraints... Secondary structure from input PDB file: 169 helices and 156 sheets defined 11.8% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.65 Creating SS restraints... Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.890A pdb=" N ARG A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 251 removed outlier: 3.757A pdb=" N ALA A 250 " --> pdb=" O ASP A 247 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 502 through 505 removed outlier: 4.204A pdb=" N ASP A 505 " --> pdb=" O SER A 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 502 through 505' Processing helix chain 'A' and resid 506 through 512 removed outlier: 3.704A pdb=" N SER A 512 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 555 removed outlier: 3.592A pdb=" N GLU A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE A 555 " --> pdb=" O ILE A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 563 removed outlier: 4.036A pdb=" N GLY A 562 " --> pdb=" O LYS A 559 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 563 " --> pdb=" O LYS A 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 559 through 563' Processing helix chain 'A' and resid 581 through 591 Processing helix chain 'A' and resid 599 through 603 removed outlier: 3.566A pdb=" N ASN A 602 " --> pdb=" O LYS A 599 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 603 " --> pdb=" O ILE A 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 599 through 603' Processing helix chain 'A' and resid 661 through 663 No H-bonds generated for 'chain 'A' and resid 661 through 663' Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.808A pdb=" N ARG B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 removed outlier: 3.555A pdb=" N PHE B 249 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA B 250 " --> pdb=" O ASP B 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 246 through 250' Processing helix chain 'B' and resid 272 through 278 Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.633A pdb=" N ARG B 290 " --> pdb=" O THR B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 472 Processing helix chain 'B' and resid 502 through 505 removed outlier: 4.263A pdb=" N ASP B 505 " --> pdb=" O SER B 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 502 through 505' Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 546 through 555 removed outlier: 3.799A pdb=" N PHE B 555 " --> pdb=" O ILE B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 563 removed outlier: 3.982A pdb=" N GLY B 562 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 589 Processing helix chain 'B' and resid 661 through 663 No H-bonds generated for 'chain 'B' and resid 661 through 663' Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'C' and resid 227 through 233 removed outlier: 3.618A pdb=" N ASN C 233 " --> pdb=" O SER C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 removed outlier: 3.541A pdb=" N LYS C 276 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.988A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 3.564A pdb=" N ALA C 337 " --> pdb=" O SER C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 502 through 505 removed outlier: 4.276A pdb=" N ASP C 505 " --> pdb=" O SER C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 546 through 555 removed outlier: 3.794A pdb=" N GLU C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE C 555 " --> pdb=" O ILE C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 590 removed outlier: 3.753A pdb=" N ALA C 585 " --> pdb=" O ASP C 581 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN C 586 " --> pdb=" O ASP C 582 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS C 587 " --> pdb=" O ASN C 583 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASP C 590 " --> pdb=" O ASN C 586 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 603 removed outlier: 3.655A pdb=" N ASN C 602 " --> pdb=" O LYS C 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL C 603 " --> pdb=" O ILE C 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 599 through 603' Processing helix chain 'C' and resid 760 through 764 removed outlier: 3.839A pdb=" N ASP C 763 " --> pdb=" O GLU C 760 " (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 'D' and resid 226 through 230 Processing helix chain 'D' and resid 246 through 250 removed outlier: 3.561A pdb=" N PHE D 249 " --> pdb=" O GLU D 246 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA D 250 " --> pdb=" O ASP D 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 246 through 250' Processing helix chain 'D' and resid 273 through 278 Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.605A pdb=" N ARG D 290 " --> pdb=" O THR D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 506 through 511 Processing helix chain 'D' and resid 546 through 555 removed outlier: 3.527A pdb=" N GLU D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE D 555 " --> pdb=" O ILE D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 559 through 563 removed outlier: 3.917A pdb=" N GLY D 562 " --> pdb=" O LYS D 559 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 563 " --> pdb=" O LYS D 560 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 559 through 563' Processing helix chain 'D' and resid 581 through 589 Processing helix chain 'D' and resid 661 through 663 No H-bonds generated for 'chain 'D' and resid 661 through 663' Processing helix chain 'D' and resid 796 through 800 Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'E' and resid 227 through 233 removed outlier: 3.656A pdb=" N ASN E 233 " --> pdb=" O SER E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 removed outlier: 3.537A pdb=" N LYS E 276 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 removed outlier: 3.541A pdb=" N ARG E 290 " --> pdb=" O THR E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 502 through 505 removed outlier: 4.202A pdb=" N ASP E 505 " --> pdb=" O SER E 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 502 through 505' Processing helix chain 'E' and resid 506 through 511 Processing helix chain 'E' and resid 546 through 555 removed outlier: 3.817A pdb=" N GLU E 552 " --> pdb=" O GLY E 548 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 590 removed outlier: 3.707A pdb=" N ALA E 585 " --> pdb=" O ASP E 581 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN E 586 " --> pdb=" O ASP E 582 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASP E 590 " --> pdb=" O ASN E 586 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 removed outlier: 3.600A pdb=" N ASN E 602 " --> pdb=" O LYS E 599 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL E 603 " --> pdb=" O ILE E 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 599 through 603' Processing helix chain 'E' and resid 760 through 764 removed outlier: 3.911A pdb=" N ASP E 763 " --> pdb=" O GLU E 760 " (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 'F' and resid 227 through 232 removed outlier: 3.675A pdb=" N ARG F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 250 removed outlier: 3.576A pdb=" N PHE F 249 " --> pdb=" O GLU F 246 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 250 " --> pdb=" O ASP F 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 246 through 250' Processing helix chain 'F' and resid 272 through 278 Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 502 through 505 removed outlier: 4.309A pdb=" N ASP F 505 " --> pdb=" O SER F 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 502 through 505' Processing helix chain 'F' and resid 506 through 512 removed outlier: 3.879A pdb=" N SER F 512 " --> pdb=" O SER F 508 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 555 removed outlier: 3.744A pdb=" N GLU F 552 " --> pdb=" O GLY F 548 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE F 555 " --> pdb=" O ILE F 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 592 Processing helix chain 'F' and resid 661 through 663 No H-bonds generated for 'chain 'F' and resid 661 through 663' Processing helix chain 'F' and resid 796 through 800 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.652A pdb=" N ASN G 233 " --> pdb=" O SER G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 272 through 279 removed outlier: 3.545A pdb=" N LYS G 276 " --> pdb=" O THR G 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.616A pdb=" N ARG G 290 " --> pdb=" O THR G 287 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 375 through 379 removed outlier: 3.629A pdb=" N LEU G 379 " --> pdb=" O ASN G 376 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 Processing helix chain 'G' and resid 463 through 472 Processing helix chain 'G' and resid 506 through 511 Processing helix chain 'G' and resid 547 through 555 removed outlier: 3.602A pdb=" N GLU G 552 " --> pdb=" O GLY G 548 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE G 555 " --> pdb=" O ILE G 551 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 590 removed outlier: 3.543A pdb=" N ALA G 585 " --> pdb=" O ASP G 581 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN G 586 " --> pdb=" O ASP G 582 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS G 587 " --> pdb=" O ASN G 583 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP G 590 " --> pdb=" O ASN G 586 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.683A pdb=" N ASN G 602 " --> pdb=" O LYS G 599 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 599 through 603' Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.935A pdb=" N ARG H 232 " --> pdb=" O ASP H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 250 removed outlier: 3.564A pdb=" N PHE H 249 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA H 250 " --> pdb=" O ASP H 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 246 through 250' Processing helix chain 'H' and resid 272 through 278 Processing helix chain 'H' and resid 286 through 290 removed outlier: 3.628A pdb=" N ARG H 290 " --> pdb=" O THR H 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 463 through 472 Processing helix chain 'H' and resid 506 through 512 removed outlier: 3.749A pdb=" N SER H 512 " --> pdb=" O SER H 508 " (cutoff:3.500A) Processing helix chain 'H' and resid 546 through 555 removed outlier: 3.774A pdb=" N GLU H 552 " --> pdb=" O GLY H 548 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE H 555 " --> pdb=" O ILE H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 559 through 563 removed outlier: 3.869A pdb=" N GLY H 562 " --> pdb=" O LYS H 559 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 591 Processing helix chain 'H' and resid 661 through 663 No H-bonds generated for 'chain 'H' and resid 661 through 663' Processing helix chain 'H' and resid 796 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 'I' and resid 227 through 233 removed outlier: 3.640A pdb=" N ASN I 233 " --> pdb=" O SER I 229 " (cutoff:3.500A) Processing helix chain 'I' and resid 272 through 279 removed outlier: 3.529A pdb=" N LYS I 276 " --> pdb=" O THR I 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 removed outlier: 4.058A pdb=" N ASP I 291 " --> pdb=" O GLU I 288 " (cutoff:3.500A) Processing helix chain 'I' and resid 425 through 429 removed outlier: 3.625A pdb=" N GLN I 428 " --> pdb=" O GLN I 425 " (cutoff:3.500A) Processing helix chain 'I' and resid 463 through 472 Processing helix chain 'I' and resid 502 through 505 removed outlier: 4.190A pdb=" N ASP I 505 " --> pdb=" O SER I 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 502 through 505' Processing helix chain 'I' and resid 506 through 511 Processing helix chain 'I' and resid 546 through 555 removed outlier: 3.699A pdb=" N GLU I 552 " --> pdb=" O GLY I 548 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE I 555 " --> pdb=" O ILE I 551 " (cutoff:3.500A) Processing helix chain 'I' and resid 581 through 590 removed outlier: 3.603A pdb=" N ALA I 585 " --> pdb=" O ASP I 581 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASN I 586 " --> pdb=" O ASP I 582 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS I 587 " --> pdb=" O ASN I 583 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP I 590 " --> pdb=" O ASN I 586 " (cutoff:3.500A) Processing helix chain 'I' and resid 599 through 603 removed outlier: 3.547A pdb=" N ASN I 602 " --> pdb=" O LYS I 599 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL I 603 " --> pdb=" O ILE I 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 599 through 603' Processing helix chain 'I' and resid 760 through 764 removed outlier: 3.894A pdb=" N ASP I 763 " --> pdb=" O GLU I 760 " (cutoff:3.500A) Processing helix chain 'I' and resid 829 through 831 No H-bonds generated for 'chain 'I' and resid 829 through 831' Processing helix chain 'J' and resid 227 through 232 removed outlier: 3.860A pdb=" N ARG J 232 " --> pdb=" O ASP J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 246 through 250 removed outlier: 3.737A pdb=" N PHE J 249 " --> pdb=" O GLU J 246 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA J 250 " --> pdb=" O ASP J 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 246 through 250' Processing helix chain 'J' and resid 272 through 278 Processing helix chain 'J' and resid 286 through 290 removed outlier: 3.660A pdb=" N ARG J 290 " --> pdb=" O THR J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 463 through 472 removed outlier: 3.543A pdb=" N ALA J 472 " --> pdb=" O LYS J 468 " (cutoff:3.500A) Processing helix chain 'J' and resid 502 through 505 removed outlier: 4.253A pdb=" N ASP J 505 " --> pdb=" O SER J 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 502 through 505' Processing helix chain 'J' and resid 506 through 512 removed outlier: 3.775A pdb=" N SER J 512 " --> pdb=" O SER J 508 " (cutoff:3.500A) Processing helix chain 'J' and resid 546 through 555 removed outlier: 3.597A pdb=" N GLU J 552 " --> pdb=" O GLY J 548 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE J 555 " --> pdb=" O ILE J 551 " (cutoff:3.500A) Processing helix chain 'J' and resid 581 through 589 Processing helix chain 'J' and resid 661 through 663 No H-bonds generated for 'chain 'J' and resid 661 through 663' Processing helix chain 'J' and resid 796 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 'K' and resid 227 through 233 removed outlier: 3.671A pdb=" N ASN K 233 " --> pdb=" O SER K 229 " (cutoff:3.500A) Processing helix chain 'K' and resid 272 through 279 removed outlier: 3.511A pdb=" N LYS K 276 " --> pdb=" O THR K 272 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 290 removed outlier: 3.502A pdb=" N ARG K 290 " --> pdb=" O THR K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 333 through 337 removed outlier: 3.542A pdb=" N ALA K 337 " --> pdb=" O SER K 334 " (cutoff:3.500A) Processing helix chain 'K' and resid 425 through 429 removed outlier: 3.516A pdb=" N GLN K 428 " --> pdb=" O GLN K 425 " (cutoff:3.500A) Processing helix chain 'K' and resid 463 through 472 Processing helix chain 'K' and resid 506 through 511 Processing helix chain 'K' and resid 546 through 555 removed outlier: 3.826A pdb=" N GLU K 552 " --> pdb=" O GLY K 548 " (cutoff:3.500A) Processing helix chain 'K' and resid 581 through 589 removed outlier: 3.537A pdb=" N ALA K 585 " --> pdb=" O ASP K 581 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN K 586 " --> pdb=" O ASP K 582 " (cutoff:3.500A) Processing helix chain 'K' and resid 599 through 603 removed outlier: 3.658A pdb=" N ASN K 602 " --> pdb=" O LYS K 599 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL K 603 " --> pdb=" O ILE K 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 599 through 603' Processing helix chain 'K' and resid 760 through 764 removed outlier: 3.951A pdb=" N ASP K 763 " --> pdb=" O GLU K 760 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 removed outlier: 3.919A pdb=" N ARG L 232 " --> pdb=" O ASP L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 250 removed outlier: 3.657A pdb=" N PHE L 249 " --> pdb=" O GLU L 246 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA L 250 " --> pdb=" O ASP L 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 246 through 250' Processing helix chain 'L' and resid 272 through 278 Processing helix chain 'L' and resid 286 through 290 removed outlier: 3.703A pdb=" N ARG L 290 " --> pdb=" O THR L 287 " (cutoff:3.500A) Processing helix chain 'L' and resid 463 through 472 removed outlier: 3.602A pdb=" N ALA L 472 " --> pdb=" O LYS L 468 " (cutoff:3.500A) Processing helix chain 'L' and resid 502 through 505 removed outlier: 4.185A pdb=" N ASP L 505 " --> pdb=" O SER L 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 502 through 505' Processing helix chain 'L' and resid 506 through 512 removed outlier: 3.732A pdb=" N SER L 512 " --> pdb=" O SER L 508 " (cutoff:3.500A) Processing helix chain 'L' and resid 546 through 555 removed outlier: 3.621A pdb=" N GLU L 552 " --> pdb=" O GLY L 548 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE L 555 " --> pdb=" O ILE L 551 " (cutoff:3.500A) Processing helix chain 'L' and resid 581 through 589 Processing helix chain 'L' and resid 661 through 663 No H-bonds generated for 'chain 'L' and resid 661 through 663' Processing helix chain 'L' and resid 796 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 'M' and resid 227 through 233 removed outlier: 3.611A pdb=" N ASN M 233 " --> pdb=" O SER M 229 " (cutoff:3.500A) Processing helix chain 'M' and resid 272 through 279 removed outlier: 3.701A pdb=" N LYS M 276 " --> pdb=" O THR M 272 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 removed outlier: 4.065A pdb=" N ASP M 291 " --> pdb=" O GLU M 288 " (cutoff:3.500A) Processing helix chain 'M' and resid 425 through 429 Processing helix chain 'M' and resid 463 through 472 Processing helix chain 'M' and resid 502 through 505 removed outlier: 4.219A pdb=" N ASP M 505 " --> pdb=" O SER M 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 502 through 505' Processing helix chain 'M' and resid 506 through 511 Processing helix chain 'M' and resid 546 through 555 removed outlier: 3.771A pdb=" N GLU M 552 " --> pdb=" O GLY M 548 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE M 555 " --> pdb=" O ILE M 551 " (cutoff:3.500A) Processing helix chain 'M' and resid 581 through 590 removed outlier: 3.885A pdb=" N ASN M 586 " --> pdb=" O ASP M 582 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS M 587 " --> pdb=" O ASN M 583 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP M 590 " --> pdb=" O ASN M 586 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 603 removed outlier: 3.681A pdb=" N ASN M 602 " --> pdb=" O LYS M 599 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N VAL M 603 " --> pdb=" O ILE M 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 599 through 603' Processing helix chain 'M' and resid 760 through 764 removed outlier: 3.942A pdb=" N ASP M 763 " --> pdb=" O GLU M 760 " (cutoff:3.500A) Processing helix chain 'M' and resid 829 through 831 No H-bonds generated for 'chain 'M' and resid 829 through 831' Processing helix chain 'Z' and resid 227 through 233 removed outlier: 3.649A pdb=" N ASN Z 233 " --> pdb=" O SER Z 229 " (cutoff:3.500A) Processing helix chain 'Z' and resid 272 through 279 removed outlier: 3.504A pdb=" N LYS Z 276 " --> pdb=" O THR Z 272 " (cutoff:3.500A) Processing helix chain 'Z' and resid 286 through 291 removed outlier: 3.973A pdb=" N ASP Z 291 " --> pdb=" O GLU Z 288 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 337 removed outlier: 3.562A pdb=" N ALA Z 337 " --> pdb=" O SER Z 334 " (cutoff:3.500A) Processing helix chain 'Z' and resid 425 through 429 removed outlier: 3.648A pdb=" N ILE Z 429 " --> pdb=" O GLU Z 426 " (cutoff:3.500A) Processing helix chain 'Z' and resid 463 through 472 Processing helix chain 'Z' and resid 506 through 511 Processing helix chain 'Z' and resid 546 through 555 removed outlier: 3.716A pdb=" N GLU Z 552 " --> pdb=" O GLY Z 548 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE Z 555 " --> pdb=" O ILE Z 551 " (cutoff:3.500A) Processing helix chain 'Z' and resid 581 through 590 removed outlier: 3.657A pdb=" N ALA Z 585 " --> pdb=" O ASP Z 581 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASN Z 586 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP Z 590 " --> pdb=" O ASN Z 586 " (cutoff:3.500A) Processing helix chain 'Z' and resid 599 through 603 removed outlier: 3.725A pdb=" N ASN Z 602 " --> pdb=" O LYS Z 599 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL Z 603 " --> pdb=" O ILE Z 600 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 599 through 603' Processing helix chain 'Z' and resid 760 through 764 removed outlier: 4.012A pdb=" N ASP Z 763 " --> pdb=" O GLU Z 760 " (cutoff:3.500A) 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 298 through 311 removed outlier: 3.615A pdb=" N ILE A 299 " --> pdb=" O THR A 398 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY A 301 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 437 through 439 removed outlier: 3.798A pdb=" N ASP A 437 " --> pdb=" O ASN A 397 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N TYR A 439 " --> pdb=" O TYR A 395 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 316 through 345 removed outlier: 3.516A pdb=" N ALA A 351 " --> pdb=" O TYR B 345 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL B 343 " --> pdb=" O VAL A 353 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 341 " --> pdb=" O THR A 355 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR A 357 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA B 337 " --> pdb=" O HIS A 359 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR A 361 " --> pdb=" O ASN B 335 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 363 " --> pdb=" O GLU B 333 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS B 331 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR B 327 " --> pdb=" O ASP A 369 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N TRP A 375 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 319 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 351 " --> pdb=" O TYR D 345 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 341 " --> pdb=" O THR B 355 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 357 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 337 " --> pdb=" O HIS B 359 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN B 363 " --> pdb=" O GLU D 333 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 331 " --> pdb=" O THR B 365 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 327 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP B 375 " --> pdb=" O LYS D 321 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS D 321 " --> pdb=" O TRP B 375 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA D 351 " --> pdb=" O TYR F 345 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL F 341 " --> pdb=" O THR D 355 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR D 357 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N HIS D 359 " --> pdb=" O ALA F 337 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA F 337 " --> pdb=" O HIS D 359 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 363 " --> pdb=" O GLU F 333 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS F 331 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR F 327 " --> pdb=" O ASP D 369 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TRP D 375 " --> pdb=" O LYS F 321 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS F 321 " --> pdb=" O TRP D 375 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN F 319 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA F 351 " --> pdb=" O TYR H 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL H 341 " --> pdb=" O THR F 355 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR F 357 " --> pdb=" O VAL H 339 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN F 363 " --> pdb=" O GLU H 333 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS H 331 " --> pdb=" O THR F 365 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASP F 369 " --> pdb=" O THR H 327 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR H 327 " --> pdb=" O ASP F 369 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP F 375 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS H 321 " --> pdb=" O TRP F 375 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN H 319 " --> pdb=" O THR F 377 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA H 351 " --> pdb=" O TYR J 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 343 " --> pdb=" O VAL H 353 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL J 341 " --> pdb=" O THR H 355 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR H 357 " --> pdb=" O VAL J 339 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA J 337 " --> pdb=" O HIS H 359 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR H 361 " --> pdb=" O ASN J 335 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASN H 363 " --> pdb=" O GLU J 333 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LYS J 331 " --> pdb=" O THR H 365 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR J 327 " --> pdb=" O ASP H 369 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP H 375 " --> pdb=" O LYS J 321 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN J 319 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA J 351 " --> pdb=" O TYR L 345 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL L 341 " --> pdb=" O THR J 355 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR J 357 " --> pdb=" O VAL L 339 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA L 337 " --> pdb=" O HIS J 359 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN J 363 " --> pdb=" O GLU L 333 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS L 331 " --> pdb=" O THR J 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR L 327 " --> pdb=" O ASP J 369 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TRP J 375 " --> pdb=" O LYS L 321 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS L 321 " --> pdb=" O TRP J 375 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN L 319 " --> pdb=" O THR J 377 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA L 351 " --> pdb=" O TYR A 345 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL A 343 " --> pdb=" O VAL L 353 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 341 " --> pdb=" O THR L 355 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR L 357 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N HIS L 359 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 337 " --> pdb=" O HIS L 359 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASN L 363 " --> pdb=" O GLU A 333 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS A 331 " --> pdb=" O THR L 365 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR A 327 " --> pdb=" O ASP L 369 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LYS A 321 " --> pdb=" O TRP L 375 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLN A 319 " --> pdb=" O THR L 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 420 through 423 removed outlier: 3.760A pdb=" N SER A 420 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 489 through 490 removed outlier: 3.652A pdb=" N THR A 489 " --> pdb=" O VAL A 497 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 525 through 531 Processing sheet with id=AA8, first strand: chain 'A' and resid 564 through 565 removed outlier: 4.143A pdb=" N LEU A 564 " --> pdb=" O ILE A 571 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 618 through 619 removed outlier: 3.571A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 651 through 659 Processing sheet with id=AB2, first strand: chain 'A' and resid 768 through 775 removed outlier: 6.246A pdb=" N PHE A 769 " --> pdb=" O MET A 786 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N MET A 786 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ASP A 771 " --> pdb=" O ASN A 784 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ASN A 780 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N MET A 786 " --> pdb=" O VAL A 840 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 816 through 822 removed outlier: 5.445A pdb=" N ASP A 817 " --> pdb=" O ALA A 808 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ALA A 808 " --> pdb=" O ASP A 817 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N GLY A 819 " --> pdb=" O VAL A 806 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 806 " --> pdb=" O GLY A 819 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR A 804 " --> pdb=" O LYS A 821 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS A 803 " --> pdb=" O TYR A 861 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N ILE A 860 " --> pdb=" O ARG A 868 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ARG A 868 " --> pdb=" O ILE A 860 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 826 through 827 removed outlier: 3.527A pdb=" N ARG A 826 " --> pdb=" O THR A 837 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB6, first strand: chain 'B' and resid 303 through 311 removed outlier: 6.738A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 303 through 311 removed outlier: 6.738A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 420 through 423 removed outlier: 3.787A pdb=" N SER B 420 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC1, first strand: chain 'B' and resid 525 through 531 Processing sheet with id=AC2, first strand: chain 'B' and resid 564 through 565 removed outlier: 4.092A pdb=" N LEU B 564 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 651 through 659 Processing sheet with id=AC4, first strand: chain 'B' and resid 707 through 712 removed outlier: 3.735A pdb=" N PHE B 711 " --> pdb=" O TYR B 669 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 669 " --> pdb=" O PHE B 711 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 768 through 775 removed outlier: 6.149A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN B 780 " --> pdb=" O ASN B 775 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET B 786 " --> pdb=" O VAL B 840 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B 840 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 788 " --> pdb=" O ASN B 838 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASN B 838 " --> pdb=" O PHE B 788 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 816 through 822 removed outlier: 5.463A pdb=" N ASP B 817 " --> pdb=" O ALA B 808 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALA B 808 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLY B 819 " --> pdb=" O VAL B 806 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL B 806 " --> pdb=" O GLY B 819 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 821 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR B 804 " --> pdb=" O LYS B 821 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LYS B 803 " --> pdb=" O TYR B 861 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU B 858 " --> pdb=" O GLU B 869 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AC8, first strand: chain 'C' and resid 366 through 367 removed outlier: 5.839A pdb=" N GLU C 305 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N MET C 304 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ARG C 394 " --> pdb=" O MET C 304 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE C 460 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.542A pdb=" N SER C 516 " --> pdb=" O ILE C 611 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE C 613 " --> pdb=" O SER C 516 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE C 518 " --> pdb=" O ILE C 613 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 362 through 364 removed outlier: 3.781A pdb=" N SER C 420 " --> pdb=" O LEU C 412 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 489 through 490 removed outlier: 3.531A pdb=" N THR C 489 " --> pdb=" O VAL C 497 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL C 497 " --> pdb=" O THR C 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'C' and resid 558 through 559 removed outlier: 3.691A pdb=" N LEU C 564 " --> pdb=" O ILE C 571 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 618 through 620 removed outlier: 6.510A pdb=" N ARG C 668 " --> pdb=" O LEU C 741 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 654 through 659 removed outlier: 3.625A pdb=" N SER C 683 " --> pdb=" O THR C 695 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR C 695 " --> pdb=" O SER C 683 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 768 through 771 Processing sheet with id=AD7, first strand: chain 'C' and resid 816 through 822 removed outlier: 4.144A pdb=" N VAL C 806 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N THR C 820 " --> pdb=" O TYR C 804 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N TYR C 804 " --> pdb=" O THR C 820 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 870 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE C 860 " --> pdb=" O ARG C 868 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ARG C 868 " --> pdb=" O ILE C 860 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 824 through 827 Processing sheet with id=AD9, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AE1, first strand: chain 'D' and resid 298 through 311 removed outlier: 3.681A pdb=" N GLY D 301 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 394 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 298 through 311 removed outlier: 3.681A pdb=" N GLY D 301 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG D 394 " --> pdb=" O GLY D 303 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASN D 392 " --> pdb=" O GLU D 305 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU D 307 " --> pdb=" O ASN D 390 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ASN D 390 " --> pdb=" O LEU D 307 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ILE D 309 " --> pdb=" O TYR D 388 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N TYR D 388 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 420 through 423 removed outlier: 3.903A pdb=" N SER D 420 " --> pdb=" O LEU D 412 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LYS D 405 " --> pdb=" O GLY D 485 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLY D 485 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 407 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL D 483 " --> pdb=" O THR D 407 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N THR D 409 " --> pdb=" O THR D 481 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 489 through 490 removed outlier: 3.559A pdb=" N THR D 489 " --> pdb=" O VAL D 497 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 525 through 531 Processing sheet with id=AE6, first strand: chain 'D' and resid 564 through 565 removed outlier: 4.119A pdb=" N LEU D 564 " --> pdb=" O ILE D 571 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 651 through 659 Processing sheet with id=AE8, first strand: chain 'D' and resid 707 through 712 removed outlier: 3.762A pdb=" N PHE D 711 " --> pdb=" O TYR D 669 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR D 669 " --> pdb=" O PHE D 711 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 770 through 775 removed outlier: 6.681A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN D 780 " --> pdb=" O ASN D 775 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET D 786 " --> pdb=" O VAL D 840 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL D 840 " --> pdb=" O MET D 786 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 816 through 822 removed outlier: 5.412A pdb=" N ASP D 817 " --> pdb=" O ALA D 808 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N ALA D 808 " --> pdb=" O ASP D 817 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N GLY D 819 " --> pdb=" O VAL D 806 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL D 806 " --> pdb=" O GLY D 819 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N TYR D 804 " --> pdb=" O LYS D 821 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS D 803 " --> pdb=" O TYR D 861 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU D 858 " --> pdb=" O GLU D 869 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AF3, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AF4, first strand: chain 'E' and resid 418 through 421 removed outlier: 3.816A pdb=" N SER E 420 " --> pdb=" O LEU E 412 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE E 476 " --> pdb=" O THR E 365 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 364 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER E 330 " --> pdb=" O SER E 364 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N GLU E 305 " --> pdb=" O THR E 327 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N ASN E 329 " --> pdb=" O GLY E 303 " (cutoff:3.500A) removed outlier: 9.459A pdb=" N GLY E 303 " --> pdb=" O ASN E 329 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN E 392 " --> pdb=" O GLU E 305 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LEU E 307 " --> pdb=" O ASN E 390 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ASN E 390 " --> pdb=" O LEU E 307 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ILE E 309 " --> pdb=" O TYR E 388 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N TYR E 388 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE E 460 " --> pdb=" O ILE E 389 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 352 through 353 removed outlier: 6.053A pdb=" N ASN E 352 " --> pdb=" O PHE E 580 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AF7, first strand: chain 'E' and resid 558 through 559 removed outlier: 3.641A pdb=" N LEU E 564 " --> pdb=" O ILE E 571 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 618 through 620 removed outlier: 6.587A pdb=" N ARG E 668 " --> pdb=" O LEU E 741 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 654 through 659 removed outlier: 3.514A pdb=" N SER E 683 " --> pdb=" O THR E 695 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 768 through 771 Processing sheet with id=AG2, first strand: chain 'E' and resid 816 through 822 removed outlier: 5.123A pdb=" N ASP E 817 " --> pdb=" O ALA E 808 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA E 808 " --> pdb=" O ASP E 817 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLY E 819 " --> pdb=" O VAL E 806 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL E 806 " --> pdb=" O GLY E 819 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS E 803 " --> pdb=" O TYR E 861 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS E 856 " --> pdb=" O LEU E 871 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU E 871 " --> pdb=" O LYS E 856 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU E 858 " --> pdb=" O GLU E 869 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 824 through 827 Processing sheet with id=AG4, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AG5, first strand: chain 'F' and resid 298 through 311 removed outlier: 3.506A pdb=" N ILE F 299 " --> pdb=" O THR F 398 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG F 394 " --> pdb=" O GLY F 303 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 437 through 439 removed outlier: 3.761A pdb=" N ASP F 437 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N TYR F 439 " --> pdb=" O TYR F 395 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 420 through 423 removed outlier: 3.898A pdb=" N SER F 420 " --> pdb=" O LEU F 412 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.552A pdb=" N THR F 489 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 525 through 531 Processing sheet with id=AH1, first strand: chain 'F' and resid 558 through 560 removed outlier: 3.697A pdb=" N THR F 558 " --> pdb=" O TYR F 565 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LEU F 564 " --> pdb=" O ILE F 571 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 651 through 659 Processing sheet with id=AH3, first strand: chain 'F' and resid 707 through 712 removed outlier: 3.629A pdb=" N PHE F 711 " --> pdb=" O TYR F 669 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR F 669 " --> pdb=" O PHE F 711 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 770 through 775 removed outlier: 6.733A pdb=" N ASP F 771 " --> pdb=" O ASN F 784 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN F 775 " --> pdb=" O ASN F 780 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN F 780 " --> pdb=" O ASN F 775 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET F 786 " --> pdb=" O VAL F 840 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL F 840 " --> pdb=" O MET F 786 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 820 through 822 removed outlier: 3.558A pdb=" N LYS F 821 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR F 804 " --> pdb=" O LYS F 821 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N LYS F 803 " --> pdb=" O TYR F 861 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS F 856 " --> pdb=" O LEU F 871 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N LEU F 871 " --> pdb=" O LYS F 856 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU F 858 " --> pdb=" O GLU F 869 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'F' and resid 826 through 827 Processing sheet with id=AH7, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AH8, first strand: chain 'G' and resid 418 through 422 removed outlier: 6.993A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE G 476 " --> pdb=" O THR G 365 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER G 364 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER G 330 " --> pdb=" O SER G 364 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU G 305 " --> pdb=" O THR G 327 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN G 329 " --> pdb=" O GLY G 303 " (cutoff:3.500A) removed outlier: 9.486A pdb=" N GLY G 303 " --> pdb=" O ASN G 329 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N MET G 304 " --> pdb=" O ARG G 394 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ARG G 394 " --> pdb=" O MET G 304 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS G 306 " --> pdb=" O ASN G 392 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE G 460 " --> pdb=" O ILE G 389 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 352 through 353 removed outlier: 6.098A pdb=" N ASN G 352 " --> pdb=" O PHE G 580 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER G 516 " --> pdb=" O ILE G 611 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N ILE G 613 " --> pdb=" O SER G 516 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G 518 " --> pdb=" O ILE G 613 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AI2, first strand: chain 'G' and resid 558 through 559 removed outlier: 3.690A pdb=" N LEU G 564 " --> pdb=" O ILE G 571 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 618 through 620 removed outlier: 6.568A pdb=" N ARG G 668 " --> pdb=" O LEU G 741 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 654 through 659 Processing sheet with id=AI5, first strand: chain 'G' and resid 768 through 771 Processing sheet with id=AI6, first strand: chain 'G' and resid 816 through 822 removed outlier: 3.542A pdb=" N ALA G 808 " --> pdb=" O LYS G 816 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL G 806 " --> pdb=" O ILE G 818 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N THR G 820 " --> pdb=" O TYR G 804 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TYR G 804 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS G 803 " --> pdb=" O TYR G 861 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS G 856 " --> pdb=" O LEU G 871 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N LEU G 871 " --> pdb=" O LYS G 856 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU G 858 " --> pdb=" O GLU G 869 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'G' and resid 824 through 827 Processing sheet with id=AI8, first strand: chain 'H' and resid 235 through 238 Processing sheet with id=AI9, first strand: chain 'H' and resid 303 through 311 removed outlier: 6.822A pdb=" N ASN H 392 " --> pdb=" O GLU H 305 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU H 307 " --> pdb=" O ASN H 390 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ASN H 390 " --> pdb=" O LEU H 307 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE H 309 " --> pdb=" O TYR H 388 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR H 388 " --> pdb=" O ILE H 309 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'H' and resid 420 through 423 removed outlier: 3.744A pdb=" N SER H 420 " --> pdb=" O LEU H 412 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LYS H 405 " --> pdb=" O ASN H 486 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN H 486 " --> pdb=" O LYS H 405 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN H 482 " --> pdb=" O THR H 409 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ASN H 411 " --> pdb=" O THR H 480 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N THR H 480 " --> pdb=" O ASN H 411 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N VAL H 413 " --> pdb=" O LEU H 478 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N LEU H 478 " --> pdb=" O VAL H 413 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'H' and resid 489 through 490 removed outlier: 3.572A pdb=" N THR H 489 " --> pdb=" O VAL H 497 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'H' and resid 525 through 531 Processing sheet with id=AJ4, first strand: chain 'H' and resid 564 through 565 removed outlier: 4.095A pdb=" N LEU H 564 " --> pdb=" O ILE H 571 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'H' and resid 651 through 659 Processing sheet with id=AJ6, first strand: chain 'H' and resid 707 through 710 Processing sheet with id=AJ7, first strand: chain 'H' and resid 770 through 775 removed outlier: 6.682A pdb=" N ASP H 771 " --> pdb=" O ASN H 784 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ASN H 780 " --> pdb=" O ASN H 775 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'H' and resid 816 through 820 removed outlier: 5.429A pdb=" N ASP H 817 " --> pdb=" O ALA H 808 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ALA H 808 " --> pdb=" O ASP H 817 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY H 819 " --> pdb=" O VAL H 806 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL H 806 " --> pdb=" O GLY H 819 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS H 803 " --> pdb=" O TYR H 861 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N LEU H 858 " --> pdb=" O GLU H 869 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'H' and resid 826 through 827 Processing sheet with id=AK1, first strand: chain 'I' and resid 235 through 238 Processing sheet with id=AK2, first strand: chain 'I' and resid 366 through 367 removed outlier: 5.171A pdb=" N GLU I 305 " --> pdb=" O THR I 327 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VAL I 302 " --> pdb=" O TYR I 396 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N TYR I 396 " --> pdb=" O VAL I 302 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N MET I 304 " --> pdb=" O ARG I 394 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ARG I 394 " --> pdb=" O MET I 304 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LYS I 306 " --> pdb=" O ASN I 392 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE I 460 " --> pdb=" O ILE I 389 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'I' and resid 352 through 353 removed outlier: 5.970A pdb=" N ASN I 352 " --> pdb=" O PHE I 580 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N SER I 516 " --> pdb=" O ILE I 611 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ILE I 613 " --> pdb=" O SER I 516 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE I 518 " --> pdb=" O ILE I 613 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'I' and resid 362 through 364 removed outlier: 3.796A pdb=" N SER I 420 " --> pdb=" O LEU I 412 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'I' and resid 489 through 490 removed outlier: 3.547A pdb=" N THR I 489 " --> pdb=" O VAL I 497 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL I 497 " --> pdb=" O THR I 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'I' and resid 558 through 559 removed outlier: 3.753A pdb=" N LEU I 564 " --> pdb=" O ILE I 571 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'I' and resid 618 through 620 removed outlier: 6.594A pdb=" N ARG I 668 " --> pdb=" O LEU I 741 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'I' and resid 654 through 659 removed outlier: 3.680A pdb=" N SER I 683 " --> pdb=" O THR I 695 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR I 695 " --> pdb=" O SER I 683 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'I' and resid 768 through 771 Processing sheet with id=AL1, first strand: chain 'I' and resid 816 through 822 removed outlier: 3.583A pdb=" N ALA I 808 " --> pdb=" O LYS I 816 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL I 806 " --> pdb=" O ILE I 818 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N THR I 820 " --> pdb=" O TYR I 804 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N TYR I 804 " --> pdb=" O THR I 820 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS I 803 " --> pdb=" O TYR I 861 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS I 856 " --> pdb=" O LEU I 871 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N LEU I 871 " --> pdb=" O LYS I 856 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU I 858 " --> pdb=" O GLU I 869 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'I' and resid 824 through 827 Processing sheet with id=AL3, first strand: chain 'J' and resid 235 through 238 Processing sheet with id=AL4, first strand: chain 'J' and resid 298 through 300 Processing sheet with id=AL5, first strand: chain 'J' and resid 303 through 311 removed outlier: 5.712A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'J' and resid 303 through 311 removed outlier: 5.712A pdb=" N MET J 304 " --> pdb=" O ARG J 394 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ARG J 394 " --> pdb=" O MET J 304 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'J' and resid 420 through 423 removed outlier: 3.856A pdb=" N SER J 420 " --> pdb=" O LEU J 412 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LYS J 405 " --> pdb=" O GLY J 485 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N GLY J 485 " --> pdb=" O LYS J 405 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N THR J 407 " --> pdb=" O VAL J 483 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N VAL J 483 " --> pdb=" O THR J 407 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N THR J 409 " --> pdb=" O THR J 481 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'J' and resid 489 through 490 removed outlier: 3.535A pdb=" N THR J 489 " --> pdb=" O VAL J 497 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'J' and resid 525 through 531 Processing sheet with id=AM1, first strand: chain 'J' and resid 558 through 560 removed outlier: 3.601A pdb=" N THR J 558 " --> pdb=" O TYR J 565 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU J 564 " --> pdb=" O ILE J 571 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'J' and resid 652 through 659 Processing sheet with id=AM3, first strand: chain 'J' and resid 707 through 712 Processing sheet with id=AM4, first strand: chain 'J' and resid 770 through 775 removed outlier: 6.799A pdb=" N ASP J 771 " --> pdb=" O ASN J 784 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN J 775 " --> pdb=" O ASN J 780 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ASN J 780 " --> pdb=" O ASN J 775 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'J' and resid 820 through 822 removed outlier: 3.509A pdb=" N LYS J 821 " --> pdb=" O TYR J 804 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR J 804 " --> pdb=" O LYS J 821 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N LYS J 803 " --> pdb=" O TYR J 861 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N LYS J 856 " --> pdb=" O LEU J 871 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU J 871 " --> pdb=" O LYS J 856 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU J 858 " --> pdb=" O GLU J 869 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'J' and resid 824 through 827 Processing sheet with id=AM7, first strand: chain 'K' and resid 235 through 238 Processing sheet with id=AM8, first strand: chain 'K' and resid 418 through 422 removed outlier: 6.920A pdb=" N LEU K 412 " --> pdb=" O LEU K 419 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N THR K 421 " --> pdb=" O THR K 410 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR K 410 " --> pdb=" O THR K 421 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE K 476 " --> pdb=" O THR K 365 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N SER K 364 " --> pdb=" O SER K 330 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER K 330 " --> pdb=" O SER K 364 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N GLU K 305 " --> pdb=" O THR K 327 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N ASN K 329 " --> pdb=" O GLY K 303 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N GLY K 303 " --> pdb=" O ASN K 329 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N VAL K 302 " --> pdb=" O TYR K 396 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR K 396 " --> pdb=" O VAL K 302 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N MET K 304 " --> pdb=" O ARG K 394 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG K 394 " --> pdb=" O MET K 304 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS K 306 " --> pdb=" O ASN K 392 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE K 460 " --> pdb=" O ILE K 389 " (cutoff:3.500A) Processing sheet with id=AM9, first strand: chain 'K' and resid 352 through 353 removed outlier: 5.925A pdb=" N ASN K 352 " --> pdb=" O PHE K 580 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER K 516 " --> pdb=" O ILE K 611 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ILE K 613 " --> pdb=" O SER K 516 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE K 518 " --> pdb=" O ILE K 613 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'K' and resid 489 through 490 Processing sheet with id=AN2, first strand: chain 'K' and resid 558 through 559 removed outlier: 3.594A pdb=" N LEU K 564 " --> pdb=" O ILE K 571 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'K' and resid 618 through 620 removed outlier: 6.563A pdb=" N ARG K 668 " --> pdb=" O LEU K 741 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'K' and resid 654 through 659 removed outlier: 3.609A pdb=" N SER K 683 " --> pdb=" O THR K 695 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR K 695 " --> pdb=" O SER K 683 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'K' and resid 768 through 771 Processing sheet with id=AN6, first strand: chain 'K' and resid 816 through 822 removed outlier: 3.751A pdb=" N ALA K 808 " --> pdb=" O LYS K 816 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL K 806 " --> pdb=" O ILE K 818 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR K 820 " --> pdb=" O TYR K 804 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR K 804 " --> pdb=" O THR K 820 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS K 856 " --> pdb=" O LEU K 871 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU K 871 " --> pdb=" O LYS K 856 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LEU K 858 " --> pdb=" O GLU K 869 " (cutoff:3.500A) Processing sheet with id=AN7, first strand: chain 'K' and resid 824 through 827 Processing sheet with id=AN8, first strand: chain 'L' and resid 235 through 238 Processing sheet with id=AN9, first strand: chain 'L' and resid 300 through 311 removed outlier: 3.714A pdb=" N GLY L 301 " --> pdb=" O TYR L 396 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN L 392 " --> pdb=" O GLU L 305 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU L 307 " --> pdb=" O ASN L 390 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ASN L 390 " --> pdb=" O LEU L 307 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ILE L 309 " --> pdb=" O TYR L 388 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N TYR L 388 " --> pdb=" O ILE L 309 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 'L' and resid 437 through 439 removed outlier: 3.747A pdb=" N ASP L 437 " --> pdb=" O ASN L 397 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR L 439 " --> pdb=" O TYR L 395 " (cutoff:3.500A) Processing sheet with id=AO2, first strand: chain 'L' and resid 420 through 423 removed outlier: 3.842A pdb=" N SER L 420 " --> pdb=" O LEU L 412 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS L 405 " --> pdb=" O GLY L 485 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLY L 485 " --> pdb=" O LYS L 405 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N THR L 407 " --> pdb=" O VAL L 483 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N VAL L 483 " --> pdb=" O THR L 407 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N THR L 409 " --> pdb=" O THR L 481 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'L' and resid 489 through 490 removed outlier: 3.577A pdb=" N THR L 489 " --> pdb=" O VAL L 497 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'L' and resid 525 through 531 Processing sheet with id=AO5, first strand: chain 'L' and resid 558 through 560 removed outlier: 3.812A pdb=" N THR L 558 " --> pdb=" O TYR L 565 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU L 564 " --> pdb=" O ILE L 571 " (cutoff:3.500A) Processing sheet with id=AO6, first strand: chain 'L' and resid 652 through 659 removed outlier: 3.808A pdb=" N THR L 695 " --> pdb=" O SER L 683 " (cutoff:3.500A) Processing sheet with id=AO7, first strand: chain 'L' and resid 707 through 709 Processing sheet with id=AO8, first strand: chain 'L' and resid 770 through 775 removed outlier: 7.159A pdb=" N ASP L 771 " --> pdb=" O ASN L 784 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN L 780 " --> pdb=" O ASN L 775 " (cutoff:3.500A) Processing sheet with id=AO9, first strand: chain 'L' and resid 820 through 822 removed outlier: 3.762A pdb=" N TYR L 804 " --> pdb=" O LYS L 821 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS L 803 " --> pdb=" O TYR L 861 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N LYS L 856 " --> pdb=" O VAL L 872 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL L 872 " --> pdb=" O LYS L 856 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ILE L 860 " --> pdb=" O ARG L 868 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ARG L 868 " --> pdb=" O ILE L 860 " (cutoff:3.500A) Processing sheet with id=AP1, first strand: chain 'L' and resid 824 through 827 Processing sheet with id=AP2, first strand: chain 'M' and resid 235 through 238 Processing sheet with id=AP3, first strand: chain 'M' and resid 418 through 422 removed outlier: 3.683A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE M 476 " --> pdb=" O THR M 365 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU M 305 " --> pdb=" O THR M 327 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA M 391 " --> pdb=" O LEU M 449 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL M 393 " --> pdb=" O LEU M 447 " (cutoff:3.500A) Processing sheet with id=AP4, first strand: chain 'M' and resid 418 through 422 removed outlier: 3.683A pdb=" N SER M 420 " --> pdb=" O LEU M 412 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE M 476 " --> pdb=" O THR M 365 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU M 305 " --> pdb=" O THR M 327 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N MET M 304 " --> pdb=" O ARG M 394 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG M 394 " --> pdb=" O MET M 304 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS M 306 " --> pdb=" O ASN M 392 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE M 460 " --> pdb=" O ILE M 389 " (cutoff:3.500A) Processing sheet with id=AP5, first strand: chain 'M' and resid 352 through 353 removed outlier: 5.885A pdb=" N ASN M 352 " --> pdb=" O PHE M 580 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER M 516 " --> pdb=" O ILE M 611 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N ILE M 613 " --> pdb=" O SER M 516 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE M 518 " --> pdb=" O ILE M 613 " (cutoff:3.500A) Processing sheet with id=AP6, first strand: chain 'M' and resid 489 through 490 Processing sheet with id=AP7, first strand: chain 'M' and resid 558 through 559 removed outlier: 3.635A pdb=" N LEU M 564 " --> pdb=" O ILE M 571 " (cutoff:3.500A) Processing sheet with id=AP8, first strand: chain 'M' and resid 618 through 621 removed outlier: 5.291A pdb=" N ASN M 735 " --> pdb=" O TYR M 674 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR M 674 " --> pdb=" O ASN M 735 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG M 668 " --> pdb=" O LEU M 741 " (cutoff:3.500A) Processing sheet with id=AP9, first strand: chain 'M' and resid 654 through 659 removed outlier: 3.706A pdb=" N SER M 683 " --> pdb=" O THR M 695 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR M 695 " --> pdb=" O SER M 683 " (cutoff:3.500A) Processing sheet with id=AQ1, first strand: chain 'M' and resid 768 through 771 Processing sheet with id=AQ2, first strand: chain 'M' and resid 816 through 822 removed outlier: 3.846A pdb=" N VAL M 806 " --> pdb=" O ILE M 818 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR M 820 " --> pdb=" O TYR M 804 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR M 804 " --> pdb=" O THR M 820 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS M 803 " --> pdb=" O TYR M 861 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR M 861 " --> pdb=" O LYS M 803 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LYS M 856 " --> pdb=" O LEU M 871 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU M 871 " --> pdb=" O LYS M 856 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LEU M 858 " --> pdb=" O GLU M 869 " (cutoff:3.500A) Processing sheet with id=AQ3, first strand: chain 'M' and resid 824 through 827 Processing sheet with id=AQ4, first strand: chain 'Z' and resid 235 through 238 Processing sheet with id=AQ5, first strand: chain 'Z' and resid 418 through 422 removed outlier: 3.899A pdb=" N SER Z 420 " --> pdb=" O LEU Z 412 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE Z 476 " --> pdb=" O THR Z 365 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N SER Z 364 " --> pdb=" O SER Z 330 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER Z 330 " --> pdb=" O SER Z 364 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU Z 305 " --> pdb=" O THR Z 327 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N ASN Z 329 " --> pdb=" O GLY Z 303 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N GLY Z 303 " --> pdb=" O ASN Z 329 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N VAL Z 302 " --> pdb=" O TYR Z 396 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N TYR Z 396 " --> pdb=" O VAL Z 302 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N MET Z 304 " --> pdb=" O ARG Z 394 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG Z 394 " --> pdb=" O MET Z 304 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS Z 306 " --> pdb=" O ASN Z 392 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE Z 460 " --> pdb=" O ILE Z 389 " (cutoff:3.500A) Processing sheet with id=AQ6, first strand: chain 'Z' and resid 352 through 353 removed outlier: 6.030A pdb=" N ASN Z 352 " --> pdb=" O PHE Z 580 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N SER Z 516 " --> pdb=" O ILE Z 611 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ILE Z 613 " --> pdb=" O SER Z 516 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE Z 518 " --> pdb=" O ILE Z 613 " (cutoff:3.500A) Processing sheet with id=AQ7, first strand: chain 'Z' and resid 489 through 490 Processing sheet with id=AQ8, first strand: chain 'Z' and resid 558 through 559 removed outlier: 3.660A pdb=" N LEU Z 564 " --> pdb=" O ILE Z 571 " (cutoff:3.500A) Processing sheet with id=AQ9, first strand: chain 'Z' and resid 618 through 620 removed outlier: 6.481A pdb=" N ARG Z 668 " --> pdb=" O LEU Z 741 " (cutoff:3.500A) Processing sheet with id=AR1, first strand: chain 'Z' and resid 654 through 659 Processing sheet with id=AR2, first strand: chain 'Z' and resid 768 through 771 removed outlier: 3.503A pdb=" N MET Z 786 " --> pdb=" O VAL Z 840 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE Z 788 " --> pdb=" O ASN Z 838 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ASN Z 838 " --> pdb=" O PHE Z 788 " (cutoff:3.500A) Processing sheet with id=AR3, first strand: chain 'Z' and resid 816 through 822 removed outlier: 3.791A pdb=" N VAL Z 806 " --> pdb=" O ILE Z 818 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR Z 820 " --> pdb=" O TYR Z 804 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N TYR Z 804 " --> pdb=" O THR Z 820 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS Z 803 " --> pdb=" O TYR Z 861 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N TYR Z 861 " --> pdb=" O LYS Z 803 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LYS Z 856 " --> pdb=" O LEU Z 871 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU Z 871 " --> pdb=" O LYS Z 856 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N LEU Z 858 " --> pdb=" O GLU Z 869 " (cutoff:3.500A) 1917 hydrogen bonds defined for protein. 4992 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: 34.28 Time building geometry restraints manager: 24.66 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: 22620 1.33 - 1.45: 11035 1.45 - 1.57: 40067 1.57 - 1.69: 7 1.69 - 1.81: 266 Bond restraints: 73995 Sorted by residual: bond pdb=" CA HIS L 314 " pdb=" CB HIS L 314 " ideal model delta sigma weight residual 1.522 1.478 0.044 1.27e-02 6.20e+03 1.20e+01 bond pdb=" CA ASP K 749 " pdb=" CB ASP K 749 " ideal model delta sigma weight residual 1.536 1.661 -0.125 4.10e-02 5.95e+02 9.25e+00 bond pdb=" CA ASP I 749 " pdb=" CB ASP I 749 " ideal model delta sigma weight residual 1.536 1.655 -0.119 4.10e-02 5.95e+02 8.43e+00 bond pdb=" CA ASP Z 749 " pdb=" CB ASP Z 749 " ideal model delta sigma weight residual 1.539 1.670 -0.131 4.88e-02 4.20e+02 7.21e+00 bond pdb=" C ASP C 677 " pdb=" N PRO C 678 " ideal model delta sigma weight residual 1.334 1.356 -0.022 8.40e-03 1.42e+04 6.92e+00 ... (remaining 73990 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.41: 1715 106.41 - 113.61: 40752 113.61 - 120.81: 31327 120.81 - 128.01: 26294 128.01 - 135.22: 357 Bond angle restraints: 100445 Sorted by residual: angle pdb=" N GLY F 652 " pdb=" CA GLY F 652 " pdb=" C GLY F 652 " ideal model delta sigma weight residual 111.21 116.85 -5.64 1.04e+00 9.25e-01 2.94e+01 angle pdb=" N THR E 864 " pdb=" CA THR E 864 " pdb=" C THR E 864 " ideal model delta sigma weight residual 109.81 121.77 -11.96 2.21e+00 2.05e-01 2.93e+01 angle pdb=" N THR C 864 " pdb=" CA THR C 864 " pdb=" C THR C 864 " ideal model delta sigma weight residual 109.81 121.72 -11.91 2.21e+00 2.05e-01 2.90e+01 angle pdb=" N THR Z 864 " pdb=" CA THR Z 864 " pdb=" C THR Z 864 " ideal model delta sigma weight residual 109.81 121.68 -11.87 2.21e+00 2.05e-01 2.89e+01 angle pdb=" N THR M 864 " pdb=" CA THR M 864 " pdb=" C THR M 864 " ideal model delta sigma weight residual 109.81 121.59 -11.78 2.21e+00 2.05e-01 2.84e+01 ... (remaining 100440 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 39623 18.00 - 36.00: 4365 36.00 - 54.00: 781 54.00 - 72.00: 83 72.00 - 89.99: 33 Dihedral angle restraints: 44885 sinusoidal: 17819 harmonic: 27066 Sorted by residual: dihedral pdb=" CA ILE G 863 " pdb=" C ILE G 863 " pdb=" N THR G 864 " pdb=" CA THR G 864 " ideal model delta harmonic sigma weight residual -180.00 -136.54 -43.46 0 5.00e+00 4.00e-02 7.55e+01 dihedral pdb=" CA ILE Z 863 " pdb=" C ILE Z 863 " pdb=" N THR Z 864 " pdb=" CA THR Z 864 " ideal model delta harmonic sigma weight residual -180.00 -137.10 -42.90 0 5.00e+00 4.00e-02 7.36e+01 dihedral pdb=" CA ILE I 863 " pdb=" C ILE I 863 " pdb=" N THR I 864 " pdb=" CA THR I 864 " ideal model delta harmonic sigma weight residual -180.00 -138.05 -41.95 0 5.00e+00 4.00e-02 7.04e+01 ... (remaining 44882 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 9350 0.074 - 0.148: 1700 0.148 - 0.222: 165 0.222 - 0.296: 32 0.296 - 0.370: 15 Chirality restraints: 11262 Sorted by residual: chirality pdb=" CB ILE B 761 " pdb=" CA ILE B 761 " pdb=" CG1 ILE B 761 " pdb=" CG2 ILE B 761 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB THR D 864 " pdb=" CA THR D 864 " pdb=" OG1 THR D 864 " pdb=" CG2 THR D 864 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.04e+00 chirality pdb=" CB THR A 864 " pdb=" CA THR A 864 " pdb=" OG1 THR A 864 " pdb=" CG2 THR A 864 " both_signs ideal model delta sigma weight residual False 2.55 2.20 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 11259 not shown) Planarity restraints: 13130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR J 230 " -0.026 2.00e-02 2.50e+03 2.06e-02 8.45e+00 pdb=" CG TYR J 230 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR J 230 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR J 230 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR J 230 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR J 230 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR J 230 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR J 230 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP Z 291 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO Z 292 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO Z 292 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO Z 292 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP K 291 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO K 292 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO K 292 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO K 292 " -0.036 5.00e-02 4.00e+02 ... (remaining 13127 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 18685 2.79 - 3.32: 60115 3.32 - 3.85: 110666 3.85 - 4.37: 119536 4.37 - 4.90: 218788 Nonbonded interactions: 527790 Sorted by model distance: nonbonded pdb=" O TYR B 618 " pdb=" OG SER B 737 " model vdw 2.266 2.440 nonbonded pdb=" OG1 THR E 266 " pdb=" O PRO E 292 " model vdw 2.273 2.440 nonbonded pdb=" OG SER Z 334 " pdb=" OG SER Z 358 " model vdw 2.278 2.440 nonbonded pdb=" OG SER E 334 " pdb=" OG SER E 358 " model vdw 2.282 2.440 nonbonded pdb=" OG SER G 334 " pdb=" OG SER G 358 " model vdw 2.283 2.440 ... (remaining 527785 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 216 through 872) selection = (chain 'B' and resid 216 through 872) selection = (chain 'C' and resid 216 through 872) selection = (chain 'D' and resid 216 through 872) selection = (chain 'E' and resid 216 through 872) selection = (chain 'F' and resid 216 through 872) selection = (chain 'G' and resid 216 through 872) selection = (chain 'H' and resid 216 through 872) selection = (chain 'I' and resid 216 through 872) selection = (chain 'J' and resid 216 through 872) selection = (chain 'K' and resid 216 through 872) selection = (chain 'L' and resid 216 through 872) selection = (chain 'M' and resid 216 through 872) selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 140 5.16 5 C 45474 2.51 5 N 11801 2.21 5 O 15222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 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: 8.900 Check model and map are aligned: 0.840 Convert atoms to be neutral: 0.490 Process input model: 156.090 Find NCS groups from input model: 4.960 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 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 : 0.006 0.131 73995 Z= 0.395 Angle : 0.931 17.344 100445 Z= 0.517 Chirality : 0.058 0.370 11262 Planarity : 0.006 0.069 13130 Dihedral : 14.998 89.994 27597 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.67 % Favored : 90.33 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.61 (0.07), residues: 9190 helix: -4.58 (0.06), residues: 959 sheet: -1.73 (0.10), residues: 2318 loop : -3.58 (0.06), residues: 5913 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 664 time to evaluate : 6.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 23 residues processed: 707 average time/residue: 0.7147 time to fit residues: 867.0448 Evaluate side-chains 471 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 448 time to evaluate : 6.879 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.5157 time to fit residues: 31.8279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 768 optimal weight: 0.5980 chunk 689 optimal weight: 3.9990 chunk 382 optimal weight: 3.9990 chunk 235 optimal weight: 8.9990 chunk 465 optimal weight: 20.0000 chunk 368 optimal weight: 1.9990 chunk 713 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 433 optimal weight: 7.9990 chunk 530 optimal weight: 0.0060 chunk 826 optimal weight: 7.9990 overall best weight: 2.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 397 ASN A 602 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 651 ASN A 735 ASN B 397 ASN B 509 GLN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 651 ASN B 682 ASN B 735 ASN ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 627 ASN C 682 ASN C 735 ASN C 811 GLN C 841 ASN D 636 ASN D 644 GLN D 651 ASN D 682 ASN D 720 ASN D 735 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN E 450 ASN E 644 GLN E 735 ASN E 775 ASN E 811 GLN E 838 ASN E 841 ASN F 432 ASN F 648 ASN F 651 ASN F 735 ASN G 450 ASN G 644 GLN G 651 ASN G 735 ASN G 811 GLN G 838 ASN G 841 ASN H 397 ASN ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 644 GLN H 651 ASN H 735 ASN H 838 ASN I 335 ASN I 735 ASN I 811 GLN ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 841 ASN J 428 GLN J 644 GLN J 651 ASN J 735 ASN J 792 GLN ** K 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 491 ASN K 682 ASN K 735 ASN K 811 GLN K 838 ASN L 431 ASN ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 644 GLN L 651 ASN L 735 ASN M 335 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN M 651 ASN M 682 ASN M 735 ASN M 811 GLN M 827 ASN M 838 ASN M 841 ASN ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 735 ASN Z 811 GLN Z 838 ASN Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 73995 Z= 0.184 Angle : 0.601 11.361 100445 Z= 0.316 Chirality : 0.045 0.223 11262 Planarity : 0.004 0.056 13130 Dihedral : 5.857 37.079 9974 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.90 (0.07), residues: 9190 helix: -3.59 (0.11), residues: 968 sheet: -1.02 (0.10), residues: 2433 loop : -3.32 (0.07), residues: 5789 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 513 time to evaluate : 7.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 67 residues processed: 608 average time/residue: 0.6432 time to fit residues: 682.3020 Evaluate side-chains 502 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 435 time to evaluate : 6.849 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.4898 time to fit residues: 72.2078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 459 optimal weight: 9.9990 chunk 256 optimal weight: 9.9990 chunk 687 optimal weight: 0.8980 chunk 562 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 827 optimal weight: 9.9990 chunk 894 optimal weight: 6.9990 chunk 737 optimal weight: 6.9990 chunk 820 optimal weight: 9.9990 chunk 282 optimal weight: 2.9990 chunk 664 optimal weight: 9.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 432 ASN ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 792 GLN B 432 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 636 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN E 432 ASN E 450 ASN E 454 GLN E 495 GLN F 397 ASN F 792 GLN F 838 ASN G 450 ASN G 775 ASN ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 73995 Z= 0.291 Angle : 0.632 9.877 100445 Z= 0.333 Chirality : 0.046 0.269 11262 Planarity : 0.004 0.056 13130 Dihedral : 5.743 35.842 9974 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.57 (0.08), residues: 9190 helix: -2.93 (0.13), residues: 968 sheet: -0.80 (0.10), residues: 2426 loop : -3.18 (0.07), residues: 5796 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 460 time to evaluate : 7.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 126 residues processed: 633 average time/residue: 0.6466 time to fit residues: 716.8755 Evaluate side-chains 551 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 425 time to evaluate : 6.874 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 0 residues processed: 126 average time/residue: 0.5089 time to fit residues: 130.8237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 817 optimal weight: 10.0000 chunk 622 optimal weight: 3.9990 chunk 429 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 395 optimal weight: 7.9990 chunk 555 optimal weight: 1.9990 chunk 830 optimal weight: 8.9990 chunk 879 optimal weight: 3.9990 chunk 434 optimal weight: 6.9990 chunk 787 optimal weight: 0.0980 chunk 237 optimal weight: 30.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- 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** B 347 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN D 636 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN E 450 ASN E 454 GLN E 495 GLN F 792 GLN ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 454 GLN ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 636 ASN M 432 ASN ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 651 ASN ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 495 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 73995 Z= 0.222 Angle : 0.589 9.643 100445 Z= 0.308 Chirality : 0.045 0.290 11262 Planarity : 0.004 0.054 13130 Dihedral : 5.435 36.474 9974 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 2.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.26 (0.08), residues: 9190 helix: -2.58 (0.14), residues: 925 sheet: -0.89 (0.10), residues: 2594 loop : -2.88 (0.07), residues: 5671 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 465 time to evaluate : 7.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 80 residues processed: 605 average time/residue: 0.6417 time to fit residues: 678.1805 Evaluate side-chains 514 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 434 time to evaluate : 6.900 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.5115 time to fit residues: 86.9944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 732 optimal weight: 7.9990 chunk 499 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 654 optimal weight: 8.9990 chunk 362 optimal weight: 9.9990 chunk 750 optimal weight: 10.0000 chunk 608 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 449 optimal weight: 5.9990 chunk 789 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 223 ASN B 610 ASN ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN C 495 GLN D 610 ASN D 636 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN ** E 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 610 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN H 346 GLN H 509 GLN ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 432 ASN ** I 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 223 ASN J 610 ASN J 794 ASN K 314 HIS K 495 GLN K 627 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 431 ASN L 610 ASN ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 495 GLN M 627 ASN ** M 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 495 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.075 73995 Z= 0.536 Angle : 0.785 12.967 100445 Z= 0.412 Chirality : 0.050 0.365 11262 Planarity : 0.005 0.055 13130 Dihedral : 6.195 37.959 9974 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.06 % Favored : 87.94 % Rotamer Outliers : 3.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.08), residues: 9190 helix: -2.53 (0.14), residues: 968 sheet: -0.88 (0.10), residues: 2522 loop : -3.06 (0.07), residues: 5700 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 246 poor density : 441 time to evaluate : 6.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 246 outliers final: 153 residues processed: 652 average time/residue: 0.6262 time to fit residues: 719.4028 Evaluate side-chains 567 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 414 time to evaluate : 6.880 Switching outliers to nearest non-outliers outliers start: 153 outliers final: 0 residues processed: 153 average time/residue: 0.5185 time to fit residues: 159.5109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 295 optimal weight: 9.9990 chunk 792 optimal weight: 3.9990 chunk 173 optimal weight: 30.0000 chunk 516 optimal weight: 0.0370 chunk 217 optimal weight: 3.9990 chunk 880 optimal weight: 9.9990 chunk 730 optimal weight: 5.9990 chunk 407 optimal weight: 8.9990 chunk 73 optimal weight: 5.9990 chunk 291 optimal weight: 3.9990 chunk 462 optimal weight: 3.9990 overall best weight: 3.2066 ------------------------------------------------------------------------------- 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 838 ASN B 636 ASN C 495 GLN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN K 329 ASN K 627 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 636 ASN L 794 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 450 ASN M 627 ASN ** M 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 495 GLN ** Z 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 73995 Z= 0.231 Angle : 0.618 11.393 100445 Z= 0.322 Chirality : 0.046 0.355 11262 Planarity : 0.004 0.055 13130 Dihedral : 5.655 38.136 9974 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.38 % Favored : 91.62 % Rotamer Outliers : 1.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.11 (0.08), residues: 9190 helix: -2.33 (0.15), residues: 925 sheet: -0.82 (0.10), residues: 2650 loop : -2.80 (0.08), residues: 5615 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 451 time to evaluate : 7.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 116 outliers final: 61 residues processed: 556 average time/residue: 0.6802 time to fit residues: 664.9342 Evaluate side-chains 487 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 426 time to evaluate : 7.036 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.5283 time to fit residues: 70.3571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 848 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 501 optimal weight: 10.0000 chunk 642 optimal weight: 6.9990 chunk 498 optimal weight: 0.0270 chunk 741 optimal weight: 10.0000 chunk 491 optimal weight: 0.0770 chunk 877 optimal weight: 0.0040 chunk 548 optimal weight: 9.9990 chunk 534 optimal weight: 8.9990 chunk 404 optimal weight: 10.0000 overall best weight: 3.0212 ------------------------------------------------------------------------------- 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** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 610 ASN ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN E 627 ASN F 794 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 636 ASN ** I 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 329 ASN K 486 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 636 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 73995 Z= 0.219 Angle : 0.602 12.694 100445 Z= 0.312 Chirality : 0.045 0.315 11262 Planarity : 0.004 0.054 13130 Dihedral : 5.360 36.465 9974 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.98 (0.08), residues: 9190 helix: -2.17 (0.15), residues: 922 sheet: -0.69 (0.10), residues: 2580 loop : -2.73 (0.08), residues: 5688 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 447 time to evaluate : 8.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 44 residues processed: 530 average time/residue: 0.6827 time to fit residues: 632.5541 Evaluate side-chains 465 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 421 time to evaluate : 6.982 Switching outliers to nearest non-outliers outliers start: 44 outliers final: 0 residues processed: 44 average time/residue: 0.5373 time to fit residues: 53.5372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 542 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 523 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 169 optimal weight: 4.9990 chunk 557 optimal weight: 8.9990 chunk 597 optimal weight: 4.9990 chunk 433 optimal weight: 30.0000 chunk 81 optimal weight: 7.9990 chunk 689 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 ASN ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN E 627 ASN E 682 ASN F 794 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 610 ASN H 636 ASN ** I 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 838 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 627 ASN ** M 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.073 73995 Z= 0.369 Angle : 0.688 15.841 100445 Z= 0.357 Chirality : 0.047 0.330 11262 Planarity : 0.004 0.055 13130 Dihedral : 5.710 36.774 9974 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer Outliers : 1.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -3.01 (0.08), residues: 9190 helix: -2.13 (0.15), residues: 916 sheet: -0.69 (0.10), residues: 2594 loop : -2.78 (0.08), residues: 5680 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 424 time to evaluate : 6.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 64 residues processed: 501 average time/residue: 0.6829 time to fit residues: 599.8789 Evaluate side-chains 480 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 416 time to evaluate : 6.985 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.5495 time to fit residues: 74.9448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 797 optimal weight: 10.0000 chunk 840 optimal weight: 10.0000 chunk 766 optimal weight: 40.0000 chunk 817 optimal weight: 10.0000 chunk 491 optimal weight: 2.9990 chunk 356 optimal weight: 0.8980 chunk 641 optimal weight: 2.9990 chunk 250 optimal weight: 9.9990 chunk 738 optimal weight: 0.9990 chunk 773 optimal weight: 1.9990 chunk 814 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 759 GLN D 794 ASN F 794 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 314 HIS ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 841 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 636 ASN ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 73995 Z= 0.173 Angle : 0.589 16.297 100445 Z= 0.304 Chirality : 0.045 0.293 11262 Planarity : 0.004 0.054 13130 Dihedral : 5.198 35.312 9974 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.98 % Favored : 92.02 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.84 (0.08), residues: 9190 helix: -2.00 (0.16), residues: 922 sheet: -0.62 (0.10), residues: 2581 loop : -2.62 (0.08), residues: 5687 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 464 time to evaluate : 7.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 11 residues processed: 486 average time/residue: 0.6676 time to fit residues: 564.9996 Evaluate side-chains 438 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 427 time to evaluate : 6.923 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.5832 time to fit residues: 20.9427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 536 optimal weight: 20.0000 chunk 864 optimal weight: 5.9990 chunk 527 optimal weight: 0.7980 chunk 410 optimal weight: 9.9990 chunk 600 optimal weight: 10.0000 chunk 906 optimal weight: 7.9990 chunk 834 optimal weight: 1.9990 chunk 721 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 557 optimal weight: 8.9990 chunk 442 optimal weight: 6.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 792 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN F 346 GLN F 794 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 794 ASN ** I 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 792 GLN L 794 ASN ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 73995 Z= 0.267 Angle : 0.636 13.694 100445 Z= 0.328 Chirality : 0.046 0.233 11262 Planarity : 0.004 0.054 13130 Dihedral : 5.303 34.655 9974 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.48 % Favored : 90.52 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.82 (0.08), residues: 9190 helix: -1.98 (0.16), residues: 922 sheet: -0.62 (0.10), residues: 2580 loop : -2.61 (0.08), residues: 5688 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18380 Ramachandran restraints generated. 9190 Oldfield, 0 Emsley, 9190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 434 time to evaluate : 7.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 20 residues processed: 459 average time/residue: 0.6832 time to fit residues: 547.6039 Evaluate side-chains 445 residues out of total 8182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 425 time to evaluate : 7.036 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5390 time to fit residues: 29.7277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 910 random chunks: chunk 573 optimal weight: 6.9990 chunk 769 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 665 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 200 optimal weight: 5.9990 chunk 723 optimal weight: 2.9990 chunk 302 optimal weight: 3.9990 chunk 742 optimal weight: 0.9990 chunk 91 optimal weight: 0.0770 chunk 133 optimal weight: 1.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- 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** ** B 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 794 ASN F 759 GLN F 794 ASN ** G 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 794 ASN ** I 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 794 ASN ** K 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 329 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 411 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.113775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.090255 restraints weight = 159762.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.092284 restraints weight = 87858.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.092627 restraints weight = 60349.460| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 73995 Z= 0.173 Angle : 0.589 16.033 100445 Z= 0.302 Chirality : 0.045 0.225 11262 Planarity : 0.004 0.062 13130 Dihedral : 5.018 33.747 9974 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.85 % 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: -2.63 (0.08), residues: 9190 helix: -1.77 (0.16), residues: 892 sheet: -0.52 (0.10), residues: 2581 loop : -2.48 (0.08), residues: 5717 =============================================================================== Job complete usr+sys time: 11783.41 seconds wall clock time: 212 minutes 20.73 seconds (12740.73 seconds total)