Starting phenix.real_space_refine (version: dev) on Fri Mar 17 17:41:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/03_2023/6toa_10542.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/03_2023/6toa_10542.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/03_2023/6toa_10542.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/03_2023/6toa_10542.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/03_2023/6toa_10542.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6toa_10542/03_2023/6toa_10542.pdb" } resolution = 3.47 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= 0.002 sd= 0.024 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 Process input model Symmetric amino acids flipped Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 64": "NH1" <-> "NH2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C ARG 113": "NH1" <-> "NH2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C ARG 186": "NH1" <-> "NH2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 51": "NH1" <-> "NH2" Residue "A ARG 95": "NH1" <-> "NH2" Residue "A ARG 103": "NH1" <-> "NH2" Residue "A ARG 139": "NH1" <-> "NH2" Residue "A ARG 220": "NH1" <-> "NH2" Residue "A ARG 320": "NH1" <-> "NH2" Residue "A ARG 324": "NH1" <-> "NH2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 372": "NH1" <-> "NH2" Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 38": "NH1" <-> "NH2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 51": "NH1" <-> "NH2" Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ARG 95": "NH1" <-> "NH2" Residue "B ARG 103": "NH1" <-> "NH2" Residue "B ARG 139": "NH1" <-> "NH2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 320": "NH1" <-> "NH2" Residue "B TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ARG 333": "NH1" <-> "NH2" Residue "B ARG 372": "NH1" <-> "NH2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 61": "NH1" <-> "NH2" Residue "D ARG 64": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 186": "NH1" <-> "NH2" Residue "D ARG 188": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "E ARG 5": "NH1" <-> "NH2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 73": "NH1" <-> "NH2" Residue "E ARG 75": "NH1" <-> "NH2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G ARG 31": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 60": "NH1" <-> "NH2" Residue "G ARG 80": "NH1" <-> "NH2" Residue "H ARG 61": "NH1" <-> "NH2" Residue "H ARG 64": "NH1" <-> "NH2" Residue "H ARG 71": "NH1" <-> "NH2" Residue "H ARG 113": "NH1" <-> "NH2" Residue "H ARG 115": "NH1" <-> "NH2" Residue "H ARG 186": "NH1" <-> "NH2" Residue "H ARG 188": "NH1" <-> "NH2" Residue "I ARG 38": "NH1" <-> "NH2" Residue "I ARG 51": "NH1" <-> "NH2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "I ARG 139": "NH1" <-> "NH2" Residue "I ARG 220": "NH1" <-> "NH2" Residue "I ARG 320": "NH1" <-> "NH2" Residue "I ARG 324": "NH1" <-> "NH2" Residue "I ARG 333": "NH1" <-> "NH2" Residue "I ARG 372": "NH1" <-> "NH2" Residue "I PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 38": "NH1" <-> "NH2" Residue "J ARG 44": "NH1" <-> "NH2" Residue "J ARG 51": "NH1" <-> "NH2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "J ARG 139": "NH1" <-> "NH2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J ARG 320": "NH1" <-> "NH2" Residue "J TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 324": "NH1" <-> "NH2" Residue "J ARG 333": "NH1" <-> "NH2" Residue "J ARG 372": "NH1" <-> "NH2" Residue "J PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 24": "NH1" <-> "NH2" Residue "K ARG 61": "NH1" <-> "NH2" Residue "K ARG 64": "NH1" <-> "NH2" Residue "K ARG 113": "NH1" <-> "NH2" Residue "K ARG 115": "NH1" <-> "NH2" Residue "K ARG 131": "NH1" <-> "NH2" Residue "K ARG 186": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 101": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 72": "NH1" <-> "NH2" Residue "M ARG 73": "NH1" <-> "NH2" Residue "M ARG 75": "NH1" <-> "NH2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 97": "NH1" <-> "NH2" Residue "N ARG 28": "NH1" <-> "NH2" Residue "N ARG 31": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N ARG 80": "NH1" <-> "NH2" Residue "O ARG 61": "NH1" <-> "NH2" Residue "O ARG 64": "NH1" <-> "NH2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O ARG 113": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "O ARG 186": "NH1" <-> "NH2" Residue "O ARG 188": "NH1" <-> "NH2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 95": "NH1" <-> "NH2" Residue "P ARG 103": "NH1" <-> "NH2" Residue "P ARG 139": "NH1" <-> "NH2" Residue "P ARG 220": "NH1" <-> "NH2" Residue "P ARG 320": "NH1" <-> "NH2" Residue "P ARG 324": "NH1" <-> "NH2" Residue "P ARG 333": "NH1" <-> "NH2" Residue "P ARG 372": "NH1" <-> "NH2" Residue "P PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 38": "NH1" <-> "NH2" Residue "Q ARG 44": "NH1" <-> "NH2" Residue "Q ARG 51": "NH1" <-> "NH2" Residue "Q ASP 80": "OD1" <-> "OD2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q ARG 103": "NH1" <-> "NH2" Residue "Q ARG 139": "NH1" <-> "NH2" Residue "Q ARG 220": "NH1" <-> "NH2" Residue "Q ARG 320": "NH1" <-> "NH2" Residue "Q TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 333": "NH1" <-> "NH2" Residue "Q ARG 372": "NH1" <-> "NH2" Residue "Q PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 24": "NH1" <-> "NH2" Residue "R ARG 61": "NH1" <-> "NH2" Residue "R ARG 64": "NH1" <-> "NH2" Residue "R ARG 113": "NH1" <-> "NH2" Residue "R ARG 115": "NH1" <-> "NH2" Residue "R ARG 131": "NH1" <-> "NH2" Residue "R ARG 186": "NH1" <-> "NH2" Residue "R ARG 188": "NH1" <-> "NH2" Residue "S ARG 18": "NH1" <-> "NH2" Residue "S TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 101": "NH1" <-> "NH2" Residue "T ARG 5": "NH1" <-> "NH2" Residue "T ARG 47": "NH1" <-> "NH2" Residue "T ARG 72": "NH1" <-> "NH2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T ARG 75": "NH1" <-> "NH2" Residue "T ARG 81": "NH1" <-> "NH2" Residue "T ARG 97": "NH1" <-> "NH2" Residue "U ARG 28": "NH1" <-> "NH2" Residue "U ARG 31": "NH1" <-> "NH2" Residue "U ARG 51": "NH1" <-> "NH2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "V ARG 61": "NH1" <-> "NH2" Residue "V ARG 64": "NH1" <-> "NH2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "V ARG 113": "NH1" <-> "NH2" Residue "V ARG 115": "NH1" <-> "NH2" Residue "V ARG 186": "NH1" <-> "NH2" Residue "V ARG 188": "NH1" <-> "NH2" Residue "W ARG 38": "NH1" <-> "NH2" Residue "W ARG 51": "NH1" <-> "NH2" Residue "W ARG 95": "NH1" <-> "NH2" Residue "W ARG 103": "NH1" <-> "NH2" Residue "W ARG 139": "NH1" <-> "NH2" Residue "W ARG 220": "NH1" <-> "NH2" Residue "W ARG 320": "NH1" <-> "NH2" Residue "W ARG 324": "NH1" <-> "NH2" Residue "W ARG 333": "NH1" <-> "NH2" Residue "W ARG 372": "NH1" <-> "NH2" Residue "W PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 38": "NH1" <-> "NH2" Residue "X ARG 44": "NH1" <-> "NH2" Residue "X ARG 51": "NH1" <-> "NH2" Residue "X ASP 80": "OD1" <-> "OD2" Residue "X ARG 95": "NH1" <-> "NH2" Residue "X ARG 103": "NH1" <-> "NH2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "X ARG 220": "NH1" <-> "NH2" Residue "X ARG 320": "NH1" <-> "NH2" Residue "X TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 324": "NH1" <-> "NH2" Residue "X ARG 333": "NH1" <-> "NH2" Residue "X ARG 372": "NH1" <-> "NH2" Residue "X PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 24": "NH1" <-> "NH2" Residue "Y ARG 61": "NH1" <-> "NH2" Residue "Y ARG 64": "NH1" <-> "NH2" Residue "Y ARG 113": "NH1" <-> "NH2" Residue "Y ARG 115": "NH1" <-> "NH2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "Y ARG 186": "NH1" <-> "NH2" Residue "Y ARG 188": "NH1" <-> "NH2" Residue "Z ARG 18": "NH1" <-> "NH2" Residue "Z TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 101": "NH1" <-> "NH2" Residue "0 ARG 5": "NH1" <-> "NH2" Residue "0 ARG 47": "NH1" <-> "NH2" Residue "0 ARG 72": "NH1" <-> "NH2" Residue "0 ARG 73": "NH1" <-> "NH2" Residue "0 ARG 75": "NH1" <-> "NH2" Residue "0 ARG 81": "NH1" <-> "NH2" Residue "0 ARG 97": "NH1" <-> "NH2" Residue "1 ARG 28": "NH1" <-> "NH2" Residue "1 ARG 31": "NH1" <-> "NH2" Residue "1 ARG 51": "NH1" <-> "NH2" Residue "1 ARG 60": "NH1" <-> "NH2" Residue "1 ARG 80": "NH1" <-> "NH2" Residue "2 ARG 61": "NH1" <-> "NH2" Residue "2 ARG 64": "NH1" <-> "NH2" Residue "2 ARG 71": "NH1" <-> "NH2" Residue "2 ARG 113": "NH1" <-> "NH2" Residue "2 ARG 115": "NH1" <-> "NH2" Residue "2 ARG 186": "NH1" <-> "NH2" Residue "2 ARG 188": "NH1" <-> "NH2" Residue "3 ARG 38": "NH1" <-> "NH2" Residue "3 ARG 51": "NH1" <-> "NH2" Residue "3 ARG 95": "NH1" <-> "NH2" Residue "3 ARG 103": "NH1" <-> "NH2" Residue "3 ARG 139": "NH1" <-> "NH2" Residue "3 ARG 220": "NH1" <-> "NH2" Residue "3 ARG 320": "NH1" <-> "NH2" Residue "3 ARG 324": "NH1" <-> "NH2" Residue "3 ARG 333": "NH1" <-> "NH2" Residue "3 ARG 372": "NH1" <-> "NH2" Residue "3 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 38": "NH1" <-> "NH2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "4 ARG 51": "NH1" <-> "NH2" Residue "4 ASP 80": "OD1" <-> "OD2" Residue "4 ARG 95": "NH1" <-> "NH2" Residue "4 ARG 103": "NH1" <-> "NH2" Residue "4 ARG 139": "NH1" <-> "NH2" Residue "4 ARG 220": "NH1" <-> "NH2" Residue "4 ARG 320": "NH1" <-> "NH2" Residue "4 TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 ARG 324": "NH1" <-> "NH2" Residue "4 ARG 333": "NH1" <-> "NH2" Residue "4 ARG 372": "NH1" <-> "NH2" Residue "4 PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 24": "NH1" <-> "NH2" Residue "5 ARG 61": "NH1" <-> "NH2" Residue "5 ARG 64": "NH1" <-> "NH2" Residue "5 ARG 113": "NH1" <-> "NH2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 131": "NH1" <-> "NH2" Residue "5 ARG 186": "NH1" <-> "NH2" Residue "5 ARG 188": "NH1" <-> "NH2" Residue "6 ARG 18": "NH1" <-> "NH2" Residue "6 TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 101": "NH1" <-> "NH2" Residue "7 ARG 5": "NH1" <-> "NH2" Residue "7 ARG 47": "NH1" <-> "NH2" Residue "7 ARG 72": "NH1" <-> "NH2" Residue "7 ARG 73": "NH1" <-> "NH2" Residue "7 ARG 75": "NH1" <-> "NH2" Residue "7 ARG 81": "NH1" <-> "NH2" Residue "7 ARG 97": "NH1" <-> "NH2" Residue "8 ARG 28": "NH1" <-> "NH2" Residue "8 ARG 31": "NH1" <-> "NH2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 60": "NH1" <-> "NH2" Residue "8 ARG 80": "NH1" <-> "NH2" Residue "9 ARG 61": "NH1" <-> "NH2" Residue "9 ARG 64": "NH1" <-> "NH2" Residue "9 ARG 71": "NH1" <-> "NH2" Residue "9 ARG 113": "NH1" <-> "NH2" Residue "9 ARG 115": "NH1" <-> "NH2" Residue "9 ARG 186": "NH1" <-> "NH2" Residue "9 ARG 188": "NH1" <-> "NH2" Residue "a ARG 38": "NH1" <-> "NH2" Residue "a ARG 51": "NH1" <-> "NH2" Residue "a ARG 95": "NH1" <-> "NH2" Residue "a ARG 103": "NH1" <-> "NH2" Residue "a ARG 139": "NH1" <-> "NH2" Residue "a ARG 220": "NH1" <-> "NH2" Residue "a ARG 320": "NH1" <-> "NH2" Residue "a ARG 324": "NH1" <-> "NH2" Residue "a ARG 333": "NH1" <-> "NH2" Residue "a ARG 372": "NH1" <-> "NH2" Residue "a PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 38": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "b ARG 51": "NH1" <-> "NH2" Residue "b ASP 80": "OD1" <-> "OD2" Residue "b ARG 95": "NH1" <-> "NH2" Residue "b ARG 103": "NH1" <-> "NH2" Residue "b ARG 139": "NH1" <-> "NH2" Residue "b ARG 220": "NH1" <-> "NH2" Residue "b ARG 320": "NH1" <-> "NH2" Residue "b TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 324": "NH1" <-> "NH2" Residue "b ARG 333": "NH1" <-> "NH2" Residue "b ARG 372": "NH1" <-> "NH2" Residue "b PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 24": "NH1" <-> "NH2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "c ARG 64": "NH1" <-> "NH2" Residue "c ARG 113": "NH1" <-> "NH2" Residue "c ARG 115": "NH1" <-> "NH2" Residue "c ARG 131": "NH1" <-> "NH2" Residue "c ARG 186": "NH1" <-> "NH2" Residue "c ARG 188": "NH1" <-> "NH2" Residue "d ARG 18": "NH1" <-> "NH2" Residue "d TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 101": "NH1" <-> "NH2" Residue "e ARG 5": "NH1" <-> "NH2" Residue "e ARG 47": "NH1" <-> "NH2" Residue "e ARG 72": "NH1" <-> "NH2" Residue "e ARG 73": "NH1" <-> "NH2" Residue "e ARG 75": "NH1" <-> "NH2" Residue "e ARG 81": "NH1" <-> "NH2" Residue "e ARG 97": "NH1" <-> "NH2" Residue "f ARG 28": "NH1" <-> "NH2" Residue "f ARG 31": "NH1" <-> "NH2" Residue "f ARG 51": "NH1" <-> "NH2" Residue "f ARG 60": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/chem_data/mon_lib" Total number of atoms: 67896 Number of models: 1 Model: "" Number of chains: 42 Chain: "C" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "A" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "B" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "D" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "F" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "E" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "H" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "I" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "J" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "K" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "L" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "M" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "N" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "O" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "P" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "Q" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "R" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "S" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "T" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "U" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "V" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "W" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "X" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "Y" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "Z" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "0" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "1" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "2" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "3" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "4" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "5" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "6" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "7" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "8" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "9" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1440 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 12, 'TRANS': 179} Chain breaks: 2 Chain: "a" Number of atoms: 2815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2815 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 28, 'TRANS': 341} Chain: "b" Number of atoms: 2781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2781 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 27, 'TRANS': 338} Chain breaks: 1 Chain: "c" Number of atoms: 1460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1460 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Chain breaks: 1 Chain: "d" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 968 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "e" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 859 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "f" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 993 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 3, 'TRANS': 130} Time building chain proxies: 30.16, per 1000 atoms: 0.44 Number of scatterers: 67896 At special positions: 0 Unit cell: (158.387, 158.387, 248.742, 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 276 16.00 O 12270 8.00 N 12198 7.00 C 43152 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: 20.39 Conformation dependent library (CDL) restraints added in 7.6 seconds 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16212 Finding SS restraints... Secondary structure from input PDB file: 252 helices and 102 sheets defined 33.8% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.54 Creating SS restraints... Processing helix chain 'C' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP C 21 " --> pdb=" O ALA C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 removed outlier: 3.623A pdb=" N SER C 41 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG C 44 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA C 45 " --> pdb=" O SER C 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY C 52 " --> pdb=" O ALA C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN C 161 " --> pdb=" O LEU C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 Processing helix chain 'A' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL A 30 " --> pdb=" O THR A 26 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA A 33 " --> pdb=" O ILE A 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER A 34 " --> pdb=" O VAL A 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY A 35 " --> pdb=" O ALA A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 54 " --> pdb=" O MET A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA A 72 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.953A pdb=" N ARG A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA A 109 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU A 116 " --> pdb=" O GLY A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA A 196 " --> pdb=" O SER A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN A 257 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA A 258 " --> pdb=" O ALA A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 254 through 258' Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 297 " --> pdb=" O ILE A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE A 304 " --> pdb=" O PRO A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 344 removed outlier: 4.075A pdb=" N ARG A 333 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 343 " --> pdb=" O ALA A 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 369 " --> pdb=" O GLU A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 389 removed outlier: 4.317A pdb=" N VAL A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL B 30 " --> pdb=" O THR B 26 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET B 32 " --> pdb=" O ARG B 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA B 33 " --> pdb=" O ILE B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 54 Processing helix chain 'B' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU B 116 " --> pdb=" O GLY B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP B 202 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG B 243 " --> pdb=" O GLU B 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS B 251 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN B 257 " --> pdb=" O GLY B 254 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA B 258 " --> pdb=" O ALA B 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 254 through 258' Processing helix chain 'B' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA B 294 " --> pdb=" O ALA B 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE B 304 " --> pdb=" O PRO B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 326 removed outlier: 3.517A pdb=" N ARG B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG B 333 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 343 " --> pdb=" O ALA B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 361 No H-bonds generated for 'chain 'B' and resid 359 through 361' Processing helix chain 'B' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 369 " --> pdb=" O GLU B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU B 387 " --> pdb=" O GLU B 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU B 388 " --> pdb=" O LYS B 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP D 21 " --> pdb=" O ALA D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU D 40 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA D 45 " --> pdb=" O SER D 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA D 49 " --> pdb=" O ALA D 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY D 52 " --> pdb=" O ALA D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA D 146 " --> pdb=" O SER D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU D 165 " --> pdb=" O GLN D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 Processing helix chain 'F' and resid 5 through 17 removed outlier: 3.532A pdb=" N GLN F 10 " --> pdb=" O ALA F 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA F 11 " --> pdb=" O GLY F 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU F 17 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS F 82 " --> pdb=" O PHE F 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP F 90 " --> pdb=" O ALA F 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 80 " --> pdb=" O ASP G 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG H 20 " --> pdb=" O VAL H 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP H 21 " --> pdb=" O ALA H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER H 41 " --> pdb=" O ALA H 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG H 44 " --> pdb=" O LEU H 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA H 45 " --> pdb=" O SER H 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA H 49 " --> pdb=" O ALA H 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 148 through 165 removed outlier: 3.657A pdb=" N GLN H 161 " --> pdb=" O LEU H 157 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 185 Processing helix chain 'I' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL I 30 " --> pdb=" O THR I 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA I 33 " --> pdb=" O ILE I 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER I 34 " --> pdb=" O VAL I 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY I 35 " --> pdb=" O ALA I 31 " (cutoff:3.500A) Processing helix chain 'I' and resid 45 through 54 removed outlier: 3.617A pdb=" N MET I 50 " --> pdb=" O THR I 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG I 51 " --> pdb=" O VAL I 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE I 54 " --> pdb=" O MET I 50 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG I 96 " --> pdb=" O ASP I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA I 109 " --> pdb=" O GLU I 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU I 116 " --> pdb=" O GLY I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA I 196 " --> pdb=" O SER I 192 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER I 211 " --> pdb=" O ALA I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 237 through 250 Processing helix chain 'I' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN I 257 " --> pdb=" O GLY I 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA I 258 " --> pdb=" O ALA I 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 254 through 258' Processing helix chain 'I' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE I 293 " --> pdb=" O ALA I 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE I 297 " --> pdb=" O ILE I 293 " (cutoff:3.500A) Processing helix chain 'I' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE I 304 " --> pdb=" O PRO I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG I 324 " --> pdb=" O ARG I 320 " (cutoff:3.500A) Processing helix chain 'I' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG I 333 " --> pdb=" O PRO I 329 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER I 343 " --> pdb=" O ALA I 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY I 344 " --> pdb=" O TRP I 340 " (cutoff:3.500A) Processing helix chain 'I' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN I 368 " --> pdb=" O VAL I 364 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU I 369 " --> pdb=" O GLU I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL I 386 " --> pdb=" O SER I 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU I 387 " --> pdb=" O GLU I 383 " (cutoff:3.500A) Processing helix chain 'J' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL J 30 " --> pdb=" O THR J 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET J 32 " --> pdb=" O ARG J 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA J 33 " --> pdb=" O ILE J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 54 Processing helix chain 'J' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 Processing helix chain 'J' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU J 116 " --> pdb=" O GLY J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP J 202 " --> pdb=" O ALA J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG J 243 " --> pdb=" O GLU J 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS J 251 " --> pdb=" O GLU J 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN J 253 " --> pdb=" O GLU J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN J 257 " --> pdb=" O GLY J 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA J 258 " --> pdb=" O ALA J 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 254 through 258' Processing helix chain 'J' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA J 294 " --> pdb=" O ALA J 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) Processing helix chain 'J' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE J 304 " --> pdb=" O PRO J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG J 320 " --> pdb=" O ALA J 316 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG J 324 " --> pdb=" O ARG J 320 " (cutoff:3.500A) Processing helix chain 'J' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG J 333 " --> pdb=" O PRO J 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER J 343 " --> pdb=" O ALA J 339 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 361 No H-bonds generated for 'chain 'J' and resid 359 through 361' Processing helix chain 'J' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN J 368 " --> pdb=" O VAL J 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU J 369 " --> pdb=" O GLU J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 389 removed outlier: 4.035A pdb=" N VAL J 386 " --> pdb=" O SER J 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU J 387 " --> pdb=" O GLU J 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU J 388 " --> pdb=" O LYS J 384 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP K 21 " --> pdb=" O ALA K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU K 40 " --> pdb=" O ASP K 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER K 41 " --> pdb=" O ALA K 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA K 45 " --> pdb=" O SER K 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA K 49 " --> pdb=" O ALA K 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY K 52 " --> pdb=" O ALA K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 143 through 147 removed outlier: 3.789A pdb=" N ALA K 146 " --> pdb=" O SER K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 148 through 165 removed outlier: 3.535A pdb=" N PHE K 156 " --> pdb=" O ALA K 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN K 161 " --> pdb=" O LEU K 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU K 165 " --> pdb=" O GLN K 161 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 185 Processing helix chain 'L' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN L 10 " --> pdb=" O ALA L 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA L 11 " --> pdb=" O GLY L 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU L 17 " --> pdb=" O VAL L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 90 removed outlier: 3.556A pdb=" N LYS L 82 " --> pdb=" O PHE L 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP L 90 " --> pdb=" O ALA L 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA N 79 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE N 83 " --> pdb=" O ALA N 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG O 20 " --> pdb=" O VAL O 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP O 21 " --> pdb=" O ALA O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER O 41 " --> pdb=" O ALA O 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR O 42 " --> pdb=" O ALA O 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG O 44 " --> pdb=" O LEU O 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA O 45 " --> pdb=" O SER O 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA O 49 " --> pdb=" O ALA O 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY O 52 " --> pdb=" O ALA O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN O 161 " --> pdb=" O LEU O 157 " (cutoff:3.500A) Processing helix chain 'O' and resid 180 through 185 Processing helix chain 'P' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL P 30 " --> pdb=" O THR P 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA P 33 " --> pdb=" O ILE P 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER P 34 " --> pdb=" O VAL P 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY P 35 " --> pdb=" O ALA P 31 " (cutoff:3.500A) Processing helix chain 'P' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET P 50 " --> pdb=" O THR P 46 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG P 51 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE P 54 " --> pdb=" O MET P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL P 64 " --> pdb=" O GLY P 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA P 72 " --> pdb=" O ALA P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG P 96 " --> pdb=" O ASP P 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA P 109 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN P 113 " --> pdb=" O ALA P 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU P 116 " --> pdb=" O GLY P 112 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA P 196 " --> pdb=" O SER P 192 " (cutoff:3.500A) Processing helix chain 'P' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER P 211 " --> pdb=" O ALA P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 237 through 250 Processing helix chain 'P' and resid 254 through 258 removed outlier: 3.714A pdb=" N ASN P 257 " --> pdb=" O GLY P 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA P 258 " --> pdb=" O ALA P 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 254 through 258' Processing helix chain 'P' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE P 293 " --> pdb=" O ALA P 289 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE P 297 " --> pdb=" O ILE P 293 " (cutoff:3.500A) Processing helix chain 'P' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE P 304 " --> pdb=" O PRO P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG P 324 " --> pdb=" O ARG P 320 " (cutoff:3.500A) Processing helix chain 'P' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG P 333 " --> pdb=" O PRO P 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER P 343 " --> pdb=" O ALA P 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY P 344 " --> pdb=" O TRP P 340 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN P 368 " --> pdb=" O VAL P 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU P 369 " --> pdb=" O GLU P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL P 386 " --> pdb=" O SER P 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU P 387 " --> pdb=" O GLU P 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL Q 30 " --> pdb=" O THR Q 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET Q 32 " --> pdb=" O ARG Q 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA Q 33 " --> pdb=" O ILE Q 29 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 54 Processing helix chain 'Q' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL Q 64 " --> pdb=" O GLY Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 96 Processing helix chain 'Q' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU Q 116 " --> pdb=" O GLY Q 112 " (cutoff:3.500A) Processing helix chain 'Q' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP Q 202 " --> pdb=" O ALA Q 198 " (cutoff:3.500A) Processing helix chain 'Q' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG Q 243 " --> pdb=" O GLU Q 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS Q 251 " --> pdb=" O GLU Q 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN Q 253 " --> pdb=" O GLU Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 258 removed outlier: 3.747A pdb=" N ASN Q 257 " --> pdb=" O GLY Q 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Q 258 " --> pdb=" O ALA Q 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 254 through 258' Processing helix chain 'Q' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA Q 294 " --> pdb=" O ALA Q 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA Q 296 " --> pdb=" O GLU Q 292 " (cutoff:3.500A) Processing helix chain 'Q' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE Q 304 " --> pdb=" O PRO Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG Q 320 " --> pdb=" O ALA Q 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG Q 324 " --> pdb=" O ARG Q 320 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG Q 333 " --> pdb=" O PRO Q 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER Q 343 " --> pdb=" O ALA Q 339 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 361 No H-bonds generated for 'chain 'Q' and resid 359 through 361' Processing helix chain 'Q' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN Q 368 " --> pdb=" O VAL Q 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL Q 386 " --> pdb=" O SER Q 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU Q 387 " --> pdb=" O GLU Q 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU Q 388 " --> pdb=" O LYS Q 384 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP R 21 " --> pdb=" O ALA R 17 " (cutoff:3.500A) Processing helix chain 'R' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU R 40 " --> pdb=" O ASP R 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER R 41 " --> pdb=" O ALA R 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA R 45 " --> pdb=" O SER R 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA R 49 " --> pdb=" O ALA R 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY R 52 " --> pdb=" O ALA R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA R 146 " --> pdb=" O SER R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN R 161 " --> pdb=" O LEU R 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU R 165 " --> pdb=" O GLN R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 180 through 185 Processing helix chain 'S' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN S 10 " --> pdb=" O ALA S 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU S 17 " --> pdb=" O VAL S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS S 82 " --> pdb=" O PHE S 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG U 80 " --> pdb=" O ASP U 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE U 83 " --> pdb=" O ALA U 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG V 20 " --> pdb=" O VAL V 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP V 21 " --> pdb=" O ALA V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 54 removed outlier: 3.623A pdb=" N SER V 41 " --> pdb=" O ALA V 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR V 42 " --> pdb=" O ALA V 38 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG V 44 " --> pdb=" O LEU V 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA V 45 " --> pdb=" O SER V 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA V 49 " --> pdb=" O ALA V 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY V 52 " --> pdb=" O ALA V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN V 161 " --> pdb=" O LEU V 157 " (cutoff:3.500A) Processing helix chain 'V' and resid 180 through 185 Processing helix chain 'W' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL W 30 " --> pdb=" O THR W 26 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA W 33 " --> pdb=" O ILE W 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER W 34 " --> pdb=" O VAL W 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY W 35 " --> pdb=" O ALA W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET W 50 " --> pdb=" O THR W 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG W 51 " --> pdb=" O VAL W 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE W 54 " --> pdb=" O MET W 50 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL W 64 " --> pdb=" O GLY W 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA W 72 " --> pdb=" O ALA W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.953A pdb=" N ARG W 96 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing helix chain 'W' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA W 109 " --> pdb=" O GLU W 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU W 116 " --> pdb=" O GLY W 112 " (cutoff:3.500A) Processing helix chain 'W' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA W 196 " --> pdb=" O SER W 192 " (cutoff:3.500A) Processing helix chain 'W' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER W 211 " --> pdb=" O ALA W 207 " (cutoff:3.500A) Processing helix chain 'W' and resid 237 through 250 Processing helix chain 'W' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN W 257 " --> pdb=" O GLY W 254 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA W 258 " --> pdb=" O ALA W 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 254 through 258' Processing helix chain 'W' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE W 293 " --> pdb=" O ALA W 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE W 297 " --> pdb=" O ILE W 293 " (cutoff:3.500A) Processing helix chain 'W' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE W 304 " --> pdb=" O PRO W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG W 324 " --> pdb=" O ARG W 320 " (cutoff:3.500A) Processing helix chain 'W' and resid 327 through 344 removed outlier: 4.075A pdb=" N ARG W 333 " --> pdb=" O PRO W 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER W 343 " --> pdb=" O ALA W 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY W 344 " --> pdb=" O TRP W 340 " (cutoff:3.500A) Processing helix chain 'W' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN W 368 " --> pdb=" O VAL W 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU W 369 " --> pdb=" O GLU W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 389 removed outlier: 4.317A pdb=" N VAL W 386 " --> pdb=" O SER W 382 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LEU W 387 " --> pdb=" O GLU W 383 " (cutoff:3.500A) Processing helix chain 'X' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL X 30 " --> pdb=" O THR X 26 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET X 32 " --> pdb=" O ARG X 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA X 33 " --> pdb=" O ILE X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 54 Processing helix chain 'X' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL X 64 " --> pdb=" O GLY X 60 " (cutoff:3.500A) Processing helix chain 'X' and resid 91 through 96 Processing helix chain 'X' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU X 116 " --> pdb=" O GLY X 112 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP X 202 " --> pdb=" O ALA X 198 " (cutoff:3.500A) Processing helix chain 'X' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG X 243 " --> pdb=" O GLU X 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS X 251 " --> pdb=" O GLU X 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN X 253 " --> pdb=" O GLU X 249 " (cutoff:3.500A) Processing helix chain 'X' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN X 257 " --> pdb=" O GLY X 254 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ALA X 258 " --> pdb=" O ALA X 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 254 through 258' Processing helix chain 'X' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA X 294 " --> pdb=" O ALA X 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA X 296 " --> pdb=" O GLU X 292 " (cutoff:3.500A) Processing helix chain 'X' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE X 304 " --> pdb=" O PRO X 300 " (cutoff:3.500A) Processing helix chain 'X' and resid 315 through 326 removed outlier: 3.517A pdb=" N ARG X 320 " --> pdb=" O ALA X 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG X 324 " --> pdb=" O ARG X 320 " (cutoff:3.500A) Processing helix chain 'X' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG X 333 " --> pdb=" O PRO X 329 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER X 343 " --> pdb=" O ALA X 339 " (cutoff:3.500A) Processing helix chain 'X' and resid 359 through 361 No H-bonds generated for 'chain 'X' and resid 359 through 361' Processing helix chain 'X' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN X 368 " --> pdb=" O VAL X 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU X 369 " --> pdb=" O GLU X 365 " (cutoff:3.500A) Processing helix chain 'X' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL X 386 " --> pdb=" O SER X 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU X 387 " --> pdb=" O GLU X 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU X 388 " --> pdb=" O LYS X 384 " (cutoff:3.500A) Processing helix chain 'Y' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP Y 21 " --> pdb=" O ALA Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU Y 40 " --> pdb=" O ASP Y 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER Y 41 " --> pdb=" O ALA Y 37 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA Y 45 " --> pdb=" O SER Y 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA Y 49 " --> pdb=" O ALA Y 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY Y 52 " --> pdb=" O ALA Y 48 " (cutoff:3.500A) Processing helix chain 'Y' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA Y 146 " --> pdb=" O SER Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE Y 156 " --> pdb=" O ALA Y 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN Y 161 " --> pdb=" O LEU Y 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU Y 165 " --> pdb=" O GLN Y 161 " (cutoff:3.500A) Processing helix chain 'Y' and resid 180 through 185 Processing helix chain 'Z' and resid 5 through 17 removed outlier: 3.532A pdb=" N GLN Z 10 " --> pdb=" O ALA Z 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA Z 11 " --> pdb=" O GLY Z 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU Z 17 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS Z 82 " --> pdb=" O PHE Z 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP Z 90 " --> pdb=" O ALA Z 86 " (cutoff:3.500A) Processing helix chain '1' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA 1 79 " --> pdb=" O THR 1 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG 1 80 " --> pdb=" O ASP 1 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 1 83 " --> pdb=" O ALA 1 79 " (cutoff:3.500A) Processing helix chain '2' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG 2 20 " --> pdb=" O VAL 2 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP 2 21 " --> pdb=" O ALA 2 17 " (cutoff:3.500A) Processing helix chain '2' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER 2 41 " --> pdb=" O ALA 2 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR 2 42 " --> pdb=" O ALA 2 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG 2 44 " --> pdb=" O LEU 2 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA 2 45 " --> pdb=" O SER 2 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 2 49 " --> pdb=" O ALA 2 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY 2 52 " --> pdb=" O ALA 2 48 " (cutoff:3.500A) Processing helix chain '2' and resid 148 through 165 removed outlier: 3.657A pdb=" N GLN 2 161 " --> pdb=" O LEU 2 157 " (cutoff:3.500A) Processing helix chain '2' and resid 180 through 185 Processing helix chain '3' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL 3 30 " --> pdb=" O THR 3 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA 3 33 " --> pdb=" O ILE 3 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER 3 34 " --> pdb=" O VAL 3 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY 3 35 " --> pdb=" O ALA 3 31 " (cutoff:3.500A) Processing helix chain '3' and resid 45 through 54 removed outlier: 3.617A pdb=" N MET 3 50 " --> pdb=" O THR 3 46 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG 3 51 " --> pdb=" O VAL 3 47 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE 3 54 " --> pdb=" O MET 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL 3 64 " --> pdb=" O GLY 3 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA 3 72 " --> pdb=" O ALA 3 68 " (cutoff:3.500A) Processing helix chain '3' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG 3 96 " --> pdb=" O ASP 3 92 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA 3 109 " --> pdb=" O GLU 3 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU 3 116 " --> pdb=" O GLY 3 112 " (cutoff:3.500A) Processing helix chain '3' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA 3 196 " --> pdb=" O SER 3 192 " (cutoff:3.500A) Processing helix chain '3' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER 3 211 " --> pdb=" O ALA 3 207 " (cutoff:3.500A) Processing helix chain '3' and resid 237 through 250 Processing helix chain '3' and resid 254 through 258 removed outlier: 3.713A pdb=" N ASN 3 257 " --> pdb=" O GLY 3 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA 3 258 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 254 through 258' Processing helix chain '3' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE 3 293 " --> pdb=" O ALA 3 289 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE 3 297 " --> pdb=" O ILE 3 293 " (cutoff:3.500A) Processing helix chain '3' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE 3 304 " --> pdb=" O PRO 3 300 " (cutoff:3.500A) Processing helix chain '3' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG 3 324 " --> pdb=" O ARG 3 320 " (cutoff:3.500A) Processing helix chain '3' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG 3 333 " --> pdb=" O PRO 3 329 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER 3 343 " --> pdb=" O ALA 3 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY 3 344 " --> pdb=" O TRP 3 340 " (cutoff:3.500A) Processing helix chain '3' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN 3 368 " --> pdb=" O VAL 3 364 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU 3 369 " --> pdb=" O GLU 3 365 " (cutoff:3.500A) Processing helix chain '3' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL 3 386 " --> pdb=" O SER 3 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU 3 387 " --> pdb=" O GLU 3 383 " (cutoff:3.500A) Processing helix chain '4' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL 4 30 " --> pdb=" O THR 4 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET 4 32 " --> pdb=" O ARG 4 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA 4 33 " --> pdb=" O ILE 4 29 " (cutoff:3.500A) Processing helix chain '4' and resid 49 through 54 Processing helix chain '4' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL 4 64 " --> pdb=" O GLY 4 60 " (cutoff:3.500A) Processing helix chain '4' and resid 91 through 96 Processing helix chain '4' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU 4 116 " --> pdb=" O GLY 4 112 " (cutoff:3.500A) Processing helix chain '4' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP 4 202 " --> pdb=" O ALA 4 198 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG 4 243 " --> pdb=" O GLU 4 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS 4 251 " --> pdb=" O GLU 4 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN 4 253 " --> pdb=" O GLU 4 249 " (cutoff:3.500A) Processing helix chain '4' and resid 254 through 258 removed outlier: 3.748A pdb=" N ASN 4 257 " --> pdb=" O GLY 4 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA 4 258 " --> pdb=" O ALA 4 255 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 254 through 258' Processing helix chain '4' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA 4 294 " --> pdb=" O ALA 4 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA 4 296 " --> pdb=" O GLU 4 292 " (cutoff:3.500A) Processing helix chain '4' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE 4 304 " --> pdb=" O PRO 4 300 " (cutoff:3.500A) Processing helix chain '4' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG 4 320 " --> pdb=" O ALA 4 316 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG 4 324 " --> pdb=" O ARG 4 320 " (cutoff:3.500A) Processing helix chain '4' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG 4 333 " --> pdb=" O PRO 4 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER 4 343 " --> pdb=" O ALA 4 339 " (cutoff:3.500A) Processing helix chain '4' and resid 359 through 361 No H-bonds generated for 'chain '4' and resid 359 through 361' Processing helix chain '4' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN 4 368 " --> pdb=" O VAL 4 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU 4 369 " --> pdb=" O GLU 4 365 " (cutoff:3.500A) Processing helix chain '4' and resid 380 through 389 removed outlier: 4.035A pdb=" N VAL 4 386 " --> pdb=" O SER 4 382 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU 4 387 " --> pdb=" O GLU 4 383 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU 4 388 " --> pdb=" O LYS 4 384 " (cutoff:3.500A) Processing helix chain '5' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP 5 21 " --> pdb=" O ALA 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER 5 41 " --> pdb=" O ALA 5 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA 5 45 " --> pdb=" O SER 5 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 143 through 147 removed outlier: 3.789A pdb=" N ALA 5 146 " --> pdb=" O SER 5 143 " (cutoff:3.500A) Processing helix chain '5' and resid 148 through 165 removed outlier: 3.535A pdb=" N PHE 5 156 " --> pdb=" O ALA 5 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN 5 161 " --> pdb=" O LEU 5 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 5 165 " --> pdb=" O GLN 5 161 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 185 Processing helix chain '6' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN 6 10 " --> pdb=" O ALA 6 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA 6 11 " --> pdb=" O GLY 6 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU 6 17 " --> pdb=" O VAL 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 78 through 90 removed outlier: 3.556A pdb=" N LYS 6 82 " --> pdb=" O PHE 6 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP 6 90 " --> pdb=" O ALA 6 86 " (cutoff:3.500A) Processing helix chain '8' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA 8 79 " --> pdb=" O THR 8 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG 8 80 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE 8 83 " --> pdb=" O ALA 8 79 " (cutoff:3.500A) Processing helix chain '9' and resid 15 through 24 removed outlier: 3.882A pdb=" N ARG 9 20 " --> pdb=" O VAL 9 16 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP 9 21 " --> pdb=" O ALA 9 17 " (cutoff:3.500A) Processing helix chain '9' and resid 35 through 54 removed outlier: 3.624A pdb=" N SER 9 41 " --> pdb=" O ALA 9 37 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG 9 44 " --> pdb=" O LEU 9 40 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA 9 45 " --> pdb=" O SER 9 41 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALA 9 49 " --> pdb=" O ALA 9 45 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY 9 52 " --> pdb=" O ALA 9 48 " (cutoff:3.500A) Processing helix chain '9' and resid 148 through 165 removed outlier: 3.658A pdb=" N GLN 9 161 " --> pdb=" O LEU 9 157 " (cutoff:3.500A) Processing helix chain '9' and resid 180 through 185 Processing helix chain 'a' and resid 26 through 35 removed outlier: 3.658A pdb=" N VAL a 30 " --> pdb=" O THR a 26 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA a 33 " --> pdb=" O ILE a 29 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER a 34 " --> pdb=" O VAL a 30 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY a 35 " --> pdb=" O ALA a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 54 removed outlier: 3.618A pdb=" N MET a 50 " --> pdb=" O THR a 46 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG a 51 " --> pdb=" O VAL a 47 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE a 54 " --> pdb=" O MET a 50 " (cutoff:3.500A) Processing helix chain 'a' and resid 57 through 72 removed outlier: 3.707A pdb=" N VAL a 64 " --> pdb=" O GLY a 60 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA a 72 " --> pdb=" O ALA a 68 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 96 removed outlier: 3.952A pdb=" N ARG a 96 " --> pdb=" O ASP a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 118 removed outlier: 3.576A pdb=" N ALA a 109 " --> pdb=" O GLU a 105 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN a 113 " --> pdb=" O ALA a 109 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LEU a 116 " --> pdb=" O GLY a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 197 removed outlier: 3.743A pdb=" N ALA a 196 " --> pdb=" O SER a 192 " (cutoff:3.500A) Processing helix chain 'a' and resid 197 through 217 removed outlier: 3.744A pdb=" N SER a 211 " --> pdb=" O ALA a 207 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 250 Processing helix chain 'a' and resid 254 through 258 removed outlier: 3.714A pdb=" N ASN a 257 " --> pdb=" O GLY a 254 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA a 258 " --> pdb=" O ALA a 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 254 through 258' Processing helix chain 'a' and resid 282 through 298 removed outlier: 3.520A pdb=" N ILE a 293 " --> pdb=" O ALA a 289 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE a 297 " --> pdb=" O ILE a 293 " (cutoff:3.500A) Processing helix chain 'a' and resid 300 through 305 removed outlier: 3.698A pdb=" N ILE a 304 " --> pdb=" O PRO a 300 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 326 removed outlier: 3.674A pdb=" N ARG a 324 " --> pdb=" O ARG a 320 " (cutoff:3.500A) Processing helix chain 'a' and resid 327 through 344 removed outlier: 4.074A pdb=" N ARG a 333 " --> pdb=" O PRO a 329 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER a 343 " --> pdb=" O ALA a 339 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY a 344 " --> pdb=" O TRP a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 362 through 376 removed outlier: 3.800A pdb=" N GLN a 368 " --> pdb=" O VAL a 364 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU a 369 " --> pdb=" O GLU a 365 " (cutoff:3.500A) Processing helix chain 'a' and resid 380 through 389 removed outlier: 4.316A pdb=" N VAL a 386 " --> pdb=" O SER a 382 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU a 387 " --> pdb=" O GLU a 383 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 35 removed outlier: 3.559A pdb=" N VAL b 30 " --> pdb=" O THR b 26 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N MET b 32 " --> pdb=" O ARG b 28 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA b 33 " --> pdb=" O ILE b 29 " (cutoff:3.500A) Processing helix chain 'b' and resid 49 through 54 Processing helix chain 'b' and resid 57 through 72 removed outlier: 3.831A pdb=" N VAL b 64 " --> pdb=" O GLY b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 96 Processing helix chain 'b' and resid 102 through 118 removed outlier: 3.887A pdb=" N LEU b 116 " --> pdb=" O GLY b 112 " (cutoff:3.500A) Processing helix chain 'b' and resid 197 through 217 removed outlier: 3.612A pdb=" N ASP b 202 " --> pdb=" O ALA b 198 " (cutoff:3.500A) Processing helix chain 'b' and resid 237 through 253 removed outlier: 3.610A pdb=" N ARG b 243 " --> pdb=" O GLU b 239 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N HIS b 251 " --> pdb=" O GLU b 247 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN b 253 " --> pdb=" O GLU b 249 " (cutoff:3.500A) Processing helix chain 'b' and resid 254 through 258 removed outlier: 3.747A pdb=" N ASN b 257 " --> pdb=" O GLY b 254 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA b 258 " --> pdb=" O ALA b 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 254 through 258' Processing helix chain 'b' and resid 283 through 298 removed outlier: 3.909A pdb=" N ALA b 294 " --> pdb=" O ALA b 290 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA b 296 " --> pdb=" O GLU b 292 " (cutoff:3.500A) Processing helix chain 'b' and resid 300 through 305 removed outlier: 4.129A pdb=" N ILE b 304 " --> pdb=" O PRO b 300 " (cutoff:3.500A) Processing helix chain 'b' and resid 315 through 326 removed outlier: 3.516A pdb=" N ARG b 320 " --> pdb=" O ALA b 316 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG b 324 " --> pdb=" O ARG b 320 " (cutoff:3.500A) Processing helix chain 'b' and resid 327 through 343 removed outlier: 3.787A pdb=" N ARG b 333 " --> pdb=" O PRO b 329 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER b 343 " --> pdb=" O ALA b 339 " (cutoff:3.500A) Processing helix chain 'b' and resid 359 through 361 No H-bonds generated for 'chain 'b' and resid 359 through 361' Processing helix chain 'b' and resid 362 through 373 removed outlier: 3.927A pdb=" N GLN b 368 " --> pdb=" O VAL b 364 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU b 369 " --> pdb=" O GLU b 365 " (cutoff:3.500A) Processing helix chain 'b' and resid 380 through 389 removed outlier: 4.036A pdb=" N VAL b 386 " --> pdb=" O SER b 382 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU b 387 " --> pdb=" O GLU b 383 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU b 388 " --> pdb=" O LYS b 384 " (cutoff:3.500A) Processing helix chain 'c' and resid 15 through 23 removed outlier: 3.798A pdb=" N ASP c 21 " --> pdb=" O ALA c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 55 removed outlier: 3.556A pdb=" N LEU c 40 " --> pdb=" O ASP c 36 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER c 41 " --> pdb=" O ALA c 37 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA c 45 " --> pdb=" O SER c 41 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY c 52 " --> pdb=" O ALA c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 143 through 147 removed outlier: 3.788A pdb=" N ALA c 146 " --> pdb=" O SER c 143 " (cutoff:3.500A) Processing helix chain 'c' and resid 148 through 165 removed outlier: 3.536A pdb=" N PHE c 156 " --> pdb=" O ALA c 152 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN c 161 " --> pdb=" O LEU c 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU c 165 " --> pdb=" O GLN c 161 " (cutoff:3.500A) Processing helix chain 'c' and resid 180 through 185 Processing helix chain 'd' and resid 5 through 17 removed outlier: 3.531A pdb=" N GLN d 10 " --> pdb=" O ALA d 6 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA d 11 " --> pdb=" O GLY d 7 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LEU d 17 " --> pdb=" O VAL d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 78 through 90 removed outlier: 3.555A pdb=" N LYS d 82 " --> pdb=" O PHE d 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASP d 90 " --> pdb=" O ALA d 86 " (cutoff:3.500A) Processing helix chain 'f' and resid 75 through 85 removed outlier: 3.613A pdb=" N ALA f 79 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG f 80 " --> pdb=" O ASP f 76 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE f 83 " --> pdb=" O ALA f 79 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG C 61 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 138 " --> pdb=" O ARG C 61 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU C 133 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU C 89 " --> pdb=" O GLU C 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP C 135 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR C 137 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR C 85 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU C 89 " --> pdb=" O VAL C 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR C 99 " --> pdb=" O LEU C 91 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= 3, first strand: chain 'A' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU A 134 " --> pdb=" O VAL A 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU A 122 " --> pdb=" O CYS A 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS A 177 " --> pdb=" O LEU A 122 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY A 155 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 224 through 227 Processing sheet with id= 6, first strand: chain 'B' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS B 353 " --> pdb=" O ILE B 77 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU B 134 " --> pdb=" O VAL B 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS B 177 " --> pdb=" O LEU B 122 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY B 155 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 224 through 227 Processing sheet with id= 10, first strand: chain 'D' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG D 61 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR D 137 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL D 86 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU D 91 " --> pdb=" O THR D 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR D 99 " --> pdb=" O LEU D 91 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 45 through 46 Processing sheet with id= 12, first strand: chain 'F' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG F 130 " --> pdb=" O LEU F 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU F 107 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG F 132 " --> pdb=" O VAL F 105 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 85 through 88 removed outlier: 4.274A pdb=" N GLY E 33 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU E 14 " --> pdb=" O ALA E 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA E 31 " --> pdb=" O GLU E 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP E 36 " --> pdb=" O ARG E 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG E 64 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL E 63 " --> pdb=" O LEU E 102 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 17 through 19 Processing sheet with id= 15, first strand: chain 'E' and resid 45 through 48 Processing sheet with id= 16, first strand: chain 'G' and resid 10 through 12 removed outlier: 5.380A pdb=" N ILE G 107 " --> pdb=" O ALA G 127 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA G 127 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE G 64 " --> pdb=" O MET G 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA G 62 " --> pdb=" O SER G 128 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 10 through 12 Processing sheet with id= 18, first strand: chain 'H' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG H 61 " --> pdb=" O ALA H 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA H 138 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU H 133 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU H 89 " --> pdb=" O GLU H 133 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP H 135 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR H 137 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR H 85 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU H 89 " --> pdb=" O VAL H 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR H 99 " --> pdb=" O LEU H 91 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 76 through 79 Processing sheet with id= 20, first strand: chain 'I' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU I 134 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU I 122 " --> pdb=" O CYS I 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS I 177 " --> pdb=" O LEU I 122 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY I 155 " --> pdb=" O VAL I 146 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 224 through 227 Processing sheet with id= 23, first strand: chain 'J' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS J 353 " --> pdb=" O ILE J 77 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 134 through 136 removed outlier: 3.775A pdb=" N GLU J 134 " --> pdb=" O VAL J 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS J 177 " --> pdb=" O LEU J 122 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY J 155 " --> pdb=" O VAL J 146 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 224 through 227 Processing sheet with id= 27, first strand: chain 'K' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG K 61 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR K 137 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL K 86 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU K 91 " --> pdb=" O THR K 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR K 99 " --> pdb=" O LEU K 91 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 45 through 46 Processing sheet with id= 29, first strand: chain 'L' and resid 62 through 68 removed outlier: 6.296A pdb=" N ARG L 130 " --> pdb=" O LEU L 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU L 107 " --> pdb=" O ARG L 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG L 132 " --> pdb=" O VAL L 105 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY M 33 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU M 14 " --> pdb=" O ALA M 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA M 31 " --> pdb=" O GLU M 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP M 36 " --> pdb=" O ARG M 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG M 64 " --> pdb=" O TRP M 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL M 63 " --> pdb=" O LEU M 102 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'M' and resid 17 through 19 Processing sheet with id= 32, first strand: chain 'M' and resid 45 through 48 Processing sheet with id= 33, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE N 107 " --> pdb=" O ALA N 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA N 127 " --> pdb=" O ILE N 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE N 64 " --> pdb=" O MET N 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA N 62 " --> pdb=" O SER N 128 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'N' and resid 10 through 12 Processing sheet with id= 35, first strand: chain 'O' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG O 61 " --> pdb=" O ALA O 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA O 138 " --> pdb=" O ARG O 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU O 133 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU O 89 " --> pdb=" O GLU O 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP O 135 " --> pdb=" O THR O 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR O 137 " --> pdb=" O THR O 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR O 85 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU O 89 " --> pdb=" O VAL O 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR O 99 " --> pdb=" O LEU O 91 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'P' and resid 76 through 79 Processing sheet with id= 37, first strand: chain 'P' and resid 134 through 136 removed outlier: 3.761A pdb=" N GLU P 134 " --> pdb=" O VAL P 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU P 122 " --> pdb=" O CYS P 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS P 177 " --> pdb=" O LEU P 122 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'P' and resid 143 through 146 removed outlier: 3.796A pdb=" N GLY P 155 " --> pdb=" O VAL P 146 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'P' and resid 224 through 227 Processing sheet with id= 40, first strand: chain 'Q' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS Q 353 " --> pdb=" O ILE Q 77 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Q' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU Q 134 " --> pdb=" O VAL Q 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS Q 177 " --> pdb=" O LEU Q 122 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Q' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY Q 155 " --> pdb=" O VAL Q 146 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Q' and resid 224 through 227 Processing sheet with id= 44, first strand: chain 'R' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG R 61 " --> pdb=" O ALA R 138 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR R 137 " --> pdb=" O VAL R 86 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL R 86 " --> pdb=" O THR R 137 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU R 91 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR R 99 " --> pdb=" O LEU R 91 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'S' and resid 45 through 46 Processing sheet with id= 46, first strand: chain 'S' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG S 130 " --> pdb=" O LEU S 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU S 107 " --> pdb=" O ARG S 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG S 132 " --> pdb=" O VAL S 105 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'T' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY T 33 " --> pdb=" O LEU T 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU T 14 " --> pdb=" O ALA T 31 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA T 31 " --> pdb=" O GLU T 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP T 36 " --> pdb=" O ARG T 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG T 64 " --> pdb=" O TRP T 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL T 63 " --> pdb=" O LEU T 102 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'T' and resid 17 through 19 Processing sheet with id= 49, first strand: chain 'T' and resid 45 through 48 Processing sheet with id= 50, first strand: chain 'U' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE U 107 " --> pdb=" O ALA U 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA U 127 " --> pdb=" O ILE U 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE U 64 " --> pdb=" O MET U 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA U 62 " --> pdb=" O SER U 128 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'U' and resid 10 through 12 Processing sheet with id= 52, first strand: chain 'V' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG V 61 " --> pdb=" O ALA V 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA V 138 " --> pdb=" O ARG V 61 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N GLU V 133 " --> pdb=" O LEU V 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU V 89 " --> pdb=" O GLU V 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP V 135 " --> pdb=" O THR V 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR V 137 " --> pdb=" O THR V 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR V 85 " --> pdb=" O THR V 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU V 89 " --> pdb=" O VAL V 101 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR V 99 " --> pdb=" O LEU V 91 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'W' and resid 76 through 79 Processing sheet with id= 54, first strand: chain 'W' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU W 134 " --> pdb=" O VAL W 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU W 122 " --> pdb=" O CYS W 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS W 177 " --> pdb=" O LEU W 122 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'W' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY W 155 " --> pdb=" O VAL W 146 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'W' and resid 224 through 227 Processing sheet with id= 57, first strand: chain 'X' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS X 353 " --> pdb=" O ILE X 77 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'X' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU X 134 " --> pdb=" O VAL X 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS X 177 " --> pdb=" O LEU X 122 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'X' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY X 155 " --> pdb=" O VAL X 146 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 224 through 227 Processing sheet with id= 61, first strand: chain 'Y' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG Y 61 " --> pdb=" O ALA Y 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR Y 137 " --> pdb=" O VAL Y 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL Y 86 " --> pdb=" O THR Y 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU Y 91 " --> pdb=" O THR Y 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Y 99 " --> pdb=" O LEU Y 91 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'Z' and resid 45 through 46 Processing sheet with id= 63, first strand: chain 'Z' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG Z 130 " --> pdb=" O LEU Z 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU Z 107 " --> pdb=" O ARG Z 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG Z 132 " --> pdb=" O VAL Z 105 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain '0' and resid 85 through 88 removed outlier: 4.274A pdb=" N GLY 0 33 " --> pdb=" O LEU 0 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU 0 14 " --> pdb=" O ALA 0 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA 0 31 " --> pdb=" O GLU 0 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP 0 36 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG 0 64 " --> pdb=" O TRP 0 36 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL 0 63 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain '0' and resid 17 through 19 Processing sheet with id= 66, first strand: chain '0' and resid 45 through 48 Processing sheet with id= 67, first strand: chain '1' and resid 10 through 12 removed outlier: 5.380A pdb=" N ILE 1 107 " --> pdb=" O ALA 1 127 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA 1 127 " --> pdb=" O ILE 1 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE 1 64 " --> pdb=" O MET 1 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA 1 62 " --> pdb=" O SER 1 128 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '1' and resid 10 through 12 Processing sheet with id= 69, first strand: chain '2' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG 2 61 " --> pdb=" O ALA 2 138 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA 2 138 " --> pdb=" O ARG 2 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU 2 133 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU 2 89 " --> pdb=" O GLU 2 133 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP 2 135 " --> pdb=" O THR 2 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR 2 137 " --> pdb=" O THR 2 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR 2 85 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU 2 89 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR 2 99 " --> pdb=" O LEU 2 91 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '3' and resid 76 through 79 Processing sheet with id= 71, first strand: chain '3' and resid 134 through 136 removed outlier: 3.762A pdb=" N GLU 3 134 " --> pdb=" O VAL 3 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 3 122 " --> pdb=" O CYS 3 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS 3 177 " --> pdb=" O LEU 3 122 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '3' and resid 143 through 146 removed outlier: 3.797A pdb=" N GLY 3 155 " --> pdb=" O VAL 3 146 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain '3' and resid 224 through 227 Processing sheet with id= 74, first strand: chain '4' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS 4 353 " --> pdb=" O ILE 4 77 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain '4' and resid 134 through 136 removed outlier: 3.775A pdb=" N GLU 4 134 " --> pdb=" O VAL 4 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS 4 177 " --> pdb=" O LEU 4 122 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain '4' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY 4 155 " --> pdb=" O VAL 4 146 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain '4' and resid 224 through 227 Processing sheet with id= 78, first strand: chain '5' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG 5 61 " --> pdb=" O ALA 5 138 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR 5 137 " --> pdb=" O VAL 5 86 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL 5 86 " --> pdb=" O THR 5 137 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 5 91 " --> pdb=" O THR 5 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR 5 99 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '6' and resid 45 through 46 Processing sheet with id= 80, first strand: chain '6' and resid 62 through 68 removed outlier: 6.296A pdb=" N ARG 6 130 " --> pdb=" O LEU 6 107 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU 6 107 " --> pdb=" O ARG 6 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG 6 132 " --> pdb=" O VAL 6 105 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '7' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY 7 33 " --> pdb=" O LEU 7 12 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU 7 14 " --> pdb=" O ALA 7 31 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA 7 31 " --> pdb=" O GLU 7 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP 7 36 " --> pdb=" O ARG 7 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG 7 64 " --> pdb=" O TRP 7 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL 7 63 " --> pdb=" O LEU 7 102 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '7' and resid 17 through 19 Processing sheet with id= 83, first strand: chain '7' and resid 45 through 48 Processing sheet with id= 84, first strand: chain '8' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE 8 107 " --> pdb=" O ALA 8 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA 8 127 " --> pdb=" O ILE 8 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE 8 64 " --> pdb=" O MET 8 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA 8 62 " --> pdb=" O SER 8 128 " (cutoff:3.500A) Processing sheet with id= 85, first strand: chain '8' and resid 10 through 12 Processing sheet with id= 86, first strand: chain '9' and resid 4 through 5 removed outlier: 3.802A pdb=" N ARG 9 61 " --> pdb=" O ALA 9 138 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA 9 138 " --> pdb=" O ARG 9 61 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N GLU 9 133 " --> pdb=" O LEU 9 89 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N LEU 9 89 " --> pdb=" O GLU 9 133 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ASP 9 135 " --> pdb=" O THR 9 87 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N THR 9 137 " --> pdb=" O THR 9 85 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR 9 85 " --> pdb=" O THR 9 137 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU 9 89 " --> pdb=" O VAL 9 101 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR 9 99 " --> pdb=" O LEU 9 91 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'a' and resid 76 through 79 Processing sheet with id= 88, first strand: chain 'a' and resid 134 through 136 removed outlier: 3.761A pdb=" N GLU a 134 " --> pdb=" O VAL a 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU a 122 " --> pdb=" O CYS a 177 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N CYS a 177 " --> pdb=" O LEU a 122 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'a' and resid 143 through 146 removed outlier: 3.796A pdb=" N GLY a 155 " --> pdb=" O VAL a 146 " (cutoff:3.500A) Processing sheet with id= 90, first strand: chain 'a' and resid 224 through 227 Processing sheet with id= 91, first strand: chain 'b' and resid 76 through 79 removed outlier: 3.623A pdb=" N LYS b 353 " --> pdb=" O ILE b 77 " (cutoff:3.500A) Processing sheet with id= 92, first strand: chain 'b' and resid 134 through 136 removed outlier: 3.776A pdb=" N GLU b 134 " --> pdb=" O VAL b 125 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS b 177 " --> pdb=" O LEU b 122 " (cutoff:3.500A) Processing sheet with id= 93, first strand: chain 'b' and resid 143 through 146 removed outlier: 3.682A pdb=" N GLY b 155 " --> pdb=" O VAL b 146 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'b' and resid 224 through 227 Processing sheet with id= 95, first strand: chain 'c' and resid 4 through 5 removed outlier: 3.861A pdb=" N ARG c 61 " --> pdb=" O ALA c 138 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR c 137 " --> pdb=" O VAL c 86 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL c 86 " --> pdb=" O THR c 137 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU c 91 " --> pdb=" O THR c 99 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR c 99 " --> pdb=" O LEU c 91 " (cutoff:3.500A) Processing sheet with id= 96, first strand: chain 'd' and resid 45 through 46 Processing sheet with id= 97, first strand: chain 'd' and resid 62 through 68 removed outlier: 6.297A pdb=" N ARG d 130 " --> pdb=" O LEU d 107 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU d 107 " --> pdb=" O ARG d 130 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N ARG d 132 " --> pdb=" O VAL d 105 " (cutoff:3.500A) Processing sheet with id= 98, first strand: chain 'e' and resid 85 through 88 removed outlier: 4.275A pdb=" N GLY e 33 " --> pdb=" O LEU e 12 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N GLU e 14 " --> pdb=" O ALA e 31 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ALA e 31 " --> pdb=" O GLU e 14 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N TRP e 36 " --> pdb=" O ARG e 64 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N ARG e 64 " --> pdb=" O TRP e 36 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL e 63 " --> pdb=" O LEU e 102 " (cutoff:3.500A) Processing sheet with id= 99, first strand: chain 'e' and resid 17 through 19 Processing sheet with id=100, first strand: chain 'e' and resid 45 through 48 Processing sheet with id=101, first strand: chain 'f' and resid 10 through 12 removed outlier: 5.381A pdb=" N ILE f 107 " --> pdb=" O ALA f 127 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA f 127 " --> pdb=" O ILE f 107 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ILE f 64 " --> pdb=" O MET f 126 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA f 62 " --> pdb=" O SER f 128 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain 'f' and resid 10 through 12 2370 hydrogen bonds defined for protein. 6714 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: 26.93 Time building geometry restraints manager: 22.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 22130 1.34 - 1.46: 12284 1.46 - 1.58: 34490 1.58 - 1.70: 6 1.70 - 1.82: 510 Bond restraints: 69420 Sorted by residual: bond pdb=" N PRO Y 109 " pdb=" CD PRO Y 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.90e+01 bond pdb=" N PRO D 109 " pdb=" CD PRO D 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.90e+01 bond pdb=" N PRO R 109 " pdb=" CD PRO R 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" N PRO c 109 " pdb=" CD PRO c 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 bond pdb=" N PRO K 109 " pdb=" CD PRO K 109 " ideal model delta sigma weight residual 1.473 1.548 -0.075 1.40e-02 5.10e+03 2.85e+01 ... (remaining 69415 not shown) Histogram of bond angle deviations from ideal: 96.52 - 105.08: 1906 105.08 - 113.64: 38050 113.64 - 122.21: 41544 122.21 - 130.77: 12496 130.77 - 139.33: 402 Bond angle restraints: 94398 Sorted by residual: angle pdb=" N ASP X 150 " pdb=" CA ASP X 150 " pdb=" C ASP X 150 " ideal model delta sigma weight residual 109.50 125.38 -15.88 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP B 150 " pdb=" CA ASP B 150 " pdb=" C ASP B 150 " ideal model delta sigma weight residual 109.50 125.38 -15.88 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP b 150 " pdb=" CA ASP b 150 " pdb=" C ASP b 150 " ideal model delta sigma weight residual 109.50 125.36 -15.86 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP Q 150 " pdb=" CA ASP Q 150 " pdb=" C ASP Q 150 " ideal model delta sigma weight residual 109.50 125.36 -15.86 1.58e+00 4.01e-01 1.01e+02 angle pdb=" N ASP 4 150 " pdb=" CA ASP 4 150 " pdb=" C ASP 4 150 " ideal model delta sigma weight residual 109.50 125.34 -15.84 1.58e+00 4.01e-01 1.01e+02 ... (remaining 94393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.75: 38208 14.75 - 29.51: 2336 29.51 - 44.26: 538 44.26 - 59.02: 48 59.02 - 73.77: 60 Dihedral angle restraints: 41190 sinusoidal: 15828 harmonic: 25362 Sorted by residual: dihedral pdb=" CA ALA D 102 " pdb=" C ALA D 102 " pdb=" N ALA D 103 " pdb=" CA ALA D 103 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA Y 102 " pdb=" C ALA Y 102 " pdb=" N ALA Y 103 " pdb=" CA ALA Y 103 " ideal model delta harmonic sigma weight residual 180.00 150.61 29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ALA c 102 " pdb=" C ALA c 102 " pdb=" N ALA c 103 " pdb=" CA ALA c 103 " ideal model delta harmonic sigma weight residual 180.00 150.62 29.38 0 5.00e+00 4.00e-02 3.45e+01 ... (remaining 41187 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 8840 0.087 - 0.174: 1442 0.174 - 0.260: 200 0.260 - 0.347: 6 0.347 - 0.434: 24 Chirality restraints: 10512 Sorted by residual: chirality pdb=" CB ILE W 225 " pdb=" CA ILE W 225 " pdb=" CG1 ILE W 225 " pdb=" CG2 ILE W 225 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB ILE A 225 " pdb=" CA ILE A 225 " pdb=" CG1 ILE A 225 " pdb=" CG2 ILE A 225 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" CB ILE 3 225 " pdb=" CA ILE 3 225 " pdb=" CG1 ILE 3 225 " pdb=" CG2 ILE 3 225 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 10509 not shown) Planarity restraints: 12396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY d 48 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO d 49 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO d 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO d 49 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY S 48 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO S 49 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO S 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO S 49 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY Z 48 " -0.049 5.00e-02 4.00e+02 7.37e-02 8.69e+00 pdb=" N PRO Z 49 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO Z 49 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO Z 49 " -0.042 5.00e-02 4.00e+02 ... (remaining 12393 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1510 2.67 - 3.23: 60710 3.23 - 3.78: 106932 3.78 - 4.34: 143156 4.34 - 4.90: 239630 Nonbonded interactions: 551938 Sorted by model distance: nonbonded pdb=" OD1 ASP b 150 " pdb=" N GLY b 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP Q 150 " pdb=" N GLY Q 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP J 150 " pdb=" N GLY J 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP 4 150 " pdb=" N GLY 4 151 " model vdw 2.110 2.520 nonbonded pdb=" OD1 ASP X 150 " pdb=" N GLY X 151 " model vdw 2.111 2.520 ... (remaining 551933 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '7' selection = chain 'E' selection = chain 'M' selection = chain 'T' selection = chain 'e' } ncs_group { reference = chain '1' selection = chain '8' selection = chain 'G' selection = chain 'N' selection = chain 'U' selection = chain 'f' } ncs_group { reference = chain '2' selection = (chain '5' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain '9' selection = chain 'C' selection = (chain 'D' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain 'H' selection = (chain 'K' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain 'O' selection = (chain 'R' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = chain 'V' selection = (chain 'Y' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) selection = (chain 'c' and (resid 1 through 30 or resid 33 through 171 or resid 175 through \ 197)) } ncs_group { reference = (chain '3' and (resid 24 through 85 or resid 90 through 393)) selection = chain '4' selection = (chain 'A' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'B' selection = (chain 'I' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'J' selection = (chain 'P' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'Q' selection = (chain 'W' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'X' selection = (chain 'a' and (resid 24 through 85 or resid 90 through 393)) selection = chain 'b' } ncs_group { reference = chain '6' selection = chain 'F' selection = chain 'L' selection = chain 'S' selection = chain 'Z' selection = chain 'd' } 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 276 5.16 5 C 43152 2.51 5 N 12198 2.21 5 O 12270 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.100 Extract box with map and model: 10.000 Check model and map are aligned: 0.750 Process input model: 137.450 Find NCS groups from input model: 3.840 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Set scattering table: 0.460 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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 : 0.009 0.075 69420 Z= 0.583 Angle : 1.238 15.877 94398 Z= 0.678 Chirality : 0.068 0.434 10512 Planarity : 0.009 0.074 12396 Dihedral : 10.848 73.774 24978 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.83 % Favored : 88.03 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.85 (0.06), residues: 8874 helix: -4.84 (0.03), residues: 2766 sheet: -2.76 (0.11), residues: 1638 loop : -3.69 (0.07), residues: 4470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17748 Ramachandran restraints generated. 8874 Oldfield, 0 Emsley, 8874 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1969 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1933 time to evaluate : 5.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 1957 average time/residue: 0.7314 time to fit residues: 2331.5933 Evaluate side-chains 1378 residues out of total 6690 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1360 time to evaluate : 5.587 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.7723 time to fit residues: 29.5228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 888 random chunks: chunk 749 optimal weight: 9.9990 chunk 673 optimal weight: 0.9990 chunk 373 optimal weight: 0.8980 chunk 229 optimal weight: 0.6980 chunk 454 optimal weight: 2.9990 chunk 359 optimal weight: 1.9990 chunk 696 optimal weight: 9.9990 chunk 269 optimal weight: 0.9990 chunk 423 optimal weight: 2.9990 chunk 518 optimal weight: 0.9990 chunk 806 optimal weight: 8.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN A 204 HIS ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 GLN A 381 ASN B 119 ASN B 204 HIS ** B 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS G 35 ASN ** I 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 204 HIS ** I 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 358 GLN J 204 HIS ** J 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 HIS L 15 GLN P 119 ASN P 204 HIS P 233 GLN ** P 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 358 GLN Q 204 HIS ** Q 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 283 HIS R 22 HIS S 15 GLN W 79 GLN ** W 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 358 GLN W 381 ASN X 119 ASN X 204 HIS ** X 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 35 ASN ** 3 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 204 HIS ** 3 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 358 GLN 4 119 ASN 4 204 HIS ** 4 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 22 HIS 6 15 GLN a 119 ASN a 204 HIS a 233 GLN ** a 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 358 GLN b 204 HIS ** b 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 22 HIS d 15 GLN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 69420 Z= 0.209 Angle : 0.742 14.797 94398 Z= 0.369 Chirality : 0.047 0.320 10512 Planarity : 0.006 0.066 12396 Dihedral : 6.104 27.682 9864 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.52 % Favored : 91.46 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.53 (0.07), residues: 8874 helix: -2.94 (0.07), residueTraceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/iotbx/cli_parser.py", line 865, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 285, in __init__ self.caller(self.update_phi_psi_targets) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 318, in caller self.log.flush() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4893/modules/cctbx_project/libtbx/utils.py", line 1570, in flush if (flush is not None): flush() IOError: [Errno 28] No space left on device