Starting phenix.real_space_refine (version: dev) on Thu Apr 21 23:15:04 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcj_0194/04_2022/6hcj_0194.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcj_0194/04_2022/6hcj_0194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcj_0194/04_2022/6hcj_0194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcj_0194/04_2022/6hcj_0194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcj_0194/04_2022/6hcj_0194.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hcj_0194/04_2022/6hcj_0194.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B2 ARG 128": "NH1" <-> "NH2" Residue "C2 ARG 51": "NH1" <-> "NH2" Residue "C2 PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 ARG 82": "NH1" <-> "NH2" Residue "C2 ARG 107": "NH1" <-> "NH2" Residue "C2 ARG 136": "NH1" <-> "NH2" Residue "C2 ARG 162": "NH1" <-> "NH2" Residue "C2 ARG 165": "NH1" <-> "NH2" Residue "C2 ARG 213": "NH1" <-> "NH2" Residue "D2 ARG 68": "NH1" <-> "NH2" Residue "D2 ARG 117": "NH1" <-> "NH2" Residue "D2 ARG 123": "NH1" <-> "NH2" Residue "D2 ARG 166": "NH1" <-> "NH2" Residue "D2 ARG 167": "NH1" <-> "NH2" Residue "D2 ARG 200": "NH1" <-> "NH2" Residue "D2 ARG 227": "NH1" <-> "NH2" Residue "E2 ARG 67": "NH1" <-> "NH2" Residue "E2 ARG 146": "NH1" <-> "NH2" Residue "F2 ARG 11": "NH1" <-> "NH2" Residue "F2 ARG 49": "NH1" <-> "NH2" Residue "F2 ARG 68": "NH1" <-> "NH2" Residue "F2 ARG 77": "NH1" <-> "NH2" Residue "F2 ARG 108": "NH1" <-> "NH2" Residue "F2 ARG 191": "NH1" <-> "NH2" Residue "F2 ARG 198": "NH1" <-> "NH2" Residue "F2 ARG 221": "NH1" <-> "NH2" Residue "F2 ARG 252": "NH1" <-> "NH2" Residue "G2 ARG 55": "NH1" <-> "NH2" Residue "G2 ARG 62": "NH1" <-> "NH2" Residue "G2 ARG 71": "NH1" <-> "NH2" Residue "G2 ARG 81": "NH1" <-> "NH2" Residue "G2 ARG 127": "NH1" <-> "NH2" Residue "G2 ARG 135": "NH1" <-> "NH2" Residue "G2 ARG 164": "NH1" <-> "NH2" Residue "G2 ARG 198": "NH1" <-> "NH2" Residue "H2 ARG 31": "NH1" <-> "NH2" Residue "H2 ARG 72": "NH1" <-> "NH2" Residue "H2 ARG 131": "NH1" <-> "NH2" Residue "H2 ARG 132": "NH1" <-> "NH2" Residue "H2 ARG 178": "NH1" <-> "NH2" Residue "H2 ARG 198": "NH1" <-> "NH2" Residue "H2 ARG 216": "NH1" <-> "NH2" Residue "H2 ARG 231": "NH1" <-> "NH2" Residue "H2 ARG 233": "NH1" <-> "NH2" Residue "I2 ARG 41": "NH1" <-> "NH2" Residue "I2 ARG 81": "NH1" <-> "NH2" Residue "I2 ARG 143": "NH1" <-> "NH2" Residue "J2 ARG 25": "NH1" <-> "NH2" Residue "J2 ARG 41": "NH1" <-> "NH2" Residue "J2 ARG 47": "NH1" <-> "NH2" Residue "J2 ARG 123": "NH1" <-> "NH2" Residue "J2 ARG 141": "NH1" <-> "NH2" Residue "K2 ARG 18": "NH1" <-> "NH2" Residue "K2 ARG 38": "NH1" <-> "NH2" Residue "K2 ARG 54": "NH1" <-> "NH2" Residue "K2 ARG 69": "NH1" <-> "NH2" Residue "K2 ARG 83": "NH1" <-> "NH2" Residue "K2 ARG 138": "NH1" <-> "NH2" Residue "K2 ARG 162": "NH1" <-> "NH2" Residue "L2 ARG 65": "NH1" <-> "NH2" Residue "L2 ARG 95": "NH1" <-> "NH2" Residue "L2 ARG 96": "NH1" <-> "NH2" Residue "M2 ARG 97": "NH1" <-> "NH2" Residue "N2 ARG 45": "NH1" <-> "NH2" Residue "O2 ARG 20": "NH1" <-> "NH2" Residue "O2 ARG 104": "NH1" <-> "NH2" Residue "O2 ARG 114": "NH1" <-> "NH2" Residue "O2 ARG 121": "NH1" <-> "NH2" Residue "P2 ARG 104": "NH1" <-> "NH2" Residue "P2 ARG 117": "NH1" <-> "NH2" Residue "P2 ARG 128": "NH1" <-> "NH2" Residue "P2 ARG 141": "NH1" <-> "NH2" Residue "P2 ARG 150": "NH1" <-> "NH2" Residue "Q2 ARG 42": "NH1" <-> "NH2" Residue "Q2 ARG 51": "NH1" <-> "NH2" Residue "Q2 ARG 59": "NH1" <-> "NH2" Residue "Q2 TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q2 ARG 130": "NH1" <-> "NH2" Residue "R2 ARG 126": "NH1" <-> "NH2" Residue "R2 ARG 140": "NH1" <-> "NH2" Residue "S2 ARG 5": "NH1" <-> "NH2" Residue "S2 ARG 63": "NH1" <-> "NH2" Residue "S2 ARG 81": "NH1" <-> "NH2" Residue "T2 ARG 14": "NH1" <-> "NH2" Residue "T2 ARG 39": "NH1" <-> "NH2" Residue "T2 ARG 55": "NH1" <-> "NH2" Residue "T2 ARG 86": "NH1" <-> "NH2" Residue "T2 ARG 121": "NH1" <-> "NH2" Residue "T2 ARG 142": "NH1" <-> "NH2" Residue "U2 ARG 16": "NH1" <-> "NH2" Residue "U2 ARG 62": "NH1" <-> "NH2" Residue "U2 ARG 84": "NH1" <-> "NH2" Residue "U2 ARG 102": "NH1" <-> "NH2" Residue "U2 ARG 121": "NH1" <-> "NH2" Residue "V2 ARG 19": "NH1" <-> "NH2" Residue "V2 ARG 87": "NH1" <-> "NH2" Residue "X2 ARG 36": "NH1" <-> "NH2" Residue "X2 PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y2 ARG 8": "NH1" <-> "NH2" Residue "Y2 ARG 17": "NH1" <-> "NH2" Residue "Y2 ARG 18": "NH1" <-> "NH2" Residue "Y2 ARG 67": "NH1" <-> "NH2" Residue "Y2 ARG 107": "NH1" <-> "NH2" Residue "Z2 ARG 20": "NH1" <-> "NH2" Residue "Z2 ARG 61": "NH1" <-> "NH2" Residue "Z2 ARG 110": "NH1" <-> "NH2" Residue "a2 ARG 80": "NH1" <-> "NH2" Residue "a2 ARG 85": "NH1" <-> "NH2" Residue "b2 ARG 10": "NH1" <-> "NH2" Residue "b2 ARG 85": "NH1" <-> "NH2" Residue "b2 ARG 87": "NH1" <-> "NH2" Residue "b2 ARG 89": "NH1" <-> "NH2" Residue "c2 ARG 72": "NH1" <-> "NH2" Residue "d2 ARG 13": "NH1" <-> "NH2" Residue "d2 ARG 40": "NH1" <-> "NH2" Residue "d2 ARG 44": "NH1" <-> "NH2" Residue "d2 ARG 66": "NH1" <-> "NH2" Residue "d2 ARG 67": "NH1" <-> "NH2" Residue "f2 ARG 101": "NH1" <-> "NH2" Residue "f2 ARG 104": "NH1" <-> "NH2" Residue "g2 ARG 138": "NH1" <-> "NH2" Residue "h2 ARG 47": "NH1" <-> "NH2" Residue "h2 ARG 60": "NH1" <-> "NH2" Residue "h2 ARG 100": "NH1" <-> "NH2" Residue "A3 ARG 193": "NH1" <-> "NH2" Residue "A3 ARG 242": "NH1" <-> "NH2" Residue "B3 ARG 10": "NH1" <-> "NH2" Residue "B3 ARG 268": "NH1" <-> "NH2" Residue "C3 ARG 5": "NH1" <-> "NH2" Residue "C3 ARG 49": "NH1" <-> "NH2" Residue "C3 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C3 ARG 306": "NH1" <-> "NH2" Residue "C3 ARG 323": "NH1" <-> "NH2" Residue "C3 ARG 337": "NH1" <-> "NH2" Residue "D3 ARG 15": "NH1" <-> "NH2" Residue "D3 ARG 23": "NH1" <-> "NH2" Residue "D3 ARG 24": "NH1" <-> "NH2" Residue "D3 ARG 33": "NH1" <-> "NH2" Residue "D3 ARG 50": "NH1" <-> "NH2" Residue "D3 ARG 108": "NH1" <-> "NH2" Residue "D3 ARG 179": "NH1" <-> "NH2" Residue "D3 ARG 209": "NH1" <-> "NH2" Residue "D3 ARG 259": "NH1" <-> "NH2" Residue "E3 ARG 61": "NH1" <-> "NH2" Residue "E3 ARG 126": "NH1" <-> "NH2" Residue "E3 ARG 164": "NH1" <-> "NH2" Residue "E3 ARG 191": "NH1" <-> "NH2" Residue "F3 ARG 45": "NH1" <-> "NH2" Residue "F3 ARG 93": "NH1" <-> "NH2" Residue "F3 ARG 156": "NH1" <-> "NH2" Residue "F3 ARG 235": "NH1" <-> "NH2" Residue "F3 ARG 244": "NH1" <-> "NH2" Residue "G3 ARG 166": "NH1" <-> "NH2" Residue "G3 ARG 242": "NH1" <-> "NH2" Residue "G3 ARG 287": "NH1" <-> "NH2" Residue "H3 ARG 23": "NH1" <-> "NH2" Residue "H3 ARG 89": "NH1" <-> "NH2" Residue "H3 ARG 127": "NH1" <-> "NH2" Residue "I3 ARG 4": "NH1" <-> "NH2" Residue "I3 ARG 69": "NH1" <-> "NH2" Residue "I3 ARG 98": "NH1" <-> "NH2" Residue "I3 ARG 116": "NH1" <-> "NH2" Residue "I3 ARG 153": "NH1" <-> "NH2" Residue "I3 ARG 162": "NH1" <-> "NH2" Residue "I3 ARG 203": "NH1" <-> "NH2" Residue "I3 ARG 210": "NH1" <-> "NH2" Residue "J3 ARG 35": "NH1" <-> "NH2" Residue "J3 ARG 64": "NH1" <-> "NH2" Residue "J3 ARG 146": "NH1" <-> "NH2" Residue "J3 ARG 164": "NH1" <-> "NH2" Residue "L3 ARG 31": "NH1" <-> "NH2" Residue "L3 ARG 49": "NH1" <-> "NH2" Residue "L3 ARG 65": "NH1" <-> "NH2" Residue "L3 ARG 102": "NH1" <-> "NH2" Residue "L3 ARG 116": "NH1" <-> "NH2" Residue "L3 ARG 158": "NH1" <-> "NH2" Residue "M3 ARG 11": "NH1" <-> "NH2" Residue "M3 ARG 98": "NH1" <-> "NH2" Residue "M3 ARG 109": "NH1" <-> "NH2" Residue "M3 ARG 119": "NH1" <-> "NH2" Residue "M3 ARG 121": "NH1" <-> "NH2" Residue "N3 ARG 24": "NH1" <-> "NH2" Residue "N3 ARG 50": "NH1" <-> "NH2" Residue "N3 ARG 65": "NH1" <-> "NH2" Residue "N3 ARG 96": "NH1" <-> "NH2" Residue "N3 ARG 169": "NH1" <-> "NH2" Residue "N3 ARG 189": "NH1" <-> "NH2" Residue "N3 ARG 194": "NH1" <-> "NH2" Residue "O3 ARG 78": "NH1" <-> "NH2" Residue "O3 ARG 128": "NH1" <-> "NH2" Residue "O3 ARG 140": "NH1" <-> "NH2" Residue "P3 ARG 3": "NH1" <-> "NH2" Residue "P3 ARG 62": "NH1" <-> "NH2" Residue "Q3 ARG 37": "NH1" <-> "NH2" Residue "Q3 ARG 55": "NH1" <-> "NH2" Residue "Q3 ARG 91": "NH1" <-> "NH2" Residue "Q3 ARG 134": "NH1" <-> "NH2" Residue "Q3 ARG 180": "NH1" <-> "NH2" Residue "Q3 ARG 181": "NH1" <-> "NH2" Residue "R3 ARG 38": "NH1" <-> "NH2" Residue "R3 ARG 42": "NH1" <-> "NH2" Residue "R3 ARG 74": "NH1" <-> "NH2" Residue "R3 ARG 117": "NH1" <-> "NH2" Residue "R3 ARG 173": "NH1" <-> "NH2" Residue "R3 ARG 176": "NH1" <-> "NH2" Residue "S3 ARG 31": "NH1" <-> "NH2" Residue "S3 ARG 43": "NH1" <-> "NH2" Residue "S3 ARG 83": "NH1" <-> "NH2" Residue "S3 ARG 111": "NH1" <-> "NH2" Residue "S3 ARG 118": "NH1" <-> "NH2" Residue "S3 ARG 139": "NH1" <-> "NH2" Residue "S3 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S3 ARG 161": "NH1" <-> "NH2" Residue "S3 ARG 166": "NH1" <-> "NH2" Residue "T3 ARG 130": "NH1" <-> "NH2" Residue "U3 ARG 65": "NH1" <-> "NH2" Residue "V3 ARG 48": "NH1" <-> "NH2" Residue "V3 ARG 51": "NH1" <-> "NH2" Residue "V3 ARG 85": "NH1" <-> "NH2" Residue "V3 ARG 89": "NH1" <-> "NH2" Residue "V3 TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V3 ARG 131": "NH1" <-> "NH2" Residue "X3 ARG 53": "NH1" <-> "NH2" Residue "X3 ARG 129": "NH1" <-> "NH2" Residue "X3 ARG 139": "NH1" <-> "NH2" Residue "Y3 ARG 27": "NH1" <-> "NH2" Residue "Y3 ARG 87": "NH1" <-> "NH2" Residue "Z3 ARG 65": "NH1" <-> "NH2" Residue "a3 ARG 4": "NH1" <-> "NH2" Residue "a3 ARG 9": "NH1" <-> "NH2" Residue "a3 ARG 21": "NH1" <-> "NH2" Residue "a3 ARG 65": "NH1" <-> "NH2" Residue "a3 ARG 105": "NH1" <-> "NH2" Residue "b3 ARG 14": "NH1" <-> "NH2" Residue "b3 ARG 18": "NH1" <-> "NH2" Residue "b3 ARG 25": "NH1" <-> "NH2" Residue "b3 ARG 28": "NH1" <-> "NH2" Residue "b3 ARG 95": "NH1" <-> "NH2" Residue "b3 ARG 109": "NH1" <-> "NH2" Residue "b3 ARG 111": "NH1" <-> "NH2" Residue "c3 ARG 39": "NH1" <-> "NH2" Residue "c3 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d3 ARG 90": "NH1" <-> "NH2" Residue "e3 ARG 36": "NH1" <-> "NH2" Residue "e3 ARG 39": "NH1" <-> "NH2" Residue "e3 ARG 108": "NH1" <-> "NH2" Residue "e3 ARG 128": "NH1" <-> "NH2" Residue "f3 ARG 89": "NH1" <-> "NH2" Residue "g3 ARG 29": "NH1" <-> "NH2" Residue "g3 ARG 60": "NH1" <-> "NH2" Residue "h3 ARG 48": "NH1" <-> "NH2" Residue "h3 ARG 84": "NH1" <-> "NH2" Residue "h3 ARG 89": "NH1" <-> "NH2" Residue "h3 ARG 94": "NH1" <-> "NH2" Residue "i3 ARG 68": "NH1" <-> "NH2" Residue "i3 ARG 76": "NH1" <-> "NH2" Residue "j3 ARG 11": "NH1" <-> "NH2" Residue "j3 ARG 20": "NH1" <-> "NH2" Residue "j3 ARG 45": "NH1" <-> "NH2" Residue "j3 ARG 55": "NH1" <-> "NH2" Residue "j3 ARG 56": "NH1" <-> "NH2" Residue "j3 ARG 72": "NH1" <-> "NH2" Residue "j3 ARG 79": "NH1" <-> "NH2" Residue "k3 ARG 3": "NH1" <-> "NH2" Residue "l3 ARG 8": "NH1" <-> "NH2" Residue "l3 ARG 21": "NH1" <-> "NH2" Residue "l3 ARG 36": "NH1" <-> "NH2" Residue "m3 ARG 71": "NH1" <-> "NH2" Residue "m3 ARG 85": "NH1" <-> "NH2" Residue "n3 ARG 2": "NH1" <-> "NH2" Residue "n3 ARG 9": "NH1" <-> "NH2" Residue "n3 ARG 15": "NH1" <-> "NH2" Residue "n3 ARG 23": "NH1" <-> "NH2" Residue "o3 ARG 40": "NH1" <-> "NH2" Residue "o3 ARG 43": "NH1" <-> "NH2" Residue "o3 ARG 69": "NH1" <-> "NH2" Residue "o3 ARG 78": "NH1" <-> "NH2" Residue "p3 ARG 17": "NH1" <-> "NH2" Residue "p3 ARG 49": "NH1" <-> "NH2" Residue "p3 ARG 84": "NH1" <-> "NH2" Residue "r3 ARG 35": "NH1" <-> "NH2" Residue "r3 ARG 39": "NH1" <-> "NH2" Residue "r3 ARG 71": "NH1" <-> "NH2" Residue "r3 ARG 107": "NH1" <-> "NH2" Residue "r3 ARG 112": "NH1" <-> "NH2" Residue "r3 ARG 113": "NH1" <-> "NH2" Residue "u3 ARG 16": "NH1" <-> "NH2" Residue "u3 ARG 57": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 219683 Number of models: 1 Model: "" Number of chains: 106 Chain: "51" Number of atoms: 77827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3635, 77827 Classifications: {'RNA': 3630, 'DNA': 5} Modifications used: {'rna3p_pyr': 1414, 'rna2p_pur': 364, 'rna3p_pur': 1629, 'rna2p_pyr': 219} Link IDs: {'rna3p': 3051, 'rna2p': 583} Chain breaks: 32 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {' U:plan': 4, ' G:plan2': 2, ' C:plan': 3, ' C:plan2': 3, ' G:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "71" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 7, 'rna3p_pyr': 52} Link IDs: {'rna3p': 106, 'rna2p': 13} Chain: "81" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3208 Classifications: {'RNA': 151} Modifications used: {'rna3p_pyr': 63, 'rna2p_pur': 14, 'rna3p_pur': 59, 'rna2p_pyr': 15, '5*END': 1} Link IDs: {'rna3p': 122, 'rna2p': 28} Chain breaks: 1 Chain: "A2" Number of atoms: 37141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1740, 37141 Classifications: {'RNA': 1740} Modifications used: {'5*END': 1, 'rna2p_pur': 150, 'rna3p_pur': 768, 'rna2p_pyr': 115, 'rna3p_pyr': 707} Link IDs: {'rna3p': 1475, 'rna2p': 264} Chain breaks: 22 Chain: "B2" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1710 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 204} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C2" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1729 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 5, 'TRANS': 207} Chain: "D2" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1716 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 12, 'TRANS': 208} Chain: "E2" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1765 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 11, 'TRANS': 216} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F2" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2076 Classifications: {'peptide': 262} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 247} Chain: "G2" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1471 Classifications: {'peptide': 185} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain breaks: 1 Chain: "H2" Number of atoms: 1923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1923 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 10, 'TRANS': 226} Chain: "I2" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1488 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain breaks: 1 Chain: "J2" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1686 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "K2" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1525 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'CIS': 1, 'TRANS': 177} Chain: "L2" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 810 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 7, 'TRANS': 88} Chain: "M2" Number of atoms: 1175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1175 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "N2" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "O2" Number of atoms: 1202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1202 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 8, 'TRANS': 140} Chain: "P2" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1016 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain: "Q2" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 997 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 7, 'TRANS': 112} Chain: "R2" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S2" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1068 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 6, 'TRANS': 125} Chain: "T2" Number of atoms: 1190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1190 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "U2" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1097 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "V2" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 795 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 5, 'TRANS': 94} Chain: "W2" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 636 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "X2" Number of atoms: 1034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1034 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 125, 'PCIS': 1} Chain: "Y2" Number of atoms: 1098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1098 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 5, 'TRANS': 135} Chain: "Z2" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1011 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "a2" Number of atoms: 598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 598 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "b2" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 814 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "c2" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 651 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "d2" Number of atoms: 488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 488 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "e2" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "f2" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 443 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "g2" Number of atoms: 555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 555 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "h2" Number of atoms: 2436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2436 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain: "A3" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'CIS': 1, 'TRANS': 232} Chain: "B3" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3172 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "C3" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D3" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2391 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "E3" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain breaks: 3 Chain: "F3" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1875 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "G3" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain breaks: 2 Chain: "H3" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I3" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1664 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "J3" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1362 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "L3" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1674 Classifications: {'peptide': 207} Link IDs: {'PTRANS': 14, 'TRANS': 192} Chain: "M3" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N3" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "O3" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1630 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P3" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q3" Number of atoms: 1515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1515 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R3" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'CIS': 1, 'TRANS': 175} Chain: "S3" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1462 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "T3" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U3" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 809 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V3" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "X3" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "Y3" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1102 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 5, 'TRANS': 126} Chain: "Z3" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a3" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b3" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Chain: "c3" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 761 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "d3" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e3" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f3" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "g3" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "h3" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i3" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j3" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k3" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l3" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 447 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m3" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "n3" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "o3" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p3" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "r3" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "q3" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1579 Classifications: {'RNA': 74} Modifications used: {'5*END': 1, 'rna2p_pur': 8, 'rna3p_pur': 31, 'rna2p_pyr': 5, 'rna3p_pyr': 30} Link IDs: {'rna3p': 60, 'rna2p': 13} Chain breaks: 3 Chain: "t3" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "u3" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1160 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "v3" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 463 Classifications: {'RNA': 22} Modifications used: {'rna3p_pyr': 10, 'rna2p_pur': 4, 'rna3p_pur': 5, 'rna2p_pyr': 3} Link IDs: {'rna3p': 14, 'rna2p': 7} Chain: "33" Number of atoms: 1604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1604 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna3p_pur': 32, 'rna2p_pyr': 2, 'rna3p_pyr': 31} Link IDs: {'rna3p': 63, 'rna2p': 11} Chain: "w3" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1741 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 208} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "1" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "51" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 200 Unusual residues: {' MG': 200} Classifications: {'undetermined': 200} Link IDs: {None: 199} Chain: "71" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "81" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "A2" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 76 Unusual residues: {' MG': 76} Classifications: {'undetermined': 76} Link IDs: {None: 75} Chain: "G2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "b2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "g2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B3" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "q3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A15HG SG CYSb2 23 112.908 167.889 178.896 1.00 32.02 S ATOM A15SO SG CYSb2 74 112.681 170.006 174.886 1.00 32.73 S ATOM A15T7 SG CYSb2 77 110.845 166.992 175.482 1.00 35.11 S ATOM A16ZD SG CYSe2 21 70.824 166.729 110.262 1.00 37.35 S ATOM A1701 SG CYSe2 24 74.801 169.973 110.591 1.00 43.22 S ATOM A173E SG CYSe2 39 72.956 166.896 113.142 1.00 36.49 S ATOM A285Q SG CYSg3 46 176.646 168.372 219.627 1.00 32.63 S ATOM A2867 SG CYSg3 49 176.821 172.346 218.125 1.00 41.08 S ATOM A28DI SG CYSg3 83 179.087 171.828 221.424 1.00 28.73 S ATOM A28E2 SG CYSg3 86 175.256 170.729 221.928 1.00 28.00 S ATOM A2A3T SG CYSj3 19 204.762 121.129 195.608 1.00 21.79 S ATOM A2A4L SG CYSj3 22 206.007 118.767 193.096 1.00 21.88 S ATOM A2A74 SG CYSj3 34 202.286 120.791 192.172 1.00 21.16 S ATOM A2A7N SG CYSj3 37 202.799 117.694 194.332 1.00 18.32 S ATOM A2BG8 SG CYSm3 70 187.608 143.006 79.718 1.00 25.62 S ATOM A2BGY SG CYSm3 73 191.045 143.951 81.447 1.00 25.58 S ATOM A2BJG SG CYSm3 84 191.652 142.708 78.050 1.00 26.21 S ATOM A2BKO SG CYSm3 89 191.116 140.404 80.755 1.00 29.27 S ATOM A2BWT SG CYSo3 12 135.695 68.271 149.812 1.00 37.37 S ATOM A2BXH SG CYSo3 15 133.385 65.348 150.932 1.00 38.18 S ATOM A2CBJ SG CYSo3 77 134.429 67.910 153.268 1.00 69.30 S Time building chain proxies: 82.34, per 1000 atoms: 0.37 Number of scatterers: 219683 At special positions: 0 Unit cell: (299.44, 308.56, 288.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 430 16.00 P 5812 15.00 Mg 300 11.99 O 56736 8.00 N 40909 7.00 C 115488 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSp3 42 " - pdb=" SG CYSp3 60 " distance=2.03 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: 68.68 Conformation dependent library (CDL) restraints added in 9.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZNb2 202 " pdb="ZN ZNb2 202 " - pdb=" SG CYSb2 77 " pdb="ZN ZNb2 202 " - pdb=" SG CYSb2 74 " pdb="ZN ZNb2 202 " - pdb=" SG CYSb2 23 " pdb=" ZNe2 100 " pdb="ZN ZNe2 100 " - pdb=" SG CYSe2 39 " pdb="ZN ZNe2 100 " - pdb=" SG CYSe2 21 " pdb="ZN ZNe2 100 " - pdb=" SG CYSe2 24 " pdb=" ZNg3 201 " pdb="ZN ZNg3 201 " - pdb=" SG CYSg3 46 " pdb="ZN ZNg3 201 " - pdb=" SG CYSg3 86 " pdb="ZN ZNg3 201 " - pdb=" SG CYSg3 49 " pdb="ZN ZNg3 201 " - pdb=" SG CYSg3 83 " pdb=" ZNj3 101 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 22 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 34 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 19 " pdb="ZN ZNj3 101 " - pdb=" SG CYSj3 37 " pdb=" ZNm3 200 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 89 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 84 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 70 " pdb="ZN ZNm3 200 " - pdb=" SG CYSm3 73 " pdb=" ZNo3 200 " pdb="ZN ZNo3 200 " - pdb=" SG CYSo3 15 " pdb="ZN ZNo3 200 " - pdb=" SG CYSo3 12 " pdb="ZN ZNo3 200 " - pdb=" SG CYSo3 77 " Number of angles added : 18 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21998 Finding SS restraints... Secondary structure from input PDB file: 377 helices and 131 sheets defined 27.2% alpha, 11.0% beta 447 base pairs and 2265 stacking pairs defined. Time for finding SS restraints: 46.99 Creating SS restraints... Processing helix chain 'B2' and resid 11 through 22 removed outlier: 3.968A pdb=" N LYSB2 17 " --> pdb=" O GLUB2 13 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALAB2 21 " --> pdb=" O LYSB2 17 " (cutoff:3.500A) Processing helix chain 'B2' and resid 31 through 36 removed outlier: 4.096A pdb=" N GLUB2 35 " --> pdb=" O PHEB2 32 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N GLNB2 36 " --> pdb=" O GLNB2 33 " (cutoff:3.500A) Processing helix chain 'B2' and resid 51 through 66 removed outlier: 3.811A pdb=" N LYSB2 57 " --> pdb=" O ARGB2 53 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEUB2 59 " --> pdb=" O TRPB2 55 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEUB2 60 " --> pdb=" O GLUB2 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALAB2 64 " --> pdb=" O LEUB2 60 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VALB2 66 " --> pdb=" O ALAB2 62 " (cutoff:3.500A) Processing helix chain 'B2' and resid 70 through 74 removed outlier: 4.121A pdb=" N ASPB2 73 " --> pdb=" O ASNB2 70 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N VALB2 74 " --> pdb=" O PROB2 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'B2' and resid 70 through 74' Processing helix chain 'B2' and resid 85 through 94 removed outlier: 4.276A pdb=" N ALAB2 91 " --> pdb=" O VALB2 87 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALAB2 92 " --> pdb=" O LEUB2 88 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALAB2 93 " --> pdb=" O LYSB2 89 " (cutoff:3.500A) Processing helix chain 'B2' and resid 132 through 137 Processing helix chain 'B2' and resid 167 through 182 removed outlier: 4.023A pdb=" N VALB2 171 " --> pdb=" O GLYB2 167 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLYB2 172 " --> pdb=" O ALAB2 168 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TRPB2 175 " --> pdb=" O VALB2 171 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRPB2 176 " --> pdb=" O GLYB2 172 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLUB2 181 " --> pdb=" O METB2 177 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VALB2 182 " --> pdb=" O LEUB2 178 " (cutoff:3.500A) Processing helix chain 'B2' and resid 208 through 213 Processing helix chain 'C2' and resid 23 through 27 removed outlier: 3.818A pdb=" N SERC2 26 " --> pdb=" O ASPC2 23 " (cutoff:3.500A) Processing helix chain 'C2' and resid 59 through 64 removed outlier: 4.403A pdb=" N GLYC2 64 " --> pdb=" O ASPC2 60 " (cutoff:3.500A) Processing helix chain 'C2' and resid 72 through 74 No H-bonds generated for 'chain 'C2' and resid 72 through 74' Processing helix chain 'C2' and resid 106 through 111 removed outlier: 3.504A pdb=" N CYSC2 111 " --> pdb=" O ARGC2 107 " (cutoff:3.500A) Processing helix chain 'C2' and resid 158 through 175 removed outlier: 3.507A pdb=" N GLNC2 163 " --> pdb=" O GLNC2 159 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ILEC2 164 " --> pdb=" O GLNC2 160 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYSC2 166 " --> pdb=" O ARGC2 162 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYSC2 167 " --> pdb=" O GLNC2 163 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N METC2 169 " --> pdb=" O ARGC2 165 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THRC2 173 " --> pdb=" O METC2 169 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARGC2 174 " --> pdb=" O GLUC2 170 " (cutoff:3.500A) Processing helix chain 'C2' and resid 181 through 186 removed outlier: 3.826A pdb=" N VALC2 185 " --> pdb=" O LEUC2 181 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASNC2 186 " --> pdb=" O LYSC2 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 181 through 186' Processing helix chain 'C2' and resid 191 through 200 removed outlier: 3.606A pdb=" N ASPC2 196 " --> pdb=" O SERC2 192 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLUC2 198 " --> pdb=" O GLYC2 194 " (cutoff:3.500A) Processing helix chain 'C2' and resid 225 through 231 removed outlier: 3.945A pdb=" N METC2 229 " --> pdb=" O LEUC2 225 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEUC2 231 " --> pdb=" O LYSC2 227 " (cutoff:3.500A) Processing helix chain 'D2' and resid 64 through 72 removed outlier: 3.940A pdb=" N LEUD2 69 " --> pdb=" O LYSD2 65 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VALD2 70 " --> pdb=" O LEUD2 66 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYSD2 71 " --> pdb=" O GLYD2 67 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASPD2 72 " --> pdb=" O ARGD2 68 " (cutoff:3.500A) Processing helix chain 'D2' and resid 90 through 92 No H-bonds generated for 'chain 'D2' and resid 90 through 92' Processing helix chain 'D2' and resid 93 through 98 Processing helix chain 'D2' and resid 146 through 160 removed outlier: 3.586A pdb=" N ALAD2 150 " --> pdb=" O GLUD2 146 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILED2 151 " --> pdb=" O VALD2 147 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARGD2 152 " --> pdb=" O ALAD2 148 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ILED2 156 " --> pdb=" O ARGD2 152 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEUD2 157 " --> pdb=" O GLYD2 153 " (cutoff:3.500A) Processing helix chain 'D2' and resid 209 through 216 removed outlier: 3.991A pdb=" N LEUD2 213 " --> pdb=" O VALD2 209 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N METD2 216 " --> pdb=" O LYSD2 212 " (cutoff:3.500A) Processing helix chain 'D2' and resid 232 through 243 removed outlier: 3.855A pdb=" N LYSD2 238 " --> pdb=" O GLYD2 234 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THRD2 240 " --> pdb=" O PHED2 236 " (cutoff:3.500A) Processing helix chain 'D2' and resid 271 through 275 removed outlier: 3.840A pdb=" N VALD2 274 " --> pdb=" O ASPD2 271 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYSD2 275 " --> pdb=" O HISD2 272 " (cutoff:3.500A) No H-bonds generated for 'chain 'D2' and resid 271 through 275' Processing helix chain 'E2' and resid 9 through 14 Processing helix chain 'E2' and resid 15 through 25 removed outlier: 3.522A pdb=" N LEUE2 21 " --> pdb=" O PHEE2 17 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ASNE2 22 " --> pdb=" O LYSE2 18 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLUE2 23 " --> pdb=" O ALAE2 19 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEUE2 25 " --> pdb=" O LEUE2 21 " (cutoff:3.500A) Processing helix chain 'E2' and resid 55 through 59 removed outlier: 3.689A pdb=" N VALE2 58 " --> pdb=" O THRE2 55 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEUE2 59 " --> pdb=" O GLNE2 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'E2' and resid 55 through 59' Processing helix chain 'E2' and resid 63 through 78 removed outlier: 3.766A pdb=" N ARGE2 67 " --> pdb=" O GLYE2 63 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEUE2 69 " --> pdb=" O ARGE2 65 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALAE2 71 " --> pdb=" O ARGE2 67 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLNE2 74 " --> pdb=" O THRE2 70 " (cutoff:3.500A) Processing helix chain 'E2' and resid 93 through 96 Processing helix chain 'E2' and resid 97 through 107 removed outlier: 4.053A pdb=" N SERE2 104 " --> pdb=" O ALAE2 100 " (cutoff:3.500A) Processing helix chain 'E2' and resid 114 through 129 removed outlier: 3.628A pdb=" N ALAE2 118 " --> pdb=" O ALAE2 114 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N CYSE2 119 " --> pdb=" O VALE2 115 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N TYRE2 120 " --> pdb=" O ARGE2 116 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLYE2 121 " --> pdb=" O ARGE2 117 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N PHEE2 125 " --> pdb=" O GLYE2 121 " (cutoff:3.500A) Processing helix chain 'E2' and resid 161 through 165 removed outlier: 3.616A pdb=" N VALE2 164 " --> pdb=" O GLYE2 161 " (cutoff:3.500A) Processing helix chain 'F2' and resid 15 through 19 removed outlier: 3.706A pdb=" N TRPF2 18 " --> pdb=" O PROF2 15 " (cutoff:3.500A) Processing helix chain 'F2' and resid 44 through 48 Processing helix chain 'F2' and resid 57 through 66 removed outlier: 3.724A pdb=" N VALF2 61 " --> pdb=" O THRF2 57 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LYSF2 62 " --> pdb=" O GLYF2 58 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILEF2 64 " --> pdb=" O GLUF2 60 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N CYSF2 65 " --> pdb=" O VALF2 61 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N METF2 66 " --> pdb=" O LYSF2 62 " (cutoff:3.500A) Processing helix chain 'F2' and resid 223 through 225 No H-bonds generated for 'chain 'F2' and resid 223 through 225' Processing helix chain 'F2' and resid 250 through 257 removed outlier: 3.843A pdb=" N LYSF2 254 " --> pdb=" O GLUF2 250 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARGF2 255 " --> pdb=" O GLUF2 251 " (cutoff:3.500A) Processing helix chain 'F2' and resid 258 through 263 removed outlier: 4.118A pdb=" N SERF2 262 " --> pdb=" O ALAF2 258 " (cutoff:3.500A) Processing helix chain 'G2' and resid 62 through 66 removed outlier: 3.630A pdb=" N GLNG2 65 " --> pdb=" O ARGG2 62 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N CYSG2 66 " --> pdb=" O LYSG2 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G2' and resid 62 through 66' Processing helix chain 'G2' and resid 67 through 75 Processing helix chain 'G2' and resid 85 through 102 removed outlier: 3.817A pdb=" N THRG2 89 " --> pdb=" O LYSG2 85 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ARGG2 91 " --> pdb=" O LEUG2 87 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILEG2 92 " --> pdb=" O METG2 88 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VALG2 93 " --> pdb=" O THRG2 89 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLUG2 98 " --> pdb=" O LYSG2 94 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILEG2 99 " --> pdb=" O HISG2 95 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILEG2 100 " --> pdb=" O ALAG2 96 " (cutoff:3.500A) Processing helix chain 'G2' and resid 107 through 120 removed outlier: 3.903A pdb=" N VALG2 113 " --> pdb=" O LEUG2 109 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILEG2 117 " --> pdb=" O VALG2 113 " (cutoff:3.500A) Processing helix chain 'G2' and resid 142 through 161 removed outlier: 4.000A pdb=" N TRPG2 152 " --> pdb=" O ASNG2 148 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEUG2 154 " --> pdb=" O ALAG2 150 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARGG2 159 " --> pdb=" O CYSG2 155 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLUG2 160 " --> pdb=" O THRG2 156 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALAG2 161 " --> pdb=" O GLYG2 157 " (cutoff:3.500A) Processing helix chain 'G2' and resid 168 through 179 removed outlier: 3.720A pdb=" N ASPG2 175 " --> pdb=" O GLUG2 171 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILEG2 178 " --> pdb=" O ALAG2 174 " (cutoff:3.500A) Processing helix chain 'G2' and resid 190 through 203 removed outlier: 3.842A pdb=" N ASPG2 194 " --> pdb=" O ILEG2 190 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLUG2 195 " --> pdb=" O LYSG2 191 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N VALG2 199 " --> pdb=" O GLUG2 195 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALAG2 200 " --> pdb=" O LEUG2 196 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASNG2 203 " --> pdb=" O VALG2 199 " (cutoff:3.500A) Processing helix chain 'H2' and resid 139 through 144 removed outlier: 3.963A pdb=" N LEUH2 144 " --> pdb=" O ARGH2 140 " (cutoff:3.500A) Processing helix chain 'H2' and resid 185 through 190 removed outlier: 3.878A pdb=" N ARGH2 190 " --> pdb=" O GLNH2 186 " (cutoff:3.500A) Processing helix chain 'H2' and resid 194 through 205 removed outlier: 3.666A pdb=" N LYSH2 200 " --> pdb=" O LYSH2 196 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLUH2 205 " --> pdb=" O LYSH2 201 " (cutoff:3.500A) Processing helix chain 'H2' and resid 205 through 217 removed outlier: 3.572A pdb=" N TYRH2 209 " --> pdb=" O GLUH2 205 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARGH2 216 " --> pdb=" O LEUH2 212 " (cutoff:3.500A) Processing helix chain 'H2' and resid 217 through 237 removed outlier: 4.134A pdb=" N ARGH2 224 " --> pdb=" O ALAH2 220 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILEH2 228 " --> pdb=" O ARGH2 224 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALAH2 229 " --> pdb=" O GLNH2 225 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARGH2 233 " --> pdb=" O ALAH2 229 " (cutoff:3.500A) Processing helix chain 'I2' and resid 19 through 27 removed outlier: 3.841A pdb=" N ILEI2 23 " --> pdb=" O PHEI2 19 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLNI2 25 " --> pdb=" O SERI2 21 " (cutoff:3.500A) Processing helix chain 'I2' and resid 28 through 33 removed outlier: 3.595A pdb=" N METI2 32 " --> pdb=" O LEUI2 28 " (cutoff:3.500A) Processing helix chain 'I2' and resid 68 through 74 removed outlier: 3.761A pdb=" N PHEI2 72 " --> pdb=" O GLNI2 68 " (cutoff:3.500A) Processing helix chain 'I2' and resid 76 through 87 removed outlier: 4.350A pdb=" N ARGI2 81 " --> pdb=" O VALI2 77 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLUI2 82 " --> pdb=" O ARGI2 78 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEUI2 83 " --> pdb=" O LEUI2 79 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYSI2 85 " --> pdb=" O ARGI2 81 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHEI2 87 " --> pdb=" O LEUI2 83 " (cutoff:3.500A) Processing helix chain 'I2' and resid 121 through 126 removed outlier: 3.549A pdb=" N VALI2 125 " --> pdb=" O THRI2 121 " (cutoff:3.500A) Processing helix chain 'I2' and resid 128 through 134 removed outlier: 4.040A pdb=" N VALI2 134 " --> pdb=" O LEUI2 130 " (cutoff:3.500A) Processing helix chain 'I2' and resid 166 through 168 No H-bonds generated for 'chain 'I2' and resid 166 through 168' Processing helix chain 'I2' and resid 169 through 181 removed outlier: 3.615A pdb=" N PHEI2 173 " --> pdb=" O LYSI2 169 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SERI2 174 " --> pdb=" O VALI2 170 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLYI2 175 " --> pdb=" O GLUI2 171 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYSI2 178 " --> pdb=" O SERI2 174 " (cutoff:3.500A) Processing helix chain 'J2' and resid 49 through 51 No H-bonds generated for 'chain 'J2' and resid 49 through 51' Processing helix chain 'J2' and resid 106 through 110 Processing helix chain 'J2' and resid 133 through 138 removed outlier: 4.145A pdb=" N LEUJ2 137 " --> pdb=" O GLUJ2 133 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASNJ2 138 " --> pdb=" O GLUJ2 134 " (cutoff:3.500A) No H-bonds generated for 'chain 'J2' and resid 133 through 138' Processing helix chain 'J2' and resid 144 through 155 removed outlier: 3.820A pdb=" N GLUJ2 151 " --> pdb=" O LYSJ2 147 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARGJ2 152 " --> pdb=" O LYSJ2 148 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYSJ2 154 " --> pdb=" O ASPJ2 150 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASNJ2 155 " --> pdb=" O GLUJ2 151 " (cutoff:3.500A) Processing helix chain 'J2' and resid 159 through 164 removed outlier: 3.845A pdb=" N GLUJ2 164 " --> pdb=" O SERJ2 160 " (cutoff:3.500A) Processing helix chain 'J2' and resid 178 through 183 removed outlier: 3.683A pdb=" N GLYJ2 183 " --> pdb=" O PROJ2 179 " (cutoff:3.500A) Processing helix chain 'J2' and resid 194 through 201 removed outlier: 3.558A pdb=" N LYSJ2 201 " --> pdb=" O PHEJ2 197 " (cutoff:3.500A) Processing helix chain 'K2' and resid 23 through 34 removed outlier: 3.835A pdb=" N GLNK2 27 " --> pdb=" O SERK2 23 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEUK2 29 " --> pdb=" O LEUK2 25 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEUK2 31 " --> pdb=" O GLNK2 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILEK2 32 " --> pdb=" O GLUK2 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLYK2 33 " --> pdb=" O LEUK2 29 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLUK2 34 " --> pdb=" O LYSK2 30 " (cutoff:3.500A) Processing helix chain 'K2' and resid 40 through 58 removed outlier: 3.660A pdb=" N TRPK2 44 " --> pdb=" O LYSK2 40 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VALK2 46 " --> pdb=" O GLUK2 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THRK2 49 " --> pdb=" O ARGK2 45 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILEK2 53 " --> pdb=" O THRK2 49 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALAK2 56 " --> pdb=" O LYSK2 52 " (cutoff:3.500A) Processing helix chain 'K2' and resid 67 through 78 removed outlier: 3.923A pdb=" N PHEK2 72 " --> pdb=" O PROK2 68 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASNK2 75 " --> pdb=" O LEUK2 71 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALAK2 76 " --> pdb=" O PHEK2 72 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEUK2 78 " --> pdb=" O GLYK2 74 " (cutoff:3.500A) Processing helix chain 'K2' and resid 78 through 83 removed outlier: 3.517A pdb=" N ARGK2 83 " --> pdb=" O ARGK2 79 " (cutoff:3.500A) Processing helix chain 'K2' and resid 88 through 92 removed outlier: 3.784A pdb=" N METK2 92 " --> pdb=" O GLUK2 89 " (cutoff:3.500A) Processing helix chain 'K2' and resid 102 through 107 removed outlier: 3.858A pdb=" N LEUK2 106 " --> pdb=" O ILEK2 102 " (cutoff:3.500A) Processing helix chain 'K2' and resid 109 through 117 removed outlier: 3.914A pdb=" N PHEK2 115 " --> pdb=" O GLNK2 111 " (cutoff:3.500A) Processing helix chain 'K2' and resid 123 through 131 removed outlier: 4.248A pdb=" N ARGK2 127 " --> pdb=" O ILEK2 123 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VALK2 128 " --> pdb=" O HISK2 124 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEUK2 129 " --> pdb=" O HISK2 125 " (cutoff:3.500A) Processing helix chain 'L2' and resid 4 through 18 removed outlier: 3.601A pdb=" N ILEL2 9 " --> pdb=" O LYSL2 5 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILEL2 11 " --> pdb=" O ASNL2 7 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEUL2 14 " --> pdb=" O ALAL2 10 " (cutoff:3.500A) Processing helix chain 'L2' and resid 42 through 54 removed outlier: 3.791A pdb=" N ALAL2 48 " --> pdb=" O HISL2 44 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N METL2 49 " --> pdb=" O VALL2 45 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SERL2 51 " --> pdb=" O LYSL2 47 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEUL2 52 " --> pdb=" O ALAL2 48 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N SERL2 54 " --> pdb=" O GLNL2 50 " (cutoff:3.500A) Processing helix chain 'L2' and resid 73 through 83 removed outlier: 4.259A pdb=" N GLNL2 77 " --> pdb=" O ASNL2 73 " (cutoff:3.500A) Processing helix chain 'M2' and resid 48 through 53 removed outlier: 4.067A pdb=" N GLUM2 52 " --> pdb=" O LYSM2 48 " (cutoff:3.500A) Processing helix chain 'N2' and resid 17 through 22 removed outlier: 3.911A pdb=" N VALN2 21 " --> pdb=" O ALAN2 17 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEUN2 22 " --> pdb=" O LEUN2 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'N2' and resid 17 through 22' Processing helix chain 'N2' and resid 34 through 43 removed outlier: 3.713A pdb=" N ALAN2 39 " --> pdb=" O ILEN2 35 " (cutoff:3.500A) Processing helix chain 'N2' and resid 58 through 63 Processing helix chain 'N2' and resid 65 through 70 removed outlier: 3.604A pdb=" N CYSN2 69 " --> pdb=" O VALN2 65 " (cutoff:3.500A) Processing helix chain 'N2' and resid 84 through 89 Processing helix chain 'N2' and resid 118 through 125 removed outlier: 4.449A pdb=" N ASPN2 122 " --> pdb=" O SERN2 118 " (cutoff:3.500A) Processing helix chain 'N2' and resid 126 through 128 No H-bonds generated for 'chain 'N2' and resid 126 through 128' Processing helix chain 'O2' and resid 32 through 44 removed outlier: 3.691A pdb=" N LEUO2 40 " --> pdb=" O GLNO2 36 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYSO2 42 " --> pdb=" O TYRO2 38 " (cutoff:3.500A) Processing helix chain 'O2' and resid 46 through 54 removed outlier: 3.876A pdb=" N GLYO2 51 " --> pdb=" O PROO2 47 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VALO2 52 " --> pdb=" O SERO2 48 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILEO2 53 " --> pdb=" O GLNO2 49 " (cutoff:3.500A) Processing helix chain 'O2' and resid 62 through 67 removed outlier: 3.517A pdb=" N VALO2 66 " --> pdb=" O GLNO2 62 " (cutoff:3.500A) Processing helix chain 'O2' and resid 70 through 77 removed outlier: 3.523A pdb=" N ILEO2 74 " --> pdb=" O LYSO2 70 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SERO2 77 " --> pdb=" O ARGO2 73 " (cutoff:3.500A) Processing helix chain 'O2' and resid 85 through 90 removed outlier: 3.682A pdb=" N HISO2 90 " --> pdb=" O GLUO2 86 " (cutoff:3.500A) Processing helix chain 'O2' and resid 92 through 104 removed outlier: 3.808A pdb=" N ARGO2 99 " --> pdb=" O ALAO2 95 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N HISO2 101 " --> pdb=" O ALAO2 97 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARGO2 104 " --> pdb=" O LYSO2 100 " (cutoff:3.500A) Processing helix chain 'O2' and resid 108 through 124 removed outlier: 4.063A pdb=" N ILEO2 116 " --> pdb=" O LYSO2 112 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEUO2 117 " --> pdb=" O PHEO2 113 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARGO2 121 " --> pdb=" O LEUO2 117 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N HISO2 123 " --> pdb=" O GLUO2 119 " (cutoff:3.500A) Processing helix chain 'O2' and resid 128 through 133 removed outlier: 3.755A pdb=" N LYSO2 132 " --> pdb=" O TYRO2 128 " (cutoff:3.500A) Processing helix chain 'P2' and resid 64 through 68 removed outlier: 4.044A pdb=" N GLUP2 68 " --> pdb=" O ASPP2 65 " (cutoff:3.500A) Processing helix chain 'P2' and resid 71 through 76 removed outlier: 3.594A pdb=" N METP2 75 " --> pdb=" O PROP2 71 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEUP2 76 " --> pdb=" O TYRP2 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'P2' and resid 71 through 76' Processing helix chain 'P2' and resid 78 through 86 removed outlier: 3.955A pdb=" N LYSP2 86 " --> pdb=" O ALAP2 82 " (cutoff:3.500A) Processing helix chain 'P2' and resid 112 through 121 removed outlier: 4.210A pdb=" N ARGP2 117 " --> pdb=" O GLNP2 113 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ALAP2 118 " --> pdb=" O SERP2 114 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEUP2 119 " --> pdb=" O ALAP2 115 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 21 through 26 Processing helix chain 'Q2' and resid 29 through 34 removed outlier: 3.742A pdb=" N LEUQ2 33 " --> pdb=" O SERQ2 29 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 41 through 46 Processing helix chain 'Q2' and resid 50 through 61 removed outlier: 3.558A pdb=" N SERQ2 55 " --> pdb=" O ARGQ2 51 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEUQ2 56 " --> pdb=" O LYSQ2 52 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEUQ2 57 " --> pdb=" O GLNQ2 53 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARGQ2 59 " --> pdb=" O SERQ2 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEUQ2 60 " --> pdb=" O LEUQ2 56 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARGQ2 61 " --> pdb=" O LEUQ2 57 " (cutoff:3.500A) Processing helix chain 'R2' and resid 52 through 57 removed outlier: 3.527A pdb=" N LEUR2 57 " --> pdb=" O GLUR2 53 " (cutoff:3.500A) Processing helix chain 'R2' and resid 85 through 99 removed outlier: 3.503A pdb=" N ALAR2 94 " --> pdb=" O LYSR2 90 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYSR2 98 " --> pdb=" O ALAR2 94 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYRR2 99 " --> pdb=" O TYRR2 95 " (cutoff:3.500A) Processing helix chain 'R2' and resid 104 through 114 removed outlier: 3.924A pdb=" N ILER2 108 " --> pdb=" O SERR2 104 " (cutoff:3.500A) Processing helix chain 'R2' and resid 116 through 120 removed outlier: 3.503A pdb=" N LEUR2 119 " --> pdb=" O ASPR2 116 " (cutoff:3.500A) Processing helix chain 'S2' and resid 6 through 20 removed outlier: 3.600A pdb=" N LYSS2 10 " --> pdb=" O THRS2 6 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALAS2 12 " --> pdb=" O THRS2 8 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARGS2 14 " --> pdb=" O LYSS2 10 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VALS2 15 " --> pdb=" O LYSS2 11 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILES2 16 " --> pdb=" O ALAS2 12 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILES2 17 " --> pdb=" O ALAS2 13 " (cutoff:3.500A) Processing helix chain 'S2' and resid 27 through 35 removed outlier: 3.935A pdb=" N ASNS2 31 " --> pdb=" O ASPS2 27 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ARGS2 33 " --> pdb=" O HISS2 29 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VALS2 34 " --> pdb=" O THRS2 30 " (cutoff:3.500A) Processing helix chain 'S2' and resid 44 through 62 removed outlier: 3.579A pdb=" N TYRS2 53 " --> pdb=" O LYSS2 49 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THRS2 55 " --> pdb=" O ALAS2 51 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N HISS2 56 " --> pdb=" O GLYS2 52 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYSS2 59 " --> pdb=" O THRS2 55 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ARGS2 60 " --> pdb=" O HISS2 56 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLNS2 62 " --> pdb=" O METS2 58 " (cutoff:3.500A) Processing helix chain 'S2' and resid 74 through 84 Processing helix chain 'S2' and resid 99 through 109 removed outlier: 3.883A pdb=" N METS2 105 " --> pdb=" O ASPS2 101 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEUS2 106 " --> pdb=" O THRS2 102 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYSS2 107 " --> pdb=" O LYSS2 103 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEUS2 108 " --> pdb=" O GLUS2 104 " (cutoff:3.500A) Processing helix chain 'T2' and resid 25 through 33 removed outlier: 5.340A pdb=" N ILET2 30 " --> pdb=" O ALAT2 27 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THRT2 31 " --> pdb=" O PHET2 28 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALAT2 32 " --> pdb=" O ALAT2 29 " (cutoff:3.500A) Processing helix chain 'T2' and resid 37 through 48 removed outlier: 3.549A pdb=" N ALAT2 41 " --> pdb=" O GLYT2 37 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HIST2 42 " --> pdb=" O ARGT2 38 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VALT2 43 " --> pdb=" O ARGT2 39 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARGT2 46 " --> pdb=" O HIST2 42 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALAT2 48 " --> pdb=" O VALT2 44 " (cutoff:3.500A) Processing helix chain 'T2' and resid 66 through 73 Processing helix chain 'T2' and resid 101 through 117 removed outlier: 3.813A pdb=" N LEUT2 107 " --> pdb=" O LEUT2 103 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARGT2 108 " --> pdb=" O ASPT2 104 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEUT2 111 " --> pdb=" O LEUT2 107 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLUT2 112 " --> pdb=" O ARGT2 108 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYST2 116 " --> pdb=" O GLUT2 112 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILET2 117 " --> pdb=" O ARGT2 113 " (cutoff:3.500A) Processing helix chain 'U2' and resid 5 through 9 removed outlier: 3.998A pdb=" N ASPU2 8 " --> pdb=" O THRU2 5 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VALU2 9 " --> pdb=" O VALU2 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'U2' and resid 5 through 9' Processing helix chain 'U2' and resid 17 through 25 removed outlier: 4.009A pdb=" N LYSU2 24 " --> pdb=" O ALAU2 20 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SERU2 25 " --> pdb=" O PHEU2 21 " (cutoff:3.500A) Processing helix chain 'U2' and resid 52 through 67 removed outlier: 3.833A pdb=" N ARGU2 56 " --> pdb=" O TRPU2 52 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALAU2 58 " --> pdb=" O TYRU2 54 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALAU2 61 " --> pdb=" O ALAU2 57 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARGU2 62 " --> pdb=" O ALAU2 58 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N TYRU2 65 " --> pdb=" O ALAU2 61 " (cutoff:3.500A) Processing helix chain 'U2' and resid 96 through 107 removed outlier: 3.662A pdb=" N ALAU2 100 " --> pdb=" O SERU2 96 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARGU2 102 " --> pdb=" O SERU2 98 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VALU2 103 " --> pdb=" O VALU2 99 " (cutoff:3.500A) Processing helix chain 'U2' and resid 124 through 142 removed outlier: 4.083A pdb=" N ASPU2 130 " --> pdb=" O GLNU2 126 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILEU2 134 " --> pdb=" O ASPU2 130 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALAU2 135 " --> pdb=" O LEUU2 131 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLYU2 136 " --> pdb=" O ASPU2 132 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLNU2 137 " --> pdb=" O ARGU2 133 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALAU2 140 " --> pdb=" O GLYU2 136 " (cutoff:3.500A) Processing helix chain 'V2' and resid 29 through 37 Processing helix chain 'V2' and resid 37 through 45 removed outlier: 3.509A pdb=" N ARGV2 41 " --> pdb=" O ALAV2 37 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ALAV2 43 " --> pdb=" O LEUV2 39 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLUV2 45 " --> pdb=" O ARGV2 41 " (cutoff:3.500A) Processing helix chain 'V2' and resid 97 through 102 Processing helix chain 'W2' and resid 56 through 63 removed outlier: 3.944A pdb=" N ARGW2 60 " --> pdb=" O CYSW2 56 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARGW2 61 " --> pdb=" O GLYW2 57 " (cutoff:3.500A) Processing helix chain 'W2' and resid 64 through 76 removed outlier: 3.946A pdb=" N SERW2 68 " --> pdb=" O GLUW2 64 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASPW2 76 " --> pdb=" O LEUW2 72 " (cutoff:3.500A) Processing helix chain 'X2' and resid 6 through 11 removed outlier: 3.743A pdb=" N LEUX2 11 " --> pdb=" O LEUX2 7 " (cutoff:3.500A) Processing helix chain 'X2' and resid 31 through 42 removed outlier: 3.963A pdb=" N VALX2 40 " --> pdb=" O ARGX2 36 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N METX2 41 " --> pdb=" O PHEX2 37 " (cutoff:3.500A) Processing helix chain 'X2' and resid 113 through 120 removed outlier: 3.752A pdb=" N ARGX2 117 " --> pdb=" O HISX2 113 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARGX2 118 " --> pdb=" O GLUX2 114 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HISX2 120 " --> pdb=" O ALAX2 116 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 9 through 21 removed outlier: 3.865A pdb=" N LEUY2 13 " --> pdb=" O THRY2 9 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SERY2 15 " --> pdb=" O ARGY2 11 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASPY2 19 " --> pdb=" O SERY2 15 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 24 through 31 removed outlier: 4.048A pdb=" N LYSY2 28 " --> pdb=" O ASPY2 24 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYSY2 29 " --> pdb=" O LYSY2 25 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALAY2 30 " --> pdb=" O GLNY2 26 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 89 through 94 removed outlier: 3.599A pdb=" N PHEY2 93 " --> pdb=" O CYSY2 90 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 130 through 136 Processing helix chain 'Z2' and resid 36 through 41 removed outlier: 3.706A pdb=" N ARGZ2 41 " --> pdb=" O LYSZ2 37 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 44 through 49 removed outlier: 3.864A pdb=" N TYRZ2 48 " --> pdb=" O LEUZ2 44 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 78 through 82 Processing helix chain 'Z2' and resid 87 through 95 removed outlier: 3.899A pdb=" N LEUZ2 91 " --> pdb=" O PROZ2 87 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALAZ2 92 " --> pdb=" O LYSZ2 88 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ARGZ2 93 " --> pdb=" O HISZ2 89 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N HISZ2 94 " --> pdb=" O ARGZ2 90 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 104 through 117 removed outlier: 3.603A pdb=" N GLUZ2 109 " --> pdb=" O LYSZ2 105 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARGZ2 110 " --> pdb=" O GLNZ2 106 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYSZ2 115 " --> pdb=" O LYSZ2 111 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYSZ2 116 " --> pdb=" O ASNZ2 112 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VALZ2 117 " --> pdb=" O ARGZ2 113 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 119 through 123 removed outlier: 3.671A pdb=" N LYSZ2 122 " --> pdb=" O GLYZ2 119 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALAZ2 123 " --> pdb=" O THRZ2 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z2' and resid 119 through 123' Processing helix chain 'a2' and resid 54 through 59 removed outlier: 3.944A pdb=" N LEUa2 58 " --> pdb=" O THRa2 54 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYSa2 59 " --> pdb=" O TYRa2 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'a2' and resid 54 through 59' Processing helix chain 'a2' and resid 61 through 65 Processing helix chain 'a2' and resid 69 through 77 removed outlier: 3.590A pdb=" N SERa2 74 " --> pdb=" O PROa2 70 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLUa2 75 " --> pdb=" O ALAa2 71 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARGa2 76 " --> pdb=" O VALa2 72 " (cutoff:3.500A) Processing helix chain 'a2' and resid 83 through 88 Processing helix chain 'a2' and resid 89 through 95 removed outlier: 4.037A pdb=" N SERa2 93 " --> pdb=" O GLNa2 89 " (cutoff:3.500A) Processing helix chain 'b2' and resid 33 through 35 No H-bonds generated for 'chain 'b2' and resid 33 through 35' Processing helix chain 'b2' and resid 49 through 54 removed outlier: 3.783A pdb=" N SERb2 54 " --> pdb=" O VALb2 50 " (cutoff:3.500A) Processing helix chain 'b2' and resid 74 through 81 removed outlier: 3.561A pdb=" N HISb2 80 " --> pdb=" O SERb2 76 " (cutoff:3.500A) Processing helix chain 'e2' and resid 2 through 6 removed outlier: 3.593A pdb=" N LEUe2 6 " --> pdb=" O HISe2 3 " (cutoff:3.500A) Processing helix chain 'e2' and resid 32 through 36 removed outlier: 3.560A pdb=" N GLYe2 35 " --> pdb=" O ARGe2 32 " (cutoff:3.500A) Processing helix chain 'e2' and resid 40 through 46 removed outlier: 3.739A pdb=" N ARGe2 44 " --> pdb=" O ARGe2 40 " (cutoff:3.500A) Processing helix chain 'e2' and resid 46 through 51 removed outlier: 3.750A pdb=" N ILEe2 50 " --> pdb=" O TYRe2 46 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLYe2 51 " --> pdb=" O ALAe2 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'e2' and resid 46 through 51' Processing helix chain 'f2' and resid 85 through 89 removed outlier: 4.175A pdb=" N THRf2 89 " --> pdb=" O ARGf2 86 " (cutoff:3.500A) Processing helix chain 'f2' and resid 103 through 113 removed outlier: 3.765A pdb=" N ARGf2 107 " --> pdb=" O GLYf2 103 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASNf2 112 " --> pdb=" O ARGf2 108 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARGf2 113 " --> pdb=" O METf2 109 " (cutoff:3.500A) Processing helix chain 'g2' and resid 100 through 105 removed outlier: 3.591A pdb=" N LYSg2 104 " --> pdb=" O ALAg2 101 " (cutoff:3.500A) Processing helix chain 'A3' and resid 5 through 9 Processing helix chain 'A3' and resid 34 through 39 removed outlier: 3.686A pdb=" N HISA3 38 " --> pdb=" O PHEA3 34 " (cutoff:3.500A) Processing helix chain 'B3' and resid 13 through 17 removed outlier: 3.812A pdb=" N PHEB3 16 " --> pdb=" O SERB3 13 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEUB3 17 " --> pdb=" O LEUB3 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 13 through 17' Processing helix chain 'B3' and resid 111 through 116 removed outlier: 3.796A pdb=" N ARGB3 116 " --> pdb=" O ASPB3 112 " (cutoff:3.500A) Processing helix chain 'B3' and resid 132 through 136 Processing helix chain 'B3' and resid 142 through 151 removed outlier: 3.889A pdb=" N ASPB3 147 " --> pdb=" O LYSB3 143 " (cutoff:3.500A) Processing helix chain 'B3' and resid 189 through 200 removed outlier: 3.982A pdb=" N GLUB3 199 " --> pdb=" O ASPB3 195 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARGB3 200 " --> pdb=" O TRPB3 196 " (cutoff:3.500A) Processing helix chain 'B3' and resid 231 through 236 removed outlier: 3.912A pdb=" N TRPB3 235 " --> pdb=" O VALB3 231 " (cutoff:3.500A) Processing helix chain 'B3' and resid 381 through 386 removed outlier: 4.219A pdb=" N LYSB3 385 " --> pdb=" O THRB3 381 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYSB3 386 " --> pdb=" O VALB3 382 " (cutoff:3.500A) No H-bonds generated for 'chain 'B3' and resid 381 through 386' Processing helix chain 'C3' and resid 26 through 30 removed outlier: 3.815A pdb=" N LYSC3 29 " --> pdb=" O ALAC3 26 " (cutoff:3.500A) Processing helix chain 'C3' and resid 33 through 45 removed outlier: 3.718A pdb=" N VALC3 37 " --> pdb=" O ARGC3 33 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHEC3 39 " --> pdb=" O ASPC3 35 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THRC3 42 " --> pdb=" O ASNC3 38 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASNC3 43 " --> pdb=" O PHEC3 39 " (cutoff:3.500A) Processing helix chain 'C3' and resid 46 through 48 No H-bonds generated for 'chain 'C3' and resid 46 through 48' Processing helix chain 'C3' and resid 116 through 129 removed outlier: 3.672A pdb=" N LYSC3 120 " --> pdb=" O ASNC3 116 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N TYRC3 122 " --> pdb=" O THRC3 118 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILEC3 124 " --> pdb=" O LYSC3 120 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N CYSC3 125 " --> pdb=" O ARGC3 121 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALAC3 129 " --> pdb=" O CYSC3 125 " (cutoff:3.500A) Processing helix chain 'C3' and resid 155 through 159 removed outlier: 3.644A pdb=" N VALC3 158 " --> pdb=" O GLUC3 155 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLUC3 159 " --> pdb=" O ASPC3 156 " (cutoff:3.500A) No H-bonds generated for 'chain 'C3' and resid 155 through 159' Processing helix chain 'C3' and resid 163 through 168 removed outlier: 3.693A pdb=" N VALC3 168 " --> pdb=" O LYSC3 165 " (cutoff:3.500A) Processing helix chain 'C3' and resid 169 through 174 removed outlier: 3.613A pdb=" N LYSC3 173 " --> pdb=" O LEUC3 169 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEUC3 174 " --> pdb=" O LEUC3 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'C3' and resid 169 through 174' Processing helix chain 'C3' and resid 176 through 185 removed outlier: 4.070A pdb=" N ILEC3 180 " --> pdb=" O ALAC3 176 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYSC3 182 " --> pdb=" O ASNC3 178 " (cutoff:3.500A) Processing helix chain 'C3' and resid 217 through 221 removed outlier: 3.672A pdb=" N PHEC3 221 " --> pdb=" O VALC3 218 " (cutoff:3.500A) Processing helix chain 'C3' and resid 255 through 257 No H-bonds generated for 'chain 'C3' and resid 255 through 257' Processing helix chain 'C3' and resid 259 through 264 removed outlier: 3.600A pdb=" N TYRC3 264 " --> pdb=" O LEUC3 260 " (cutoff:3.500A) Processing helix chain 'C3' and resid 289 through 294 removed outlier: 4.051A pdb=" N LEUC3 293 " --> pdb=" O LEUC3 289 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LYSC3 294 " --> pdb=" O SERC3 290 " (cutoff:3.500A) No H-bonds generated for 'chain 'C3' and resid 289 through 294' Processing helix chain 'C3' and resid 324 through 329 Processing helix chain 'C3' and resid 330 through 333 removed outlier: 3.759A pdb=" N LYSC3 333 " --> pdb=" O PROC3 330 " (cutoff:3.500A) No H-bonds generated for 'chain 'C3' and resid 330 through 333' Processing helix chain 'C3' and resid 347 through 358 removed outlier: 3.791A pdb=" N VALC3 351 " --> pdb=" O HISC3 347 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLUC3 352 " --> pdb=" O LYSC3 348 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARGC3 353 " --> pdb=" O LEUC3 349 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ALAC3 356 " --> pdb=" O GLUC3 352 " (cutoff:3.500A) Processing helix chain 'D3' and resid 20 through 25 Processing helix chain 'D3' and resid 29 through 38 removed outlier: 4.454A pdb=" N ARGD3 35 " --> pdb=" O TYRD3 31 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEUD3 36 " --> pdb=" O ALAD3 32 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILED3 38 " --> pdb=" O LYSD3 34 " (cutoff:3.500A) Processing helix chain 'D3' and resid 94 through 114 removed outlier: 3.655A pdb=" N GLYD3 102 " --> pdb=" O ALAD3 98 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARGD3 108 " --> pdb=" O LEUD3 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARGD3 112 " --> pdb=" O ARGD3 108 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLYD3 114 " --> pdb=" O LEUD3 110 " (cutoff:3.500A) Processing helix chain 'D3' and resid 160 through 170 removed outlier: 3.884A pdb=" N GLYD3 170 " --> pdb=" O ALAD3 166 " (cutoff:3.500A) Processing helix chain 'D3' and resid 192 through 200 removed outlier: 3.568A pdb=" N HISD3 198 " --> pdb=" O VALD3 194 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N METD3 200 " --> pdb=" O ARGD3 196 " (cutoff:3.500A) Processing helix chain 'D3' and resid 201 through 206 Processing helix chain 'D3' and resid 207 through 209 No H-bonds generated for 'chain 'D3' and resid 207 through 209' Processing helix chain 'D3' and resid 239 through 246 removed outlier: 3.959A pdb=" N ALAD3 243 " --> pdb=" O METD3 239 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALAD3 246 " --> pdb=" O LYSD3 242 " (cutoff:3.500A) Processing helix chain 'D3' and resid 272 through 290 removed outlier: 3.899A pdb=" N LYSD3 276 " --> pdb=" O SERD3 272 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYSD3 277 " --> pdb=" O LEUD3 273 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ASPD3 278 " --> pdb=" O ALAD3 274 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VALD3 280 " --> pdb=" O LYSD3 276 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALAD3 281 " --> pdb=" O LYSD3 277 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLND3 282 " --> pdb=" O ASPD3 278 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYSD3 284 " --> pdb=" O VALD3 280 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALAD3 285 " --> pdb=" O ALAD3 281 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEUD3 288 " --> pdb=" O LYSD3 284 " (cutoff:3.500A) Processing helix chain 'E3' and resid 62 through 69 removed outlier: 3.544A pdb=" N SERE3 66 " --> pdb=" O SERE3 62 " (cutoff:3.500A) Processing helix chain 'E3' and resid 135 through 139 removed outlier: 3.709A pdb=" N HISE3 139 " --> pdb=" O PHEE3 136 " (cutoff:3.500A) Processing helix chain 'E3' and resid 181 through 186 removed outlier: 3.898A pdb=" N ARGE3 186 " --> pdb=" O LEUE3 182 " (cutoff:3.500A) Processing helix chain 'E3' and resid 216 through 221 removed outlier: 3.915A pdb=" N PHEE3 220 " --> pdb=" O THRE3 216 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYSE3 221 " --> pdb=" O ASPE3 217 " (cutoff:3.500A) No H-bonds generated for 'chain 'E3' and resid 216 through 221' Processing helix chain 'E3' and resid 248 through 266 removed outlier: 4.059A pdb=" N LYSE3 254 " --> pdb=" O LYSE3 250 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLNE3 259 " --> pdb=" O ALAE3 255 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEUE3 261 " --> pdb=" O ASPE3 257 " (cutoff:3.500A) Proline residue: E3 262 - end of helix removed outlier: 3.670A pdb=" N ALAE3 266 " --> pdb=" O PROE3 262 " (cutoff:3.500A) Processing helix chain 'F3' and resid 25 through 78 removed outlier: 4.178A pdb=" N ILEF3 29 " --> pdb=" O ALAF3 25 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYSF3 34 " --> pdb=" O LYSF3 30 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYSF3 35 " --> pdb=" O ARGF3 31 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLNF3 38 " --> pdb=" O LYSF3 34 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYSF3 39 " --> pdb=" O LYSF3 35 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEUF3 41 " --> pdb=" O ALAF3 37 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARGF3 42 " --> pdb=" O GLNF3 38 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEUF3 48 " --> pdb=" O ALAF3 44 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILEF3 49 " --> pdb=" O ARGF3 45 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYRF3 50 " --> pdb=" O ARGF3 46 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYRF3 56 " --> pdb=" O LYSF3 52 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARGF3 61 " --> pdb=" O HISF3 57 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLUF3 67 " --> pdb=" O METF3 63 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILEF3 68 " --> pdb=" O TYRF3 64 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N METF3 70 " --> pdb=" O THRF3 66 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALAF3 71 " --> pdb=" O GLUF3 67 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALAF3 74 " --> pdb=" O METF3 70 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARGF3 75 " --> pdb=" O ALAF3 71 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALAF3 77 " --> pdb=" O METF3 73 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLYF3 78 " --> pdb=" O ALAF3 74 " (cutoff:3.500A) Processing helix chain 'F3' and resid 101 through 108 removed outlier: 3.556A pdb=" N LYSF3 106 " --> pdb=" O PROF3 102 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VALF3 107 " --> pdb=" O LYSF3 103 " (cutoff:3.500A) Processing helix chain 'F3' and resid 125 through 130 removed outlier: 4.187A pdb=" N ASNF3 130 " --> pdb=" O LYSF3 126 " (cutoff:3.500A) Processing helix chain 'F3' and resid 146 through 154 removed outlier: 3.824A pdb=" N ASNF3 150 " --> pdb=" O LEUF3 146 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEUF3 152 " --> pdb=" O SERF3 148 " (cutoff:3.500A) Processing helix chain 'F3' and resid 170 through 172 No H-bonds generated for 'chain 'F3' and resid 170 through 172' Processing helix chain 'F3' and resid 173 through 178 removed outlier: 4.531A pdb=" N SERF3 177 " --> pdb=" O LEUF3 173 " (cutoff:3.500A) Processing helix chain 'F3' and resid 179 through 182 removed outlier: 4.039A pdb=" N ASNF3 182 " --> pdb=" O GLYF3 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'F3' and resid 179 through 182' Processing helix chain 'F3' and resid 185 through 195 removed outlier: 3.980A pdb=" N LEUF3 189 " --> pdb=" O CYSF3 185 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILEF3 190 " --> pdb=" O METF3 186 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N HISF3 191 " --> pdb=" O GLUF3 187 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THRF3 195 " --> pdb=" O HISF3 191 " (cutoff:3.500A) Processing helix chain 'F3' and resid 200 through 204 removed outlier: 3.500A pdb=" N ASNF3 204 " --> pdb=" O LYSF3 201 " (cutoff:3.500A) Processing helix chain 'F3' and resid 238 through 242 removed outlier: 3.609A pdb=" N LEUF3 242 " --> pdb=" O ILEF3 239 " (cutoff:3.500A) Processing helix chain 'G3' and resid 119 through 127 removed outlier: 4.827A pdb=" N LYSG3 125 " --> pdb=" O ALAG3 121 " (cutoff:3.500A) Processing helix chain 'G3' and resid 143 through 154 removed outlier: 3.758A pdb=" N LYSG3 150 " --> pdb=" O THRG3 146 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYSG3 154 " --> pdb=" O LYSG3 150 " (cutoff:3.500A) Processing helix chain 'G3' and resid 159 through 161 No H-bonds generated for 'chain 'G3' and resid 159 through 161' Processing helix chain 'G3' and resid 162 through 176 removed outlier: 3.928A pdb=" N LYSG3 173 " --> pdb=" O ALAG3 169 " (cutoff:3.500A) Processing helix chain 'G3' and resid 216 through 220 removed outlier: 3.786A pdb=" N LEUG3 219 " --> pdb=" O PROG3 216 " (cutoff:3.500A) Processing helix chain 'G3' and resid 222 through 227 removed outlier: 3.550A pdb=" N LEUG3 226 " --> pdb=" O PHEG3 222 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYSG3 227 " --> pdb=" O LEUG3 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'G3' and resid 222 through 227' Processing helix chain 'G3' and resid 264 through 277 removed outlier: 4.523A pdb=" N LEUG3 271 " --> pdb=" O ALAG3 267 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALAG3 274 " --> pdb=" O LYSG3 270 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILEG3 275 " --> pdb=" O LEUG3 271 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ARGG3 276 " --> pdb=" O VALG3 272 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N THRG3 277 " --> pdb=" O GLUG3 273 " (cutoff:3.500A) Processing helix chain 'G3' and resid 279 through 283 removed outlier: 4.187A pdb=" N TYRG3 283 " --> pdb=" O ASNG3 280 " (cutoff:3.500A) Processing helix chain 'G3' and resid 296 through 311 removed outlier: 3.702A pdb=" N ALAG3 301 " --> pdb=" O PROG3 297 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARGG3 302 " --> pdb=" O LYSG3 298 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILEG3 303 " --> pdb=" O SERG3 299 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYSG3 308 " --> pdb=" O ALAG3 304 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALAG3 309 " --> pdb=" O LYSG3 305 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYSG3 310 " --> pdb=" O LEUG3 306 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALAG3 311 " --> pdb=" O GLUG3 307 " (cutoff:3.500A) Processing helix chain 'G3' and resid 311 through 316 removed outlier: 4.145A pdb=" N THRG3 316 " --> pdb=" O LYSG3 312 " (cutoff:3.500A) Processing helix chain 'H3' and resid 67 through 69 No H-bonds generated for 'chain 'H3' and resid 67 through 69' Processing helix chain 'H3' and resid 70 through 86 removed outlier: 4.044A pdb=" N CYSH3 74 " --> pdb=" O VALH3 70 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N HISH3 76 " --> pdb=" O THRH3 72 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N METH3 80 " --> pdb=" O HISH3 76 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VALH3 84 " --> pdb=" O METH3 80 " (cutoff:3.500A) Processing helix chain 'H3' and resid 116 through 120 removed outlier: 3.794A pdb=" N GLYH3 119 " --> pdb=" O ASNH3 116 " (cutoff:3.500A) Processing helix chain 'H3' and resid 150 through 164 removed outlier: 3.656A pdb=" N ASNH3 156 " --> pdb=" O GLUH3 152 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SERH3 157 " --> pdb=" O LEUH3 153 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILEH3 161 " --> pdb=" O SERH3 157 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLNH3 162 " --> pdb=" O ALAH3 158 " (cutoff:3.500A) Processing helix chain 'I3' and resid 69 through 79 removed outlier: 4.175A pdb=" N TYRI3 75 " --> pdb=" O CYSI3 71 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N METI3 76 " --> pdb=" O ALAI3 72 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYSI3 78 " --> pdb=" O LYSI3 74 " (cutoff:3.500A) Processing helix chain 'I3' and resid 148 through 154 removed outlier: 3.816A pdb=" N ARGI3 154 " --> pdb=" O GLUI3 150 " (cutoff:3.500A) Processing helix chain 'I3' and resid 178 through 181 removed outlier: 3.895A pdb=" N PHEI3 181 " --> pdb=" O ALAI3 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I3' and resid 178 through 181' Processing helix chain 'I3' and resid 182 through 187 removed outlier: 3.656A pdb=" N ALAI3 186 " --> pdb=" O GLUI3 182 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLUI3 187 " --> pdb=" O ASPI3 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'I3' and resid 182 through 187' Processing helix chain 'I3' and resid 205 through 214 removed outlier: 4.075A pdb=" N TRPI3 209 " --> pdb=" O PROI3 205 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALAI3 211 " --> pdb=" O ASPI3 207 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEUI3 212 " --> pdb=" O LYSI3 208 " (cutoff:3.500A) Processing helix chain 'J3' and resid 30 through 36 removed outlier: 4.082A pdb=" N THRJ3 34 " --> pdb=" O GLYJ3 30 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALAJ3 36 " --> pdb=" O ARGJ3 32 " (cutoff:3.500A) Processing helix chain 'J3' and resid 38 through 44 removed outlier: 3.730A pdb=" N GLNJ3 42 " --> pdb=" O LYSJ3 38 " (cutoff:3.500A) Processing helix chain 'J3' and resid 76 through 88 removed outlier: 3.682A pdb=" N GLUJ3 80 " --> pdb=" O GLYJ3 76 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N GLUJ3 81 " --> pdb=" O ALAJ3 77 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILEJ3 82 " --> pdb=" O LYSJ3 78 " (cutoff:3.500A) Processing helix chain 'J3' and resid 95 through 99 removed outlier: 3.583A pdb=" N PHEJ3 99 " --> pdb=" O LYSJ3 96 " (cutoff:3.500A) Processing helix chain 'J3' and resid 111 through 116 removed outlier: 3.757A pdb=" N ASPJ3 114 " --> pdb=" O GLUJ3 111 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEUJ3 115 " --> pdb=" O HISJ3 112 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLYJ3 116 " --> pdb=" O ILEJ3 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'J3' and resid 111 through 116' Processing helix chain 'J3' and resid 138 through 142 removed outlier: 3.940A pdb=" N ILEJ3 141 " --> pdb=" O GLYJ3 138 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALAJ3 142 " --> pdb=" O PHEJ3 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'J3' and resid 138 through 142' Processing helix chain 'J3' and resid 158 through 170 removed outlier: 3.907A pdb=" N ALAJ3 162 " --> pdb=" O SERJ3 158 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N METJ3 163 " --> pdb=" O LYSJ3 159 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARGJ3 164 " --> pdb=" O GLUJ3 160 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLNJ3 168 " --> pdb=" O ARGJ3 164 " (cutoff:3.500A) Processing helix chain 'L3' and resid 27 through 31 Processing helix chain 'L3' and resid 33 through 38 Processing helix chain 'L3' and resid 41 through 46 removed outlier: 3.523A pdb=" N ARGL3 45 " --> pdb=" O ALAL3 41 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILEL3 46 " --> pdb=" O ARGL3 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'L3' and resid 41 through 46' Processing helix chain 'L3' and resid 110 through 123 removed outlier: 3.698A pdb=" N VALL3 114 " --> pdb=" O LEUL3 110 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARGL3 116 " --> pdb=" O ALAL3 112 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLUL3 119 " --> pdb=" O GLNL3 115 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SERL3 122 " --> pdb=" O LYSL3 118 " (cutoff:3.500A) Processing helix chain 'L3' and resid 142 through 147 removed outlier: 3.730A pdb=" N LYSL3 145 " --> pdb=" O GLUL3 142 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALAL3 147 " --> pdb=" O LEUL3 144 " (cutoff:3.500A) Processing helix chain 'L3' and resid 172 through 176 Processing helix chain 'L3' and resid 178 through 191 removed outlier: 4.263A pdb=" N METL3 184 " --> pdb=" O ALAL3 180 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALAL3 187 " --> pdb=" O ARGL3 183 " (cutoff:3.500A) Processing helix chain 'L3' and resid 194 through 208 removed outlier: 3.647A pdb=" N ALAL3 199 " --> pdb=" O ARGL3 195 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LYSL3 200 " --> pdb=" O ALAL3 196 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VALL3 207 " --> pdb=" O ALAL3 203 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLUL3 208 " --> pdb=" O GLUL3 204 " (cutoff:3.500A) Processing helix chain 'M3' and resid 69 through 81 removed outlier: 3.811A pdb=" N VALM3 73 " --> pdb=" O ARGM3 69 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARGM3 74 " --> pdb=" O GLNM3 70 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ALAM3 80 " --> pdb=" O ALAM3 76 " (cutoff:3.500A) Processing helix chain 'M3' and resid 81 through 86 removed outlier: 3.584A pdb=" N LYSM3 85 " --> pdb=" O ASPM3 81 " (cutoff:3.500A) Processing helix chain 'M3' and resid 92 through 101 removed outlier: 4.056A pdb=" N GLUM3 96 " --> pdb=" O ALAM3 92 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARGM3 98 " --> pdb=" O LYSM3 94 " (cutoff:3.500A) Processing helix chain 'M3' and resid 106 through 120 removed outlier: 3.979A pdb=" N TYRM3 110 " --> pdb=" O ASPM3 106 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYSM3 111 " --> pdb=" O PHEM3 107 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VALM3 112 " --> pdb=" O ASPM3 108 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ALAM3 115 " --> pdb=" O LYSM3 111 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYSM3 117 " --> pdb=" O METM3 113 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N METM3 118 " --> pdb=" O LYSM3 114 " (cutoff:3.500A) Processing helix chain 'M3' and resid 123 through 132 removed outlier: 3.558A pdb=" N LYSM3 128 " --> pdb=" O LYSM3 124 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYSM3 129 " --> pdb=" O ASNM3 125 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARGM3 132 " --> pdb=" O LYSM3 128 " (cutoff:3.500A) Processing helix chain 'N3' and resid 3 through 8 removed outlier: 4.057A pdb=" N GLNN3 8 " --> pdb=" O TYRN3 4 " (cutoff:3.500A) Processing helix chain 'N3' and resid 18 through 23 Processing helix chain 'N3' and resid 25 through 30 Processing helix chain 'N3' and resid 31 through 33 No H-bonds generated for 'chain 'N3' and resid 31 through 33' Processing helix chain 'N3' and resid 44 through 50 removed outlier: 3.690A pdb=" N ALAN3 48 " --> pdb=" O ARGN3 44 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARGN3 49 " --> pdb=" O PRON3 45 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARGN3 50 " --> pdb=" O ASPN3 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'N3' and resid 44 through 50' Processing helix chain 'N3' and resid 97 through 109 removed outlier: 4.403A pdb=" N GLUN3 104 " --> pdb=" O SERN3 100 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ALAN3 106 " --> pdb=" O ALAN3 102 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HISN3 109 " --> pdb=" O ARGN3 105 " (cutoff:3.500A) Processing helix chain 'N3' and resid 139 through 144 Processing helix chain 'N3' and resid 153 through 157 removed outlier: 3.851A pdb=" N LYSN3 157 " --> pdb=" O PRON3 154 " (cutoff:3.500A) Processing helix chain 'N3' and resid 168 through 173 removed outlier: 3.929A pdb=" N GLYN3 173 " --> pdb=" O ARGN3 169 " (cutoff:3.500A) Processing helix chain 'N3' and resid 177 through 184 removed outlier: 3.522A pdb=" N PHEN3 180 " --> pdb=" O GLYN3 177 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N HISN3 181 " --> pdb=" O HISN3 178 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HISN3 182 " --> pdb=" O LYSN3 179 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N THRN3 183 " --> pdb=" O PHEN3 180 " (cutoff:3.500A) Processing helix chain 'N3' and resid 189 through 194 removed outlier: 3.712A pdb=" N ARGN3 194 " --> pdb=" O ALAN3 190 " (cutoff:3.500A) Processing helix chain 'O3' and resid 19 through 27 removed outlier: 3.708A pdb=" N ALAO3 24 " --> pdb=" O ALAO3 20 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYSO3 25 " --> pdb=" O ALAO3 21 " (cutoff:3.500A) Processing helix chain 'O3' and resid 46 through 56 removed outlier: 3.724A pdb=" N ASNO3 50 " --> pdb=" O ASNO3 46 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N TYRO3 54 " --> pdb=" O ASNO3 50 " (cutoff:3.500A) Processing helix chain 'O3' and resid 65 through 69 Processing helix chain 'O3' and resid 81 through 86 removed outlier: 3.618A pdb=" N GLYO3 86 " --> pdb=" O ARGO3 82 " (cutoff:3.500A) Processing helix chain 'O3' and resid 109 through 113 removed outlier: 3.936A pdb=" N ASPO3 113 " --> pdb=" O PROO3 110 " (cutoff:3.500A) Processing helix chain 'O3' and resid 124 through 129 removed outlier: 3.751A pdb=" N LEUO3 129 " --> pdb=" O LYSO3 125 " (cutoff:3.500A) Processing helix chain 'O3' and resid 138 through 145 removed outlier: 3.600A pdb=" N GLUO3 144 " --> pdb=" O ARGO3 140 " (cutoff:3.500A) Processing helix chain 'O3' and resid 149 through 157 removed outlier: 3.689A pdb=" N THRO3 153 " --> pdb=" O TYRO3 149 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THRO3 155 " --> pdb=" O ALAO3 151 " (cutoff:3.500A) Processing helix chain 'O3' and resid 160 through 185 removed outlier: 4.019A pdb=" N ILEO3 166 " --> pdb=" O GLUO3 162 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N HISO3 167 " --> pdb=" O LYSO3 163 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEUO3 174 " --> pdb=" O LYSO3 170 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEUO3 177 " --> pdb=" O GLNO3 173 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYSO3 183 " --> pdb=" O LYSO3 179 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASNO3 184 " --> pdb=" O GLNO3 180 " (cutoff:3.500A) Processing helix chain 'P3' and resid 25 through 30 removed outlier: 4.057A pdb=" N THRP3 29 " --> pdb=" O HISP3 25 " (cutoff:3.500A) Processing helix chain 'P3' and resid 40 through 48 removed outlier: 3.580A pdb=" N THRP3 45 " --> pdb=" O ILEP3 41 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYSP3 46 " --> pdb=" O ARGP3 42 " (cutoff:3.500A) Processing helix chain 'P3' and resid 71 through 75 removed outlier: 4.166A pdb=" N LYSP3 74 " --> pdb=" O ALAP3 71 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLNP3 75 " --> pdb=" O GLNP3 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'P3' and resid 71 through 75' Processing helix chain 'P3' and resid 93 through 105 removed outlier: 3.513A pdb=" N ASNP3 97 " --> pdb=" O HISP3 93 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLUP3 99 " --> pdb=" O LEUP3 95 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAP3 102 " --> pdb=" O ALAP3 98 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLUP3 103 " --> pdb=" O GLUP3 99 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LYSP3 105 " --> pdb=" O ASNP3 101 " (cutoff:3.500A) Processing helix chain 'P3' and resid 108 through 110 No H-bonds generated for 'chain 'P3' and resid 108 through 110' Processing helix chain 'Q3' and resid 33 through 38 removed outlier: 3.874A pdb=" N ARGQ3 37 " --> pdb=" O ARGQ3 33 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 43 through 48 Processing helix chain 'Q3' and resid 49 through 52 removed outlier: 3.604A pdb=" N PHEQ3 52 " --> pdb=" O LYSQ3 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q3' and resid 49 through 52' Processing helix chain 'Q3' and resid 54 through 58 removed outlier: 3.607A pdb=" N ASNQ3 57 " --> pdb=" O SERQ3 54 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARGQ3 58 " --> pdb=" O ARGQ3 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q3' and resid 54 through 58' Processing helix chain 'Q3' and resid 64 through 66 No H-bonds generated for 'chain 'Q3' and resid 64 through 66' Processing helix chain 'Q3' and resid 67 through 71 removed outlier: 3.621A pdb=" N METQ3 70 " --> pdb=" O ILEQ3 67 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 124 through 130 removed outlier: 3.873A pdb=" N LEUQ3 128 " --> pdb=" O ASPQ3 124 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASPQ3 129 " --> pdb=" O GLNQ3 125 " (cutoff:3.500A) Processing helix chain 'Q3' and resid 146 through 151 removed outlier: 3.536A pdb=" N ARGQ3 150 " --> pdb=" O GLUQ3 147 " (cutoff:3.500A) Processing helix chain 'R3' and resid 5 through 10 removed outlier: 4.201A pdb=" N ARGR3 9 " --> pdb=" O ARGR3 5 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEUR3 10 " --> pdb=" O LEUR3 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'R3' and resid 5 through 10' Processing helix chain 'R3' and resid 10 through 15 removed outlier: 3.962A pdb=" N LEUR3 15 " --> pdb=" O ALAR3 11 " (cutoff:3.500A) Processing helix chain 'R3' and resid 28 through 33 removed outlier: 3.806A pdb=" N ILER3 32 " --> pdb=" O GLUR3 28 " (cutoff:3.500A) Processing helix chain 'R3' and resid 40 through 45 Processing helix chain 'R3' and resid 60 through 68 Processing helix chain 'R3' and resid 68 through 73 removed outlier: 4.064A pdb=" N LYSR3 72 " --> pdb=" O LEUR3 68 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLYR3 73 " --> pdb=" O ALAR3 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'R3' and resid 68 through 73' Processing helix chain 'R3' and resid 97 through 102 removed outlier: 3.867A pdb=" N LEUR3 102 " --> pdb=" O ARGR3 98 " (cutoff:3.500A) Processing helix chain 'R3' and resid 106 through 111 removed outlier: 3.968A pdb=" N GLUR3 111 " --> pdb=" O ARGR3 107 " (cutoff:3.500A) Processing helix chain 'R3' and resid 143 through 147 removed outlier: 3.845A pdb=" N ALAR3 147 " --> pdb=" O LYSR3 144 " (cutoff:3.500A) Processing helix chain 'R3' and resid 150 through 158 removed outlier: 3.878A pdb=" N ALAR3 156 " --> pdb=" O LYSR3 152 " (cutoff:3.500A) Processing helix chain 'R3' and resid 162 through 179 removed outlier: 3.811A pdb=" N GLUR3 168 " --> pdb=" O SERR3 164 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ARGR3 173 " --> pdb=" O ALAR3 169 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ARGR3 176 " --> pdb=" O ARGR3 172 " (cutoff:3.500A) Processing helix chain 'S3' and resid 40 through 48 removed outlier: 3.593A pdb=" N TRPS3 45 " --> pdb=" O LYSS3 41 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYRS3 46 " --> pdb=" O SERS3 42 " (cutoff:3.500A) Processing helix chain 'S3' and resid 55 through 57 No H-bonds generated for 'chain 'S3' and resid 55 through 57' Processing helix chain 'S3' and resid 103 through 118 removed outlier: 3.581A pdb=" N THRS3 107 " --> pdb=" O ALAS3 103 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N CYSS3 109 " --> pdb=" O ALAS3 105 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARGS3 111 " --> pdb=" O THRS3 107 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLYS3 114 " --> pdb=" O TYRS3 110 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ALAS3 115 " --> pdb=" O ARGS3 111 " (cutoff:3.500A) Processing helix chain 'S3' and resid 120 through 124 removed outlier: 3.734A pdb=" N SERS3 123 " --> pdb=" O ARGS3 120 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILES3 124 " --> pdb=" O ALAS3 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S3' and resid 120 through 124' Processing helix chain 'S3' and resid 142 through 146 removed outlier: 3.655A pdb=" N HISS3 146 " --> pdb=" O LYSS3 143 " (cutoff:3.500A) Processing helix chain 'T3' and resid 54 through 58 removed outlier: 3.752A pdb=" N HIST3 58 " --> pdb=" O LYST3 55 " (cutoff:3.500A) Processing helix chain 'T3' and resid 102 through 118 removed outlier: 4.565A pdb=" N ARGT3 108 " --> pdb=" O SERT3 104 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LYST3 110 " --> pdb=" O LEUT3 106 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLUT3 111 " --> pdb=" O LYST3 107 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLUT3 118 " --> pdb=" O GLNT3 114 " (cutoff:3.500A) Processing helix chain 'U3' and resid 25 through 30 Processing helix chain 'U3' and resid 81 through 93 removed outlier: 3.587A pdb=" N TYRU3 85 " --> pdb=" O ARGU3 81 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N TYRU3 90 " --> pdb=" O LEUU3 86 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYSU3 92 " --> pdb=" O LYSU3 88 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYSU3 93 " --> pdb=" O LYSU3 89 " (cutoff:3.500A) Processing helix chain 'X3' and resid 83 through 92 removed outlier: 3.888A pdb=" N LYSX3 88 " --> pdb=" O GLUX3 84 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LYSX3 89 " --> pdb=" O SERX3 85 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLUX3 91 " --> pdb=" O METX3 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASPX3 92 " --> pdb=" O LYSX3 88 " (cutoff:3.500A) Processing helix chain 'X3' and resid 109 through 114 removed outlier: 3.541A pdb=" N LYSX3 114 " --> pdb=" O LYSX3 110 " (cutoff:3.500A) Processing helix chain 'X3' and resid 146 through 154 removed outlier: 3.834A pdb=" N ASNX3 151 " --> pdb=" O LEUX3 147 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N LYSX3 152 " --> pdb=" O ASPX3 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILEX3 153 " --> pdb=" O VALX3 149 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 15 through 20 Processing helix chain 'Y3' and resid 22 through 30 removed outlier: 3.736A pdb=" N ARGY3 27 " --> pdb=" O SERY3 23 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N LYSY3 28 " --> pdb=" O HISY3 24 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILEY3 29 " --> pdb=" O ILEY3 25 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N METY3 30 " --> pdb=" O ARGY3 26 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 35 through 43 removed outlier: 3.817A pdb=" N GLNY3 40 " --> pdb=" O LYSY3 36 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYSY3 41 " --> pdb=" O GLUY3 37 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASNY3 43 " --> pdb=" O ARGY3 39 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 100 through 102 No H-bonds generated for 'chain 'Y3' and resid 100 through 102' Processing helix chain 'Y3' and resid 112 through 120 removed outlier: 3.501A pdb=" N LYSY3 117 " --> pdb=" O LYSY3 113 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILEY3 118 " --> pdb=" O ASPY3 114 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLUY3 120 " --> pdb=" O LYSY3 116 " (cutoff:3.500A) Processing helix chain 'Y3' and resid 123 through 132 removed outlier: 3.832A pdb=" N GLNY3 127 " --> pdb=" O ALAY3 123 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VALY3 128 " --> pdb=" O LYSY3 124 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLYY3 129 " --> pdb=" O SERY3 125 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYSY3 130 " --> pdb=" O ARGY3 126 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLUY3 131 " --> pdb=" O GLNY3 127 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYSY3 132 " --> pdb=" O VALY3 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y3' and resid 123 through 132' Processing helix chain 'Z3' and resid 59 through 66 Processing helix chain 'Z3' and resid 103 through 123 removed outlier: 3.804A pdb=" N ARGZ3 108 " --> pdb=" O PROZ3 104 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYSZ3 109 " --> pdb=" O ALAZ3 105 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALAZ3 110 " --> pdb=" O LEUZ3 106 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYSZ3 117 " --> pdb=" O GLUZ3 113 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHEZ3 118 " --> pdb=" O ALAZ3 114 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLUZ3 119 " --> pdb=" O LYSZ3 115 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLUZ3 120 " --> pdb=" O VALZ3 116 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARGZ3 121 " --> pdb=" O LYSZ3 117 " (cutoff:3.500A) Processing helix chain 'a3' and resid 7 through 11 Processing helix chain 'a3' and resid 43 through 48 Processing helix chain 'a3' and resid 77 through 82 removed outlier: 3.938A pdb=" N LEUa3 81 " --> pdb=" O LYSa3 77 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VALa3 82 " --> pdb=" O LEUa3 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'a3' and resid 77 through 82' Processing helix chain 'a3' and resid 83 through 93 removed outlier: 4.098A pdb=" N ARGa3 87 " --> pdb=" O SERa3 83 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VALa3 88 " --> pdb=" O GLUa3 84 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASNa3 89 " --> pdb=" O GLNa3 85 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALAa3 91 " --> pdb=" O ARGa3 87 " (cutoff:3.500A) Processing helix chain 'a3' and resid 130 through 136 removed outlier: 3.737A pdb=" N GLUa3 135 " --> pdb=" O ARGa3 131 " (cutoff:3.500A) Processing helix chain 'a3' and resid 136 through 141 removed outlier: 3.589A pdb=" N VALa3 140 " --> pdb=" O LYSa3 136 " (cutoff:3.500A) Processing helix chain 'b3' and resid 36 through 47 removed outlier: 4.063A pdb=" N ASNb3 42 " --> pdb=" O LYSb3 38 " (cutoff:3.500A) Processing helix chain 'b3' and resid 53 through 60 Processing helix chain 'b3' and resid 63 through 69 removed outlier: 3.724A pdb=" N ALAb3 69 " --> pdb=" O METb3 65 " (cutoff:3.500A) Processing helix chain 'b3' and resid 91 through 100 removed outlier: 3.605A pdb=" N TYRb3 98 " --> pdb=" O HISb3 94 " (cutoff:3.500A) Processing helix chain 'b3' and resid 103 through 106 removed outlier: 4.239A pdb=" N ARGb3 106 " --> pdb=" O LYSb3 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'b3' and resid 103 through 106' Processing helix chain 'b3' and resid 107 through 114 removed outlier: 3.826A pdb=" N ARGb3 111 " --> pdb=" O ARGb3 107 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILEb3 112 " --> pdb=" O ALAb3 108 " (cutoff:3.500A) Processing helix chain 'c3' and resid 17 through 25 removed outlier: 3.573A pdb=" N METc3 22 " --> pdb=" O LEUc3 18 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYSc3 23 " --> pdb=" O GLNc3 19 " (cutoff:3.500A) Processing helix chain 'c3' and resid 31 through 40 removed outlier: 3.915A pdb=" N LYSc3 36 " --> pdb=" O LYSc3 32 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N METc3 37 " --> pdb=" O GLNc3 33 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILEc3 38 " --> pdb=" O SERc3 34 " (cutoff:3.500A) Processing helix chain 'c3' and resid 56 through 64 removed outlier: 3.818A pdb=" N GLUc3 61 " --> pdb=" O LYSc3 57 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N TYRc3 62 " --> pdb=" O SERc3 58 " (cutoff:3.500A) Processing helix chain 'c3' and resid 79 through 85 Processing helix chain 'd3' and resid 37 through 39 No H-bonds generated for 'chain 'd3' and resid 37 through 39' Processing helix chain 'd3' and resid 40 through 54 removed outlier: 4.206A pdb=" N LYSd3 47 " --> pdb=" O PROd3 43 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILEd3 49 " --> pdb=" O ALAd3 45 " (cutoff:3.500A) Processing helix chain 'd3' and resid 65 through 73 removed outlier: 3.583A pdb=" N ASNd3 69 " --> pdb=" O ASPd3 65 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYSd3 70 " --> pdb=" O THRd3 66 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALAd3 71 " --> pdb=" O ARGd3 67 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TRPd3 73 " --> pdb=" O ASNd3 69 " (cutoff:3.500A) Processing helix chain 'e3' and resid 81 through 90 removed outlier: 3.646A pdb=" N GLUe3 84 " --> pdb=" O ASNe3 81 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLUe3 86 " --> pdb=" O LYSe3 83 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N VALe3 87 " --> pdb=" O GLUe3 84 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEUe3 88 " --> pdb=" O LEUe3 85 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEUe3 89 " --> pdb=" O GLUe3 86 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N METe3 90 " --> pdb=" O VALe3 87 " (cutoff:3.500A) Processing helix chain 'e3' and resid 107 through 118 removed outlier: 3.780A pdb=" N GLUe3 113 " --> pdb=" O LYSe3 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARGe3 114 " --> pdb=" O ALAe3 110 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALAe3 116 " --> pdb=" O VALe3 112 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLNe3 117 " --> pdb=" O GLUe3 113 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEUe3 118 " --> pdb=" O ARGe3 114 " (cutoff:3.500A) Processing helix chain 'f3' and resid 93 through 97 removed outlier: 3.798A pdb=" N ALAf3 96 " --> pdb=" O PROf3 93 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ILEf3 97 " --> pdb=" O ALAf3 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'f3' and resid 93 through 97' Processing helix chain 'g3' and resid 83 through 92 removed outlier: 3.935A pdb=" N VALg3 87 " --> pdb=" O CYSg3 83 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARGg3 88 " --> pdb=" O ALAg3 84 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASPg3 89 " --> pdb=" O LYSg3 85 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYSg3 92 " --> pdb=" O ARGg3 88 " (cutoff:3.500A) Processing helix chain 'g3' and resid 92 through 97 removed outlier: 3.750A pdb=" N LEUg3 96 " --> pdb=" O LYSg3 92 " (cutoff:3.500A) Processing helix chain 'g3' and resid 97 through 110 removed outlier: 3.679A pdb=" N ILEg3 102 " --> pdb=" O GLUg3 98 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N VALg3 103 " --> pdb=" O GLUg3 99 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VALg3 104 " --> pdb=" O GLNg3 100 " (cutoff:3.500A) Processing helix chain 'g3' and resid 110 through 115 removed outlier: 4.062A pdb=" N GLNg3 114 " --> pdb=" O GLNg3 110 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYSg3 115 " --> pdb=" O ALAg3 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'g3' and resid 110 through 115' Processing helix chain 'h3' and resid 13 through 37 removed outlier: 3.685A pdb=" N LEUh3 17 " --> pdb=" O LYSh3 13 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEUh3 18 " --> pdb=" O LYSh3 14 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASPh3 22 " --> pdb=" O LEUh3 18 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N VALh3 26 " --> pdb=" O ASPh3 22 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEUh3 31 " --> pdb=" O GLUh3 27 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VALh3 33 " --> pdb=" O SERh3 29 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ALAh3 34 " --> pdb=" O GLNh3 30 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VALh3 36 " --> pdb=" O ARGh3 32 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THRh3 37 " --> pdb=" O VALh3 33 " (cutoff:3.500A) Processing helix chain 'h3' and resid 46 through 52 Processing helix chain 'h3' and resid 54 through 73 removed outlier: 4.357A pdb=" N VALh3 60 " --> pdb=" O ARGh3 56 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THRh3 64 " --> pdb=" O VALh3 60 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYSh3 66 " --> pdb=" O ASNh3 62 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASNh3 68 " --> pdb=" O THRh3 64 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEUh3 69 " --> pdb=" O GLNh3 65 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N LYSh3 71 " --> pdb=" O GLUh3 67 " (cutoff:3.500A) Processing helix chain 'h3' and resid 96 through 101 Processing helix chain 'i3' and resid 25 through 29 removed outlier: 3.531A pdb=" N ARGi3 29 " --> pdb=" O HISi3 26 " (cutoff:3.500A) Processing helix chain 'i3' and resid 34 through 42 removed outlier: 4.040A pdb=" N PHEi3 39 " --> pdb=" O LYSi3 35 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VALi3 40 " --> pdb=" O HISi3 36 " (cutoff:3.500A) Processing helix chain 'i3' and resid 43 through 48 removed outlier: 3.687A pdb=" N VALi3 47 " --> pdb=" O METi3 43 " (cutoff:3.500A) Processing helix chain 'i3' and resid 56 through 61 Processing helix chain 'i3' and resid 67 through 76 removed outlier: 3.642A pdb=" N ILEi3 73 " --> pdb=" O ALAi3 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYSi3 75 " --> pdb=" O LYSi3 71 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARGi3 76 " --> pdb=" O PHEi3 72 " (cutoff:3.500A) Processing helix chain 'i3' and resid 80 through 88 removed outlier: 3.764A pdb=" N LYSi3 84 " --> pdb=" O HISi3 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARGi3 85 " --> pdb=" O ILEi3 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYSi3 86 " --> pdb=" O ARGi3 82 " (cutoff:3.500A) Processing helix chain 'i3' and resid 94 through 102 removed outlier: 3.590A pdb=" N ALAi3 102 " --> pdb=" O ARGi3 98 " (cutoff:3.500A) Processing helix chain 'j3' and resid 4 through 8 removed outlier: 3.645A pdb=" N SERj3 7 " --> pdb=" O GLYj3 4 " (cutoff:3.500A) Processing helix chain 'j3' and resid 66 through 70 removed outlier: 3.508A pdb=" N ILEj3 69 " --> pdb=" O HISj3 66 " (cutoff:3.500A) Processing helix chain 'j3' and resid 73 through 77 removed outlier: 3.698A pdb=" N HISj3 76 " --> pdb=" O ARGj3 73 " (cutoff:3.500A) Processing helix chain 'k3' and resid 7 through 16 removed outlier: 3.563A pdb=" N LEUk3 12 " --> pdb=" O ILEk3 8 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEUk3 13 " --> pdb=" O LYSk3 9 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THRk3 14 " --> pdb=" O ASPk3 10 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARGk3 16 " --> pdb=" O LEUk3 12 " (cutoff:3.500A) Processing helix chain 'k3' and resid 49 through 58 removed outlier: 4.389A pdb=" N GLUk3 54 " --> pdb=" O LYSk3 50 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYSk3 55 " --> pdb=" O GLUk3 51 " (cutoff:3.500A) Processing helix chain 'l3' and resid 6 through 19 removed outlier: 4.063A pdb=" N LYSl3 15 " --> pdb=" O ARGl3 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYSl3 16 " --> pdb=" O PHEl3 12 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLNl3 17 " --> pdb=" O LEUl3 13 " (cutoff:3.500A) Processing helix chain 'l3' and resid 26 through 30 removed outlier: 3.935A pdb=" N LYSl3 30 " --> pdb=" O ILEl3 27 " (cutoff:3.500A) Processing helix chain 'm3' and resid 53 through 62 removed outlier: 3.994A pdb=" N GLNm3 58 " --> pdb=" O PROm3 54 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEUm3 59 " --> pdb=" O SERm3 55 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYSm3 62 " --> pdb=" O GLNm3 58 " (cutoff:3.500A) Processing helix chain 'n3' and resid 3 through 18 removed outlier: 3.694A pdb=" N METn3 10 " --> pdb=" O ARGn3 6 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARGn3 11 " --> pdb=" O LYSn3 7 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LYSn3 16 " --> pdb=" O ARGn3 12 " (cutoff:3.500A) Processing helix chain 'n3' and resid 19 through 22 Processing helix chain 'o3' and resid 35 through 40 Processing helix chain 'o3' and resid 40 through 46 Processing helix chain 'p3' and resid 8 through 14 removed outlier: 3.818A pdb=" N VALp3 11 " --> pdb=" O VALp3 8 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLYp3 12 " --> pdb=" O GLYp3 9 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYSp3 13 " --> pdb=" O ILEp3 10 " (cutoff:3.500A) Processing helix chain 'p3' and resid 27 through 32 removed outlier: 3.621A pdb=" N SERp3 32 " --> pdb=" O LYSp3 28 " (cutoff:3.500A) Processing helix chain 'p3' and resid 74 through 92 removed outlier: 3.794A pdb=" N THRp3 78 " --> pdb=" O THRp3 74 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYSp3 80 " --> pdb=" O ALAp3 76 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALAp3 82 " --> pdb=" O THRp3 78 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARGp3 84 " --> pdb=" O LYSp3 80 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARGp3 85 " --> pdb=" O SERp3 81 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEUp3 86 " --> pdb=" O ALAp3 82 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYSp3 90 " --> pdb=" O LEUp3 86 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASPp3 91 " --> pdb=" O LYSp3 87 " (cutoff:3.500A) Processing helix chain 'r3' and resid 6 through 14 removed outlier: 5.959A pdb=" N ASNr3 12 " --> pdb=" O METr3 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N CYSr3 13 " --> pdb=" O VALr3 9 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SERr3 14 " --> pdb=" O VALr3 10 " (cutoff:3.500A) Processing helix chain 'r3' and resid 85 through 99 removed outlier: 3.609A pdb=" N THRr3 89 " --> pdb=" O ASNr3 85 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEUr3 90 " --> pdb=" O ALAr3 86 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N METr3 96 " --> pdb=" O SERr3 92 " (cutoff:3.500A) Processing helix chain 'r3' and resid 103 through 107 removed outlier: 3.564A pdb=" N ARGr3 107 " --> pdb=" O PROr3 104 " (cutoff:3.500A) Processing helix chain 'r3' and resid 108 through 121 removed outlier: 4.293A pdb=" N ALAr3 114 " --> pdb=" O ALAr3 110 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEUr3 118 " --> pdb=" O ALAr3 114 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARGr3 119 " --> pdb=" O SERr3 115 " (cutoff:3.500A) Processing helix chain 't3' and resid 18 through 22 removed outlier: 3.508A pdb=" N LEUt3 21 " --> pdb=" O ILEt3 18 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASPt3 22 " --> pdb=" O GLNt3 19 " (cutoff:3.500A) No H-bonds generated for 'chain 't3' and resid 18 through 22' Processing helix chain 't3' and resid 62 through 67 Processing helix chain 't3' and resid 168 through 178 removed outlier: 4.025A pdb=" N ALAt3 172 " --> pdb=" O GLYt3 168 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N THRt3 173 " --> pdb=" O ALAt3 169 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEUt3 174 " --> pdb=" O SERt3 170 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LEUt3 175 " --> pdb=" O GLUt3 171 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASNt3 176 " --> pdb=" O ALAt3 172 " (cutoff:3.500A) Processing helix chain 'u3' and resid 32 through 36 removed outlier: 3.592A pdb=" N GLYu3 36 " --> pdb=" O GLYu3 33 " (cutoff:3.500A) Processing helix chain 'u3' and resid 38 through 51 removed outlier: 4.062A pdb=" N VALu3 42 " --> pdb=" O SERu3 38 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLYu3 43 " --> pdb=" O PROu3 39 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ASPu3 44 " --> pdb=" O LYSu3 40 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ASPu3 45 " --> pdb=" O LYSu3 41 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALAu3 47 " --> pdb=" O GLYu3 43 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYSu3 48 " --> pdb=" O ASPu3 44 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLYu3 51 " --> pdb=" O ALAu3 47 " (cutoff:3.500A) Processing helix chain 'u3' and resid 79 through 85 Processing helix chain 'u3' and resid 107 through 113 removed outlier: 3.524A pdb=" N ASNu3 111 " --> pdb=" O ASPu3 107 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALAu3 113 " --> pdb=" O ILEu3 109 " (cutoff:3.500A) Processing helix chain 'u3' and resid 114 through 117 Processing helix chain 'u3' and resid 124 through 128 removed outlier: 3.518A pdb=" N THRu3 128 " --> pdb=" O LEUu3 125 " (cutoff:3.500A) Processing helix chain 'u3' and resid 135 through 140 Processing helix chain 'u3' and resid 148 through 153 removed outlier: 4.653A pdb=" N ILEu3 152 " --> pdb=" O PROu3 148 " (cutoff:3.500A) Processing helix chain 'w3' and resid 15 through 19 Processing helix chain 'w3' and resid 20 through 24 removed outlier: 3.806A pdb=" N LYSw3 24 " --> pdb=" O ASNw3 21 " (cutoff:3.500A) Processing helix chain 'w3' and resid 76 through 80 removed outlier: 3.722A pdb=" N ALAw3 79 " --> pdb=" O GLUw3 76 " (cutoff:3.500A) Processing helix chain 'w3' and resid 88 through 93 Processing helix chain 'w3' and resid 124 through 129 Processing helix chain 'w3' and resid 145 through 150 removed outlier: 3.509A pdb=" N ASPw3 149 " --> pdb=" O VALw3 145 " (cutoff:3.500A) Processing helix chain 'w3' and resid 175 through 180 Processing helix chain 'w3' and resid 180 through 185 removed outlier: 4.051A pdb=" N LEUw3 185 " --> pdb=" O TYRw3 181 " (cutoff:3.500A) Processing helix chain 'w3' and resid 188 through 193 removed outlier: 3.945A pdb=" N SERw3 192 " --> pdb=" O ASNw3 188 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B2' and resid 38 through 41 removed outlier: 6.919A pdb=" N ILEB2 48 " --> pdb=" O TYRB2 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B2' and resid 99 through 100 removed outlier: 6.664A pdb=" N VALB2 76 " --> pdb=" O ILEB2 99 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N SERB2 75 " --> pdb=" O VALB2 123 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEUB2 122 " --> pdb=" O ILEB2 145 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C2' and resid 32 through 34 removed outlier: 3.518A pdb=" N VALC2 33 " --> pdb=" O GLYC2 45 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLYC2 45 " --> pdb=" O VALC2 33 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C2' and resid 66 through 70 removed outlier: 3.861A pdb=" N GLYC2 102 " --> pdb=" O LYSC2 85 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILEC2 87 " --> pdb=" O PHEC2 100 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHEC2 100 " --> pdb=" O ILEC2 87 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLUC2 89 " --> pdb=" O THRC2 98 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THRC2 98 " --> pdb=" O GLUC2 89 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VALC2 91 " --> pdb=" O CYSC2 96 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYSC2 96 " --> pdb=" O VALC2 91 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N HISC2 101 " --> pdb=" O METC2 217 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N METC2 217 " --> pdb=" O HISC2 101 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N CYSC2 139 " --> pdb=" O ALAC2 123 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALAC2 123 " --> pdb=" O CYSC2 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C2' and resid 66 through 70 removed outlier: 3.861A pdb=" N GLYC2 102 " --> pdb=" O LYSC2 85 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ILEC2 87 " --> pdb=" O PHEC2 100 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N PHEC2 100 " --> pdb=" O ILEC2 87 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLUC2 89 " --> pdb=" O THRC2 98 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N THRC2 98 " --> pdb=" O GLUC2 89 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VALC2 91 " --> pdb=" O CYSC2 96 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N CYSC2 96 " --> pdb=" O VALC2 91 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N HISC2 101 " --> pdb=" O METC2 217 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N METC2 217 " --> pdb=" O HISC2 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N VALC2 140 " --> pdb=" O VALC2 210 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N VALC2 210 " --> pdb=" O VALC2 140 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHEC2 142 " --> pdb=" O HISC2 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D2' and resid 103 through 115 removed outlier: 6.080A pdb=" N ASPD2 104 " --> pdb=" O GLYD2 131 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N GLYD2 131 " --> pdb=" O ASPD2 104 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N VALD2 106 " --> pdb=" O ALAD2 129 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ALAD2 129 " --> pdb=" O VALD2 106 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LYSD2 108 " --> pdb=" O PHED2 127 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N PHED2 127 " --> pdb=" O LYSD2 108 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LYSD2 142 " --> pdb=" O ALAD2 126 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D2' and resid 187 through 188 removed outlier: 3.704A pdb=" N CYSD2 188 " --> pdb=" O VALD2 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D2' and resid 194 through 197 Processing sheet with id=AA9, first strand: chain 'E2' and resid 37 through 38 removed outlier: 3.573A pdb=" N GLUE2 38 " --> pdb=" O ILEE2 49 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILEE2 49 " --> pdb=" O GLUE2 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E2' and resid 152 through 154 removed outlier: 3.846A pdb=" N ASPE2 154 " --> pdb=" O CYSE2 134 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N CYSE2 134 " --> pdb=" O ASPE2 154 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLYE2 183 " --> pdb=" O SERE2 139 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILEE2 184 " --> pdb=" O ARGE2 173 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E2' and resid 209 through 210 removed outlier: 3.942A pdb=" N SERE2 209 " --> pdb=" O ILES2 40 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E2' and resid 223 through 224 removed outlier: 3.871A pdb=" N ILEh2 189 " --> pdb=" O ILEE2 223 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VALh2 176 " --> pdb=" O LYSh2 185 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N ASNh2 187 " --> pdb=" O VALh2 174 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VALh2 174 " --> pdb=" O ASNh2 187 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F2' and resid 42 through 43 Processing sheet with id=AB5, first strand: chain 'F2' and resid 70 through 72 removed outlier: 4.006A pdb=" N HISF2 112 " --> pdb=" O ARGF2 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F2' and resid 140 through 141 removed outlier: 7.034A pdb=" N VALF2 140 " --> pdb=" O ARGF2 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYSF2 122 " --> pdb=" O ILEF2 162 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THRF2 159 " --> pdb=" O ILEF2 173 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASPF2 171 " --> pdb=" O GLNF2 161 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N ASPF2 163 " --> pdb=" O ILEF2 169 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ILEF2 169 " --> pdb=" O ASPF2 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F2' and resid 194 through 198 removed outlier: 6.778A pdb=" N HISF2 209 " --> pdb=" O THRF2 196 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ARGF2 198 " --> pdb=" O VALF2 207 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N VALF2 207 " --> pdb=" O ARGF2 198 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G2' and resid 123 through 126 removed outlier: 8.634A pdb=" N LYSd2 47 " --> pdb=" O ALAG2 138 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ASPG2 140 " --> pdb=" O LYSd2 47 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H2' and resid 73 through 77 removed outlier: 3.635A pdb=" N VALH2 73 " --> pdb=" O VALH2 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEUH2 75 " --> pdb=" O LYSH2 95 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYSH2 93 " --> pdb=" O LEUH2 77 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I2' and resid 47 through 49 removed outlier: 3.841A pdb=" N ALAI2 47 " --> pdb=" O PHEI2 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYSI2 49 " --> pdb=" O ILEI2 61 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HISI2 91 " --> pdb=" O LYSI2 58 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VALI2 93 " --> pdb=" O ILEI2 60 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILEI2 62 " --> pdb=" O VALI2 93 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILEI2 95 " --> pdb=" O ILEI2 62 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I2' and resid 185 through 186 removed outlier: 4.122A pdb=" N GLYI2 141 " --> pdb=" O HISI2 157 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LYSI2 142 " --> pdb=" O ASPX2 54 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASPX2 54 " --> pdb=" O LYSI2 142 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J2' and resid 37 through 38 removed outlier: 5.862A pdb=" N LYSJ2 37 " --> pdb=" O LEUJ2 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'J2' and resid 45 through 47 Processing sheet with id=AC5, first strand: chain 'J2' and resid 72 through 77 removed outlier: 4.003A pdb=" N CYSJ2 72 " --> pdb=" O TRPJ2 67 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARGJ2 74 " --> pdb=" O PHEJ2 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHEJ2 65 " --> pdb=" O ARGJ2 74 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VALJ2 189 " --> pdb=" O ASNJ2 64 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N SERJ2 66 " --> pdb=" O VALJ2 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'J2' and resid 83 through 84 Processing sheet with id=AC7, first strand: chain 'L2' and resid 23 through 24 removed outlier: 3.720A pdb=" N ALAL2 23 " --> pdb=" O PHEL2 67 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M2' and resid 72 through 79 removed outlier: 17.020A pdb=" N LEUM2 73 " --> pdb=" O LEUM2 93 " (cutoff:3.500A) removed outlier: 15.470A pdb=" N LEUM2 93 " --> pdb=" O LEUM2 73 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N GLYM2 75 " --> pdb=" O ASPM2 91 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N ASPM2 91 " --> pdb=" O GLYM2 75 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VALM2 77 " --> pdb=" O ARGM2 89 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARGM2 89 " --> pdb=" O VALM2 77 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYSM2 107 " --> pdb=" O ARGM2 90 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYRM2 92 " --> pdb=" O ARGM2 105 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARGM2 105 " --> pdb=" O TYRM2 92 " (cutoff:3.500A) removed outlier: 9.288A pdb=" N VALM2 138 " --> pdb=" O ASNM2 108 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N SERM2 110 " --> pdb=" O VALM2 138 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHEM2 140 " --> pdb=" O SERM2 110 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N THRM2 127 " --> pdb=" O LEUM2 143 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N VALM2 145 " --> pdb=" O ILEM2 125 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILEM2 125 " --> pdb=" O VALM2 145 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VALM2 126 " --> pdb=" O GLYM2 75 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLYM2 75 " --> pdb=" O VALM2 126 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N2' and resid 49 through 50 removed outlier: 3.727A pdb=" N LEUN2 49 " --> pdb=" O VALN2 111 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N2' and resid 52 through 53 removed outlier: 6.405A pdb=" N LEUN2 52 " --> pdb=" O VALN2 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'P2' and resid 52 through 57 removed outlier: 6.997A pdb=" N VALP2 44 " --> pdb=" O ILEP2 53 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ARGP2 55 " --> pdb=" O VALP2 42 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VALP2 42 " --> pdb=" O ARGP2 55 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHEP2 34 " --> pdb=" O PHEP2 41 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEUP2 93 " --> pdb=" O GLYP2 127 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILEP2 129 " --> pdb=" O LEUP2 93 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILEP2 95 " --> pdb=" O ILEP2 129 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASPP2 131 " --> pdb=" O ILEP2 95 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEUP2 97 " --> pdb=" O ASPP2 131 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q2' and resid 77 through 78 Processing sheet with id=AD4, first strand: chain 'R2' and resid 13 through 14 Processing sheet with id=AD5, first strand: chain 'R2' and resid 32 through 34 Processing sheet with id=AD6, first strand: chain 'S2' and resid 96 through 98 Processing sheet with id=AD7, first strand: chain 'T2' and resid 13 through 14 removed outlier: 3.645A pdb=" N ILET2 20 " --> pdb=" O LEUT2 13 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V2' and resid 54 through 55 removed outlier: 3.964A pdb=" N THRV2 23 " --> pdb=" O GLUV2 113 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLUV2 113 " --> pdb=" O THRV2 23 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'V2' and resid 59 through 60 Processing sheet with id=AE1, first strand: chain 'W2' and resid 32 through 33 Processing sheet with id=AE2, first strand: chain 'W2' and resid 36 through 39 removed outlier: 3.586A pdb=" N GLUW2 38 " --> pdb=" O GLNW2 49 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N GLNW2 49 " --> pdb=" O GLUW2 38 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'X2' and resid 71 through 74 removed outlier: 3.763A pdb=" N PHEX2 128 " --> pdb=" O GLYX2 73 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VALX2 103 " --> pdb=" O LEUX2 126 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N PHEX2 128 " --> pdb=" O PHEX2 101 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N PHEX2 101 " --> pdb=" O PHEX2 128 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N METX2 111 " --> pdb=" O LEUX2 104 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Y2' and resid 80 through 82 removed outlier: 6.954A pdb=" N ARGY2 67 " --> pdb=" O GLYY2 56 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N GLYY2 56 " --> pdb=" O ARGY2 67 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N CYSY2 69 " --> pdb=" O LYSY2 54 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LYSY2 54 " --> pdb=" O CYSY2 69 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N ARGY2 71 " --> pdb=" O LEUY2 52 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N GLUY2 99 " --> pdb=" O VALY2 125 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VALY2 125 " --> pdb=" O GLUY2 99 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEUY2 101 " --> pdb=" O VALY2 123 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Z2' and resid 10 through 15 removed outlier: 5.969A pdb=" N LYSZ2 11 " --> pdb=" O VALZ2 24 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N VALZ2 24 " --> pdb=" O LYSZ2 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'a2' and resid 99 through 101 removed outlier: 7.093A pdb=" N ILEa2 108 " --> pdb=" O VALa2 100 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'b2' and resid 20 through 22 Processing sheet with id=AE8, first strand: chain 'b2' and resid 39 through 40 Processing sheet with id=AE9, first strand: chain 'c2' and resid 44 through 46 removed outlier: 3.571A pdb=" N THRc2 44 " --> pdb=" O VALc2 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VALc2 35 " --> pdb=" O THRc2 44 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LYSc2 36 " --> pdb=" O SERc2 78 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SERc2 78 " --> pdb=" O LYSc2 36 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c2' and resid 64 through 65 removed outlier: 3.506A pdb=" N ARGc2 72 " --> pdb=" O GLNc2 65 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd2' and resid 41 through 44 removed outlier: 6.891A pdb=" N CYSd2 27 " --> pdb=" O GLYd2 19 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLYd2 19 " --> pdb=" O CYSd2 27 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N GLNd2 29 " --> pdb=" O VALd2 17 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N VALd2 17 " --> pdb=" O GLNd2 29 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N ARGd2 31 " --> pdb=" O THRd2 15 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THRd2 15 " --> pdb=" O ARGd2 31 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYSd2 10 " --> pdb=" O LEUd2 58 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'e2' and resid 30 through 31 removed outlier: 3.869A pdb=" N METe2 38 " --> pdb=" O ILEe2 31 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'g2' and resid 138 through 140 Processing sheet with id=AF5, first strand: chain 'h2' and resid 9 through 10 removed outlier: 4.492A pdb=" N GLYh2 9 " --> pdb=" O VALh2 309 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARGh2 308 " --> pdb=" O ALAh2 300 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALAh2 300 " --> pdb=" O ARGh2 308 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N PHEh2 299 " --> pdb=" O ALAh2 290 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALAh2 290 " --> pdb=" O PHEh2 299 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'h2' and resid 41 through 42 removed outlier: 3.564A pdb=" N ARGh2 57 " --> pdb=" O METh2 42 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'h2' and resid 66 through 71 removed outlier: 3.950A pdb=" N ASPh2 68 " --> pdb=" O GLYh2 81 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N SERh2 82 " --> pdb=" O THRh2 86 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N THRh2 86 " --> pdb=" O SERh2 82 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N PHEh2 101 " --> pdb=" O LEUh2 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEUh2 89 " --> pdb=" O ARGh2 99 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ARGh2 99 " --> pdb=" O LEUh2 89 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASPh2 91 " --> pdb=" O THRh2 97 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THRh2 97 " --> pdb=" O ASPh2 91 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h2' and resid 108 through 113 removed outlier: 4.032A pdb=" N ALAh2 112 " --> pdb=" O VALh2 121 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VALh2 121 " --> pdb=" O ALAh2 112 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYSh2 130 " --> pdb=" O SERh2 122 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILEh2 129 " --> pdb=" O THRh2 141 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N THRh2 141 " --> pdb=" O ILEh2 129 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEUh2 131 " --> pdb=" O LYSh2 139 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h2' and resid 240 through 241 removed outlier: 3.627A pdb=" N CYSh2 240 " --> pdb=" O CYSh2 249 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N CYSh2 249 " --> pdb=" O CYSh2 240 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALAh2 250 " --> pdb=" O LYSh2 257 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N ILEh2 256 " --> pdb=" O GLUh2 269 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N GLUh2 269 " --> pdb=" O ILEh2 256 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ILEh2 258 " --> pdb=" O VALh2 267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A3' and resid 40 through 42 Processing sheet with id=AG2, first strand: chain 'A3' and resid 50 through 51 removed outlier: 4.646A pdb=" N ASPA3 51 " --> pdb=" O ALAA3 56 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALAA3 56 " --> pdb=" O ASPA3 51 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'A3' and resid 62 through 64 removed outlier: 3.609A pdb=" N ARGA3 72 " --> pdb=" O PHEA3 63 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'A3' and resid 101 through 103 removed outlier: 3.518A pdb=" N ALAA3 164 " --> pdb=" O LEUA3 102 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THRA3 135 " --> pdb=" O LYSA3 149 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B3' and resid 276 through 283 removed outlier: 5.375A pdb=" N THRB3 278 " --> pdb=" O GLYB3 221 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLYB3 221 " --> pdb=" O THRB3 278 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILEB3 280 " --> pdb=" O VALB3 219 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VALB3 219 " --> pdb=" O ILEB3 280 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VALB3 222 " --> pdb=" O VALB3 344 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VALB3 344 " --> pdb=" O VALB3 222 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYSB3 50 " --> pdb=" O GLUB3 80 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLUB3 80 " --> pdb=" O LYSB3 50 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLYB3 52 " --> pdb=" O ILEB3 78 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYSB3 286 " --> pdb=" O METB3 332 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B3' and resid 276 through 283 removed outlier: 5.375A pdb=" N THRB3 278 " --> pdb=" O GLYB3 221 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLYB3 221 " --> pdb=" O THRB3 278 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILEB3 280 " --> pdb=" O VALB3 219 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VALB3 219 " --> pdb=" O ILEB3 280 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VALB3 222 " --> pdb=" O VALB3 344 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VALB3 344 " --> pdb=" O VALB3 222 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VALB3 57 " --> pdb=" O LYSB3 366 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B3' and resid 101 through 106 removed outlier: 4.307A pdb=" N LYSB3 103 " --> pdb=" O GLYB3 91 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N VALB3 86 " --> pdb=" O HISB3 165 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N HISB3 165 " --> pdb=" O VALB3 86 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLYB3 88 " --> pdb=" O LEUB3 163 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VALB3 159 " --> pdb=" O TYRB3 92 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B3' and resid 101 through 106 removed outlier: 4.307A pdb=" N LYSB3 103 " --> pdb=" O GLYB3 91 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B3' and resid 292 through 293 removed outlier: 4.444A pdb=" N LEUB3 292 " --> pdb=" O ILEB3 299 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILEB3 299 " --> pdb=" O LEUB3 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'C3' and resid 7 through 11 removed outlier: 3.521A pdb=" N VALC3 10 " --> pdb=" O LYSC3 20 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LYSC3 20 " --> pdb=" O VALC3 10 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C3' and resid 64 through 65 removed outlier: 3.814A pdb=" N ARGC3 78 " --> pdb=" O GLUC3 65 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C3' and resid 152 through 154 removed outlier: 4.481A pdb=" N LEUC3 152 " --> pdb=" O CYSC3 250 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C3' and resid 188 through 189 removed outlier: 3.736A pdb=" N ARGC3 188 " --> pdb=" O ILEC3 202 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D3' and resid 74 through 79 removed outlier: 7.103A pdb=" N ILED3 64 " --> pdb=" O VALD3 75 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALAD3 77 " --> pdb=" O CYSD3 62 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N CYSD3 62 " --> pdb=" O ALAD3 77 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYRD3 79 " --> pdb=" O ILED3 60 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ILED3 60 " --> pdb=" O TYRD3 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VALD3 53 " --> pdb=" O ASPD3 147 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E3' and resid 94 through 98 removed outlier: 3.988A pdb=" N VALE3 95 " --> pdb=" O VALE3 110 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VALE3 110 " --> pdb=" O VALE3 95 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARGE3 108 " --> pdb=" O LYSE3 97 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E3' and resid 191 through 192 removed outlier: 3.832A pdb=" N LYSE3 169 " --> pdb=" O LEUE3 177 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILEE3 152 " --> pdb=" O THRE3 200 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILEE3 198 " --> pdb=" O ILEE3 154 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F3' and resid 80 through 82 removed outlier: 3.706A pdb=" N VALF3 82 " --> pdb=" O HIST3 139 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIST3 139 " --> pdb=" O VALF3 82 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'F3' and resid 139 through 140 removed outlier: 3.650A pdb=" N ILEF3 92 " --> pdb=" O ALAF3 140 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THRF3 120 " --> pdb=" O VALF3 91 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASNF3 118 " --> pdb=" O ARGF3 93 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLYF3 119 " --> pdb=" O PHEF3 210 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G3' and resid 207 through 210 removed outlier: 5.711A pdb=" N VALG3 208 " --> pdb=" O ILEG3 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'H3' and resid 3 through 5 removed outlier: 6.922A pdb=" N LEUH3 5 " --> pdb=" O TRPH3 60 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N TRPH3 60 " --> pdb=" O LEUH3 5 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'H3' and resid 8 through 11 removed outlier: 3.516A pdb=" N GLNH3 8 " --> pdb=" O VALH3 57 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H3' and resid 17 through 21 removed outlier: 3.762A pdb=" N ASPH3 17 " --> pdb=" O LYSH3 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYSH3 28 " --> pdb=" O ASPH3 17 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THRH3 24 " --> pdb=" O LYSH3 21 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VALH3 25 " --> pdb=" O ARGH3 36 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ARGH3 36 " --> pdb=" O VALH3 25 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H3' and resid 135 through 136 removed outlier: 3.671A pdb=" N GLYH3 148 " --> pdb=" O PHEH3 88 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHEH3 88 " --> pdb=" O GLYH3 148 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H3' and resid 102 through 104 removed outlier: 3.903A pdb=" N ASNH3 102 " --> pdb=" O ARGH3 115 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VALH3 104 " --> pdb=" O GLUH3 113 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'I3' and resid 35 through 37 removed outlier: 6.432A pdb=" N VALI3 134 " --> pdb=" O SERI3 54 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N SERI3 54 " --> pdb=" O VALI3 134 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N METI3 136 " --> pdb=" O METI3 52 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'I3' and resid 58 through 61 removed outlier: 3.756A pdb=" N GLUI3 58 " --> pdb=" O VALI3 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VALI3 129 " --> pdb=" O GLUI3 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILEI3 97 " --> pdb=" O GLNI3 123 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N THRI3 125 " --> pdb=" O HISI3 95 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N HISI3 95 " --> pdb=" O THRI3 125 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I3' and resid 190 through 193 Processing sheet with id=AJ1, first strand: chain 'J3' and resid 49 through 52 removed outlier: 3.528A pdb=" N HISJ3 71 " --> pdb=" O VALJ3 49 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SERJ3 51 " --> pdb=" O ALAJ3 69 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALAJ3 69 " --> pdb=" O SERJ3 51 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N VALJ3 133 " --> pdb=" O ARGJ3 18 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEUJ3 20 " --> pdb=" O TYRJ3 131 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TYRJ3 131 " --> pdb=" O LEUJ3 20 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEUJ3 22 " --> pdb=" O ASPJ3 129 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ASPJ3 129 " --> pdb=" O LEUJ3 22 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHEJ3 105 " --> pdb=" O VALJ3 132 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'L3' and resid 22 through 23 removed outlier: 3.724A pdb=" N ALAL3 23 " --> pdb=" O LEUN3 198 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'L3' and resid 58 through 59 removed outlier: 3.521A pdb=" N VALL3 59 " --> pdb=" O ARGL3 71 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'L3' and resid 124 through 126 Processing sheet with id=AJ5, first strand: chain 'M3' and resid 7 through 8 Processing sheet with id=AJ6, first strand: chain 'M3' and resid 24 through 25 removed outlier: 5.267A pdb=" N VALM3 12 " --> pdb=" O THRM3 58 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'M3' and resid 29 through 30 removed outlier: 3.659A pdb=" N METM3 50 " --> pdb=" O ALAM3 36 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'N3' and resid 36 through 39 removed outlier: 3.700A pdb=" N HISN3 37 " --> pdb=" O ARGN3 63 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ILEN3 61 " --> pdb=" O ALAN3 39 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALN3 132 " --> pdb=" O TYRN3 62 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILEN3 64 " --> pdb=" O PHEN3 130 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHEN3 129 " --> pdb=" O TRPN3 120 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N TRPN3 120 " --> pdb=" O PHEN3 129 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLUN3 131 " --> pdb=" O SERN3 118 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N SERN3 118 " --> pdb=" O GLUN3 131 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ILEN3 133 " --> pdb=" O LEUN3 116 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'O3' and resid 7 through 9 removed outlier: 3.734A pdb=" N VALO3 34 " --> pdb=" O LEUO3 7 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'O3' and resid 42 through 44 Processing sheet with id=AK2, first strand: chain 'P3' and resid 16 through 22 removed outlier: 3.760A pdb=" N ASNP3 21 " --> pdb=" O CYSP3 144 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYSP3 144 " --> pdb=" O ASNP3 21 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N HISP3 145 " --> pdb=" O VALP3 119 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VALP3 119 " --> pdb=" O HISP3 145 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLUP3 147 " --> pdb=" O ILEP3 117 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ILEP3 117 " --> pdb=" O GLUP3 147 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ILEP3 149 " --> pdb=" O GLUP3 115 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'P3' and resid 58 through 59 Processing sheet with id=AK4, first strand: chain 'P3' and resid 128 through 130 removed outlier: 3.752A pdb=" N ASNP3 137 " --> pdb=" O THRP3 129 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'Q3' and resid 61 through 62 removed outlier: 6.803A pdb=" N LEUQ3 61 " --> pdb=" O THRQ3 87 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK5 Processing sheet with id=AK6, first strand: chain 'Q3' and resid 120 through 121 removed outlier: 6.676A pdb=" N VALQ3 100 " --> pdb=" O LEUQ3 121 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N THRQ3 79 " --> pdb=" O VALQ3 137 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'S3' and resid 59 through 66 removed outlier: 5.525A pdb=" N ILES3 61 " --> pdb=" O ARGS3 15 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARGS3 15 " --> pdb=" O ILES3 61 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLYS3 65 " --> pdb=" O LYSS3 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALAS3 34 " --> pdb=" O ARGS3 8 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VALS3 12 " --> pdb=" O METS3 30 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLYS3 14 " --> pdb=" O TYRS3 28 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARGS3 29 " --> pdb=" O GLUT3 149 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'S3' and resid 95 through 96 removed outlier: 4.526A pdb=" N ASNS3 77 " --> pdb=" O ILES3 132 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYSS3 128 " --> pdb=" O TRPS3 81 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'S3' and resid 83 through 84 removed outlier: 3.590A pdb=" N TYRS3 84 " --> pdb=" O HISS3 91 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'T3' and resid 83 through 92 removed outlier: 3.597A pdb=" N LYST3 83 " --> pdb=" O VALT3 80 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ALAT3 71 " --> pdb=" O VALT3 67 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VALT3 67 " --> pdb=" O ALAT3 71 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLYT3 73 " --> pdb=" O TYRT3 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYRT3 65 " --> pdb=" O GLYT3 73 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ASNT3 77 " --> pdb=" O THRT3 61 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N THRT3 61 " --> pdb=" O ASNT3 77 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASPT3 41 " --> pdb=" O LYST3 97 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYST3 97 " --> pdb=" O ASPT3 41 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'U3' and resid 62 through 64 removed outlier: 3.772A pdb=" N SERU3 62 " --> pdb=" O THRU3 73 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THRU3 73 " --> pdb=" O SERU3 62 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'U3' and resid 102 through 104 removed outlier: 3.858A pdb=" N VALU3 103 " --> pdb=" O GLUU3 111 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'V3' and resid 25 through 27 Processing sheet with id=AL5, first strand: chain 'V3' and resid 60 through 63 Processing sheet with id=AL6, first strand: chain 'V3' and resid 88 through 89 removed outlier: 3.503A pdb=" N LEUV3 96 " --> pdb=" O TYRV3 88 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'X3' and resid 77 through 80 removed outlier: 7.018A pdb=" N ILEX3 99 " --> pdb=" O LYSX3 78 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N VALX3 97 " --> pdb=" O PROX3 80 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYSX3 134 " --> pdb=" O VALX3 100 " (cutoff:3.500A) Processing sheet with id=AL8, first strand: chain 'Y3' and resid 31 through 33 Processing sheet with id=AL9, first strand: chain 'Y3' and resid 68 through 69 removed outlier: 6.997A pdb=" N GLUY3 54 " --> pdb=" O THRY3 107 " (cutoff:3.500A) Processing sheet with id=AM1, first strand: chain 'Y3' and resid 86 through 88 Processing sheet with id=AM2, first strand: chain 'Z3' and resid 38 through 43 removed outlier: 6.180A pdb=" N TYRZ3 38 " --> pdb=" O ASPZ3 31 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASPZ3 31 " --> pdb=" O TYRZ3 38 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEUZ3 42 " --> pdb=" O LYSZ3 27 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYSZ3 27 " --> pdb=" O LEUZ3 42 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEUZ3 12 " --> pdb=" O METZ3 81 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'a3' and resid 72 through 74 removed outlier: 6.119A pdb=" N VALa3 73 " --> pdb=" O LEUa3 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM3 Processing sheet with id=AM4, first strand: chain 'a3' and resid 100 through 102 removed outlier: 6.410A pdb=" N VALa3 122 " --> pdb=" O ALAa3 143 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VALa3 145 " --> pdb=" O VALa3 122 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VALa3 124 " --> pdb=" O VALa3 145 " (cutoff:3.500A) Processing sheet with id=AM5, first strand: chain 'c3' and resid 27 through 29 removed outlier: 6.337A pdb=" N VALc3 46 " --> pdb=" O HISc3 72 " (cutoff:3.500A) Processing sheet with id=AM6, first strand: chain 'd3' and resid 22 through 28 removed outlier: 3.997A pdb=" N VALd3 86 " --> pdb=" O TYRd3 25 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'd3' and resid 63 through 64 removed outlier: 7.423A pdb=" N ARGd3 63 " --> pdb=" O VALd3 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM7 Processing sheet with id=AM8, first strand: chain 'e3' and resid 78 through 79 Processing sheet with id=AM9, first strand: chain 'f3' and resid 47 through 48 removed outlier: 10.306A pdb=" N CYSf3 7 " --> pdb=" O ILEf3 30 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ILEf3 30 " --> pdb=" O CYSf3 7 " (cutoff:3.500A) removed outlier: 8.763A pdb=" N ALAf3 9 " --> pdb=" O LEUf3 28 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEUf3 28 " --> pdb=" O ALAf3 9 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N PHEf3 11 " --> pdb=" O ALAf3 26 " (cutoff:3.500A) removed outlier: 10.911A pdb=" N ALAf3 26 " --> pdb=" O PHEf3 11 " (cutoff:3.500A) removed outlier: 12.099A pdb=" N GLYf3 13 " --> pdb=" O HISf3 24 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N HISf3 24 " --> pdb=" O GLYf3 13 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYSf3 15 " --> pdb=" O ARGf3 22 " (cutoff:3.500A) Processing sheet with id=AN1, first strand: chain 'f3' and resid 50 through 52 Processing sheet with id=AN2, first strand: chain 'g3' and resid 20 through 24 Processing sheet with id=AN3, first strand: chain 'j3' and resid 16 through 17 Processing sheet with id=AN4, first strand: chain 'k3' and resid 4 through 5 removed outlier: 3.538A pdb=" N TYRk3 43 " --> pdb=" O VALk3 36 " (cutoff:3.500A) Processing sheet with id=AN5, first strand: chain 'k3' and resid 25 through 26 removed outlier: 5.483A pdb=" N ILEk3 25 " --> pdb=" O LEUk3 69 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN5 Processing sheet with id=AN6, first strand: chain 'm3' and resid 76 through 77 Processing sheet with id=AN7, first strand: chain 'o3' and resid 9 through 11 removed outlier: 3.769A pdb=" N THRo3 24 " --> pdb=" O ARGo3 69 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILEo3 66 " --> pdb=" O ILEo3 85 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILEo3 85 " --> pdb=" O ILEo3 66 " (cutoff:3.500A) Processing sheet with id=AN8, first strand: chain 'r3' and resid 17 through 18 Processing sheet with id=AN9, first strand: chain 'r3' and resid 50 through 53 removed outlier: 3.566A pdb=" N THRr3 80 " --> pdb=" O VALr3 62 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VALr3 78 " --> pdb=" O METr3 64 " (cutoff:3.500A) Processing sheet with id=AO1, first strand: chain 't3' and resid 27 through 28 Processing sheet with id=AO2, first strand: chain 't3' and resid 145 through 148 removed outlier: 4.377A pdb=" N LYSt3 146 " --> pdb=" O GLUt3 153 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLUt3 153 " --> pdb=" O LYSt3 146 " (cutoff:3.500A) Processing sheet with id=AO3, first strand: chain 'u3' and resid 11 through 13 removed outlier: 3.672A pdb=" N VALu3 13 " --> pdb=" O LEUu3 62 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEUu3 62 " --> pdb=" O VALu3 13 " (cutoff:3.500A) Processing sheet with id=AO4, first strand: chain 'w3' and resid 31 through 36 removed outlier: 6.862A pdb=" N VALw3 32 " --> pdb=" O VALw3 169 " (cutoff:3.500A) Processing sheet with id=AO5, first strand: chain 'w3' and resid 51 through 54 1647 hydrogen bonds defined for protein. 4452 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1025 hydrogen bonds 1722 hydrogen bond angles 0 basepair planarities 447 basepair parallelities 2265 stacking parallelities Total time for adding SS restraints: 327.41 Time building geometry restraints manager: 75.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.78: 235071 1.78 - 2.51: 651 2.51 - 3.25: 5 3.25 - 3.98: 0 3.98 - 4.71: 1 Bond restraints: 235728 Sorted by residual: bond pdb=" CB GLNG3 117 " pdb=" CG GLNG3 117 " ideal model delta sigma weight residual 1.520 4.714 -3.194 3.00e-02 1.11e+03 1.13e+04 bond pdb=" CD ARGh3 89 " pdb=" NE ARGh3 89 " ideal model delta sigma weight residual 1.458 2.552 -1.094 1.40e-02 5.10e+03 6.11e+03 bond pdb=" N7 G511244 " pdb=" C5 G511244 " ideal model delta sigma weight residual 1.388 2.732 -1.344 2.00e-02 2.50e+03 4.51e+03 bond pdb=" C8 G511244 " pdb=" N7 G511244 " ideal model delta sigma weight residual 1.305 2.627 -1.322 2.00e-02 2.50e+03 4.37e+03 bond pdb=" N9 G511244 " pdb=" C4 G511244 " ideal model delta sigma weight residual 1.375 2.654 -1.279 2.00e-02 2.50e+03 4.09e+03 ... (remaining 235723 not shown) Histogram of bond angle deviations from ideal: 39.38 - 63.06: 2 63.06 - 86.75: 0 86.75 - 110.43: 113743 110.43 - 134.11: 232386 134.11 - 157.79: 73 Bond angle restraints: 346204 Sorted by residual: angle pdb=" C2 C511966 " pdb=" N1 C511966 " pdb=" C6 C511966 " ideal model delta sigma weight residual 120.20 39.38 80.82 3.00e+00 1.11e-01 7.26e+02 angle pdb=" N1 C511966 " pdb=" C2 C511966 " pdb=" N3 C511966 " ideal model delta sigma weight residual 119.20 40.11 79.09 3.00e+00 1.11e-01 6.95e+02 angle pdb=" CD ARGh3 89 " pdb=" NE ARGh3 89 " pdb=" CZ ARGh3 89 " ideal model delta sigma weight residual 124.40 157.79 -33.39 1.40e+00 5.10e-01 5.69e+02 angle pdb=" C SERH2 107 " pdb=" N VALH2 108 " pdb=" CA VALH2 108 " ideal model delta sigma weight residual 121.97 143.35 -21.38 1.80e+00 3.09e-01 1.41e+02 angle pdb=" O GLYb3 115 " pdb=" C GLYb3 115 " pdb=" N LEUb3 116 " ideal model delta sigma weight residual 122.70 107.66 15.04 1.30e+00 5.92e-01 1.34e+02 ... (remaining 346199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 123735 35.92 - 71.83: 5432 71.83 - 107.75: 385 107.75 - 143.67: 52 143.67 - 179.58: 107 Dihedral angle restraints: 129711 sinusoidal: 95613 harmonic: 34098 Sorted by residual: dihedral pdb=" CA GLUR2 43 " pdb=" C GLUR2 43 " pdb=" N PROR2 44 " pdb=" CA PROR2 44 " ideal model delta harmonic sigma weight residual -180.00 -107.11 -72.89 0 5.00e+00 4.00e-02 2.13e+02 dihedral pdb=" CA ASPG3 215 " pdb=" C ASPG3 215 " pdb=" N PROG3 216 " pdb=" CA PROG3 216 " ideal model delta harmonic sigma weight residual -180.00 -113.62 -66.38 0 5.00e+00 4.00e-02 1.76e+02 dihedral pdb=" CA PHEK2 147 " pdb=" C PHEK2 147 " pdb=" N ILEK2 148 " pdb=" CA ILEK2 148 " ideal model delta harmonic sigma weight residual -180.00 -114.62 -65.38 0 5.00e+00 4.00e-02 1.71e+02 ... (remaining 129708 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 41710 0.114 - 0.227: 1318 0.227 - 0.341: 108 0.341 - 0.454: 22 0.454 - 0.568: 4 Chirality restraints: 43162 Sorted by residual: chirality pdb=" CB ILEZ2 75 " pdb=" CA ILEZ2 75 " pdb=" CG1 ILEZ2 75 " pdb=" CG2 ILEZ2 75 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.57 2.00e-01 2.50e+01 8.05e+00 chirality pdb=" CB ILEG3 98 " pdb=" CA ILEG3 98 " pdb=" CG1 ILEG3 98 " pdb=" CG2 ILEG3 98 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.53 2.00e-01 2.50e+01 6.92e+00 chirality pdb=" CB ILEp3 54 " pdb=" CA ILEp3 54 " pdb=" CG1 ILEp3 54 " pdb=" CG2 ILEp3 54 " both_signs ideal model delta sigma weight residual False 2.64 2.13 0.52 2.00e-01 2.50e+01 6.72e+00 ... (remaining 43159 not shown) Planarity restraints: 22230 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C511966 " -0.034 2.00e-02 2.50e+03 1.23e-01 3.38e+02 pdb=" N1 C511966 " -0.197 2.00e-02 2.50e+03 pdb=" C2 C511966 " 0.253 2.00e-02 2.50e+03 pdb=" O2 C511966 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C511966 " 0.114 2.00e-02 2.50e+03 pdb=" C4 C511966 " 0.011 2.00e-02 2.50e+03 pdb=" N4 C511966 " -0.005 2.00e-02 2.50e+03 pdb=" C5 C511966 " -0.015 2.00e-02 2.50e+03 pdb=" C6 C511966 " -0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRPt3 9 " -0.052 2.00e-02 2.50e+03 2.94e-02 2.16e+01 pdb=" CG TRPt3 9 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRPt3 9 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRPt3 9 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRPt3 9 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRPt3 9 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRPt3 9 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRPt3 9 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRPt3 9 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRPt3 9 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALAR3 85 " 0.022 2.00e-02 2.50e+03 4.38e-02 1.92e+01 pdb=" C ALAR3 85 " -0.076 2.00e-02 2.50e+03 pdb=" O ALAR3 85 " 0.028 2.00e-02 2.50e+03 pdb=" N ASNR3 86 " 0.026 2.00e-02 2.50e+03 ... (remaining 22227 not shown) Histogram of nonbonded interaction distances: 1.28 - 2.01: 11 2.01 - 2.73: 26898 2.73 - 3.45: 262316 3.45 - 4.18: 581906 4.18 - 4.90: 864224 Nonbonded interactions: 1735355 Sorted by model distance: nonbonded pdb="MG MG515116 " pdb="MG MG515254 " model vdw 1.284 1.300 nonbonded pdb="MG MG515212 " pdb="MG MG515226 " model vdw 1.285 1.300 nonbonded pdb="MG MGA21955 " pdb="MG MGA21956 " model vdw 1.299 1.300 nonbonded pdb="MG MG515126 " pdb="MG MG515227 " model vdw 1.304 1.300 nonbonded pdb="MG MG515211 " pdb="MG MG515214 " model vdw 1.322 1.300 ... (remaining 1735350 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 5812 5.49 5 Mg 300 5.21 5 S 430 5.16 5 C 115488 2.51 5 N 40909 2.21 5 O 56736 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=0.10 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.200 Extract box with map and model: 21.670 Check model and map are aligned: 2.180 Convert atoms to be neutral: 1.240 Process input model: 686.210 Find NCS groups from input model: 5.610 Set up NCS constraints: 0.510 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:1.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 721.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6910 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 : 0.012 3.194 235728 Z= 0.759 Angle : 1.044 80.818 346204 Z= 0.547 Chirality : 0.050 0.568 43162 Planarity : 0.007 0.123 22230 Dihedral : 16.708 179.582 107710 Min Nonbonded Distance : 1.284 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.37 % Allowed : 10.78 % Favored : 88.85 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.65 % Twisted General : 0.44 % 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: -5.25 (0.06), residues: 11645 helix: -4.78 (0.04), residues: 2941 sheet: -2.79 (0.12), residues: 1417 loop : -3.21 (0.06), residues: 7287 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3167 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 3130 time to evaluate : 10.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 5 residues processed: 3156 average time/residue: 2.0229 time to fit residues: 10696.2907 Evaluate side-chains 1934 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1929 time to evaluate : 9.769 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 1.4834 time to fit residues: 26.1774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1458 optimal weight: 0.6980 chunk 1308 optimal weight: 0.0770 chunk 726 optimal weight: 8.9990 chunk 447 optimal weight: 9.9990 chunk 882 optimal weight: 0.4980 chunk 699 optimal weight: 9.9990 chunk 1353 optimal weight: 0.0030 chunk 523 optimal weight: 10.0000 chunk 823 optimal weight: 8.9990 chunk 1007 optimal weight: 5.9990 chunk 1568 optimal weight: 3.9990 overall best weight: 1.0550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 113 GLN C2 40 ASN C2 147 ASN C2 157 GLN D2 113 GLN E2 22 ASN E2 101 GLN E2 174 HIS F2 112 HIS F2 142 HIS F2 232 ASN G2 82 ASN G2 83 ASN G2 114 ASN G2 137 GLN H2 70 HIS I2 73 GLN I2 193 GLN J2 7 ASN J2 44 HIS J2 84 ASN J2 87 ASN J2 99 ASN ** K2 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2 7 ASN ** L2 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M2 13 GLN M2 83 GLN N2 73 GLN N2 75 ASN ** O2 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R2 80 GLN R2 97 GLN ** T2 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 12 GLN U2 85 ASN V2 47 ASN W2 82 ASN b2 17 HIS c2 26 GLN f2 112 ASN g2 111 ASN g2 135 HIS h2 133 ASN A3 100 ASN B3 55 HIS B3 109 HIS B3 179 HIS B3 245 HIS C3 38 ASN D3 17 GLN D3 111 ASN D3 202 GLN ** D3 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 45 HIS E3 193 HIS E3 253 GLN F3 38 GLN F3 79 ASN F3 118 ASN F3 130 ASN F3 205 ASN ** G3 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 293 ASN H3 15 ASN H3 138 GLN I3 92 HIS I3 100 ASN I3 213 HIS O3 5 GLN O3 50 ASN P3 25 HIS P3 56 GLN ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 118 GLN R3 36 ASN R3 75 HIS R3 86 ASN ** R3 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 143 HIS S3 117 HIS T3 69 GLN T3 95 HIS T3 98 HIS V3 36 ASN X3 93 ASN Y3 24 HIS a3 14 HIS a3 28 HIS ** a3 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN b3 101 HIS c3 73 HIS d3 18 ASN e3 68 HIS e3 107 ASN f3 21 GLN f3 99 HIS g3 18 ASN ** j3 28 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m3 94 ASN p3 92 GLN ** r3 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 23 GLN r3 45 HIS r3 103 HIS u3 147 HIS w3 40 ASN ** w3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w3 119 GLN w3 188 ASN Total number of N/Q/H flips: 99 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.850 235728 Z= 0.362 Angle : 0.760 86.745 346204 Z= 0.375 Chirality : 0.040 0.489 43162 Planarity : 0.007 0.132 22230 Dihedral : 17.298 179.961 82854 Min Nonbonded Distance : 1.093 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.36 % Favored : 92.44 % Rotamer Outliers : 3.42 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.44 % Twisted General : 0.21 % 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: -4.51 (0.06), residues: 11645 helix: -3.89 (0.06), residues: 2988 sheet: -2.29 (0.13), residues: 1477 loop : -2.86 (0.06), residues: 7180 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2520 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 347 poor density : 2173 time to evaluate : 10.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 347 outliers final: 190 residues processed: 2356 average time/residue: 1.6857 time to fit residues: 6878.9730 Evaluate side-chains 2036 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1846 time to evaluate : 11.573 Switching outliers to nearest non-outliers outliers start: 190 outliers final: 0 residues processed: 190 average time/residue: 1.3753 time to fit residues: 509.5538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 871 optimal weight: 1.9990 chunk 486 optimal weight: 10.0000 chunk 1305 optimal weight: 3.9990 chunk 1067 optimal weight: 4.9990 chunk 432 optimal weight: 10.0000 chunk 1571 optimal weight: 6.9990 chunk 1697 optimal weight: 20.0000 chunk 1399 optimal weight: 0.9980 chunk 1558 optimal weight: 5.9990 chunk 535 optimal weight: 10.0000 chunk 1260 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 33 GLN B2 113 GLN B2 131 HIS D2 113 GLN E2 165 ASN E2 174 HIS F2 138 HIS F2 224 ASN H2 177 GLN H2 225 GLN I2 186 ASN J2 138 ASN J2 155 ASN ** K2 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2 32 HIS ** L2 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M2 11 GLN N2 48 HIS N2 75 ASN O2 5 HIS O2 58 HIS O2 62 GLN Q2 104 GLN T2 11 HIS U2 63 HIS U2 83 GLN U2 105 GLN X2 24 GLN X2 56 HIS ** Y2 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z2 22 GLN Z2 124 ASN a2 64 ASN ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f2 112 ASN g2 111 ASN h2 117 ASN ** h2 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h2 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h2 191 HIS h2 311 GLN B3 322 HIS B3 328 ASN C3 198 ASN F3 98 ASN G3 96 GLN ** G3 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 153 HIS ** G3 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G3 248 HIS H3 39 ASN I3 51 HIS ** I3 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O3 5 GLN O3 184 ASN ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 137 ASN Q3 8 ASN Q3 57 ASN Q3 125 GLN ** R3 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R3 86 ASN R3 130 ASN S3 117 HIS S3 156 HIS T3 69 GLN V3 77 HIS Y3 96 HIS Z3 79 HIS a3 40 HIS a3 62 HIS ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 6 ASN b3 50 ASN b3 61 ASN d3 30 HIS ** d3 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e3 23 HIS e3 107 ASN f3 91 ASN h3 63 GLN i3 36 HIS j3 48 ASN j3 66 HIS ** j3 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m3 93 ASN p3 56 HIS r3 23 GLN u3 70 GLN ** w3 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w3 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.851 235728 Z= 0.471 Angle : 0.888 88.333 346204 Z= 0.441 Chirality : 0.045 0.645 43162 Planarity : 0.008 0.186 22230 Dihedral : 17.418 179.829 82854 Min Nonbonded Distance : 1.039 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.61 % Favored : 89.15 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.03 % Twisted General : 0.28 % 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: -4.18 (0.07), residues: 11645 helix: -3.27 (0.07), residues: 3034 sheet: -2.17 (0.13), residues: 1509 loop : -2.80 (0.06), residues: 7102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2978 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 458 poor density : 2520 time to evaluate : 13.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 458 outliers final: 199 residues processed: 2777 average time/residue: 1.8697 time to fit residues: 8944.1179 Evaluate side-chains 2148 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1949 time to evaluate : 9.908 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 199 outliers final: 1 residues processed: 199 average time/residue: 1.4528 time to fit residues: 560.0719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1552 optimal weight: 0.7980 chunk 1181 optimal weight: 0.9990 chunk 815 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 749 optimal weight: 6.9990 chunk 1055 optimal weight: 1.9990 chunk 1576 optimal weight: 4.9990 chunk 1669 optimal weight: 6.9990 chunk 823 optimal weight: 7.9990 chunk 1494 optimal weight: 10.0000 chunk 449 optimal weight: 10.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 33 GLN ** B2 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 57 ASN F2 98 ASN H2 70 HIS I2 33 ASN J2 7 ASN J2 155 ASN K2 75 ASN ** K2 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K2 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2 66 HIS ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 127 ASN T2 134 GLN U2 51 ASN X2 70 ASN ** Y2 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z2 29 HIS ** a2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e2 26 ASN h2 20 GLN ** h2 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h2 119 GLN h2 133 ASN ** h2 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h2 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 38 HIS A3 95 GLN ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 289 GLN C3 223 ASN D3 45 ASN ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 135 GLN G3 143 GLN H3 15 ASN ** J3 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M3 20 HIS N3 87 HIS O3 184 ASN ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 120 ASN Q3 125 GLN R3 143 HIS S3 117 HIS S3 125 GLN S3 146 HIS S3 162 GLN Y3 20 ASN ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN c3 19 GLN e3 24 GLN f3 91 ASN l3 19 GLN ** m3 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p3 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r3 103 HIS ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.843 235728 Z= 0.388 Angle : 0.696 88.464 346204 Z= 0.346 Chirality : 0.038 0.328 43162 Planarity : 0.006 0.115 22230 Dihedral : 16.941 179.305 82854 Min Nonbonded Distance : 1.026 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.45 % Favored : 92.37 % Rotamer Outliers : 3.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.03 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.07), residues: 11645 helix: -2.71 (0.08), residues: 3009 sheet: -1.74 (0.13), residues: 1452 loop : -2.62 (0.07), residues: 7184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2413 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 2091 time to evaluate : 11.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 322 outliers final: 181 residues processed: 2272 average time/residue: 1.7232 time to fit residues: 6822.3342 Evaluate side-chains 2059 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1878 time to evaluate : 9.858 Switching outliers to nearest non-outliers outliers start: 181 outliers final: 0 residues processed: 181 average time/residue: 1.3501 time to fit residues: 477.5755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1390 optimal weight: 4.9990 chunk 947 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 1242 optimal weight: 6.9990 chunk 688 optimal weight: 0.9990 chunk 1424 optimal weight: 7.9990 chunk 1153 optimal weight: 10.0000 chunk 1 optimal weight: 0.8980 chunk 852 optimal weight: 10.0000 chunk 1498 optimal weight: 4.9990 chunk 421 optimal weight: 10.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 33 GLN ** B2 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2 132 GLN ** C2 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2 67 GLN H2 70 HIS H2 197 GLN I2 114 GLN ** J2 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K2 75 ASN K2 113 GLN K2 124 HIS K2 156 HIS L2 32 HIS ** L2 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 104 GLN S2 127 ASN U2 51 ASN Y2 92 ASN a2 64 ASN ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h2 56 GLN ** h2 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A3 8 GLN ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 45 ASN ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F3 98 ASN ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3 113 ASN ** P3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P3 116 HIS P3 118 GLN R3 130 ASN R3 143 HIS S3 162 GLN T3 98 HIS Z3 76 ASN ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 120 GLN b3 61 ASN e3 24 GLN e3 68 HIS e3 107 ASN i3 80 HIS m3 83 ASN ** r3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 103 HIS ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.7311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.838 235728 Z= 0.389 Angle : 0.689 88.556 346204 Z= 0.341 Chirality : 0.038 0.328 43162 Planarity : 0.006 0.104 22230 Dihedral : 16.761 179.836 82854 Min Nonbonded Distance : 0.961 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.97 % Favored : 90.85 % Rotamer Outliers : 3.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.03 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.07), residues: 11645 helix: -2.34 (0.08), residues: 3035 sheet: -1.72 (0.13), residues: 1484 loop : -2.50 (0.07), residues: 7126 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2405 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 2093 time to evaluate : 10.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 312 outliers final: 176 residues processed: 2267 average time/residue: 1.6966 time to fit residues: 6678.4899 Evaluate side-chains 2069 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1893 time to evaluate : 9.904 Switching outliers to nearest non-outliers outliers start: 176 outliers final: 0 residues processed: 176 average time/residue: 1.3819 time to fit residues: 470.0969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 561 optimal weight: 7.9990 chunk 1503 optimal weight: 3.9990 chunk 329 optimal weight: 7.9990 chunk 980 optimal weight: 0.7980 chunk 412 optimal weight: 30.0000 chunk 1670 optimal weight: 8.9990 chunk 1387 optimal weight: 0.0060 chunk 773 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 chunk 552 optimal weight: 20.0000 chunk 877 optimal weight: 0.8980 overall best weight: 1.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D2 267 GLN E2 165 ASN F2 67 GLN G2 83 ASN H2 70 HIS J2 7 ASN J2 44 HIS K2 75 ASN ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 127 ASN U2 51 ASN U2 63 HIS Y2 92 ASN Z2 29 HIS ** a2 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h2 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G3 117 GLN G3 143 GLN G3 153 HIS ** G3 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L3 67 HIS O3 96 GLN ** P3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 77 ASN R3 143 HIS V3 135 ASN ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN ** c3 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 103 HIS ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 1.836 235728 Z= 0.339 Angle : 0.620 88.581 346204 Z= 0.306 Chirality : 0.034 0.414 43162 Planarity : 0.005 0.109 22230 Dihedral : 16.499 179.940 82854 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.40 % Favored : 93.47 % Rotamer Outliers : 1.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.03 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.15 (0.07), residues: 11645 helix: -2.03 (0.09), residues: 3058 sheet: -1.48 (0.13), residues: 1498 loop : -2.34 (0.07), residues: 7089 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2158 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1976 time to evaluate : 11.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 103 residues processed: 2070 average time/residue: 1.6950 time to fit residues: 6099.9471 Evaluate side-chains 1934 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1831 time to evaluate : 9.929 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 1.3504 time to fit residues: 277.9462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1611 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 952 optimal weight: 8.9990 chunk 1220 optimal weight: 5.9990 chunk 945 optimal weight: 7.9990 chunk 1406 optimal weight: 2.9990 chunk 933 optimal weight: 6.9990 chunk 1664 optimal weight: 3.9990 chunk 1041 optimal weight: 5.9990 chunk 1014 optimal weight: 5.9990 chunk 768 optimal weight: 9.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2 232 HIS D2 267 GLN F2 67 GLN H2 70 HIS K2 75 ASN K2 132 GLN ** K2 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L2 84 HIS ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 98 ASN Q2 104 GLN S2 127 ASN T2 10 GLN T2 11 HIS T2 135 HIS U2 42 HIS X2 70 ASN Y2 92 ASN a2 64 ASN ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 51 GLN h2 237 ASN ** h2 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 45 ASN ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J3 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J3 167 GLN ** P3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 77 ASN R3 143 HIS Z3 76 ASN ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN l3 17 GLN ** p3 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 103 HIS t3 68 HIS ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.8029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.841 235728 Z= 0.461 Angle : 0.746 88.811 346204 Z= 0.365 Chirality : 0.040 0.369 43162 Planarity : 0.006 0.138 22230 Dihedral : 16.716 179.796 82854 Min Nonbonded Distance : 0.993 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.00 % Favored : 89.83 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.03 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.23 (0.07), residues: 11645 helix: -2.05 (0.09), residues: 3021 sheet: -1.63 (0.13), residues: 1548 loop : -2.40 (0.07), residues: 7076 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2198 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1980 time to evaluate : 10.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 218 outliers final: 141 residues processed: 2084 average time/residue: 1.8221 time to fit residues: 6638.6855 Evaluate side-chains 2025 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1884 time to evaluate : 9.922 Switching outliers to nearest non-outliers outliers start: 141 outliers final: 0 residues processed: 141 average time/residue: 1.3319 time to fit residues: 371.8741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1029 optimal weight: 7.9990 chunk 664 optimal weight: 0.8980 chunk 994 optimal weight: 9.9990 chunk 501 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 322 optimal weight: 5.9990 chunk 1058 optimal weight: 3.9990 chunk 1134 optimal weight: 3.9990 chunk 822 optimal weight: 1.9990 chunk 155 optimal weight: 40.0000 chunk 1308 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2 67 GLN F2 138 HIS G2 203 ASN H2 70 HIS H2 225 GLN K2 75 ASN ** K2 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 98 ASN Q2 104 GLN R2 24 HIS S2 127 ASN T2 10 GLN U2 51 ASN W2 29 HIS Y2 92 ASN Z2 15 ASN ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h2 56 GLN h2 237 ASN ** h2 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G3 248 HIS ** J3 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O3 184 ASN ** P3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 77 ASN Q3 125 GLN R3 143 HIS T3 69 GLN ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN i3 36 HIS ** p3 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 103 HIS u3 115 GLN ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.8398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.835 235728 Z= 0.418 Angle : 0.698 88.965 346204 Z= 0.345 Chirality : 0.038 0.406 43162 Planarity : 0.006 0.113 22230 Dihedral : 16.656 179.694 82854 Min Nonbonded Distance : 1.020 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.42 % Favored : 91.40 % Rotamer Outliers : 1.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.03 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.14 (0.07), residues: 11645 helix: -1.94 (0.09), residues: 3021 sheet: -1.55 (0.13), residues: 1516 loop : -2.36 (0.07), residues: 7108 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2126 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1964 time to evaluate : 9.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 94 residues processed: 2041 average time/residue: 1.7319 time to fit residues: 6172.2107 Evaluate side-chains 1934 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1840 time to evaluate : 9.766 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 0 residues processed: 94 average time/residue: 1.4164 time to fit residues: 266.9224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1514 optimal weight: 1.9990 chunk 1594 optimal weight: 5.9990 chunk 1454 optimal weight: 1.9990 chunk 1551 optimal weight: 0.6980 chunk 933 optimal weight: 5.9990 chunk 675 optimal weight: 7.9990 chunk 1218 optimal weight: 3.9990 chunk 476 optimal weight: 10.0000 chunk 1401 optimal weight: 0.9980 chunk 1467 optimal weight: 6.9990 chunk 1545 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F2 67 GLN F2 138 HIS H2 70 HIS K2 75 ASN ** K2 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 98 ASN S2 127 ASN T2 10 GLN ** T2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 70 ASN ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 275 HIS ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 282 ASN ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O3 50 ASN ** P3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 77 ASN Q3 125 GLN R3 143 HIS ** Z3 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z3 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a3 28 HIS ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN i3 36 HIS ** p3 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r3 103 HIS ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.8449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.836 235728 Z= 0.368 Angle : 0.690 88.522 346204 Z= 0.339 Chirality : 0.036 0.463 43162 Planarity : 0.006 0.122 22230 Dihedral : 16.589 179.980 82854 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 8.07 % Favored : 91.76 % Rotamer Outliers : 0.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.23 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.07), residues: 11645 helix: -1.81 (0.09), residues: 3011 sheet: -1.49 (0.13), residues: 1525 loop : -2.29 (0.07), residues: 7109 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1999 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1918 time to evaluate : 10.056 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: 81 outliers final: 46 residues processed: 1950 average time/residue: 1.6957 time to fit residues: 5778.6387 Evaluate side-chains 1889 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1843 time to evaluate : 9.936 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 0 residues processed: 46 average time/residue: 1.3980 time to fit residues: 133.3778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1018 optimal weight: 20.0000 chunk 1640 optimal weight: 0.9980 chunk 1001 optimal weight: 5.9990 chunk 778 optimal weight: 3.9990 chunk 1140 optimal weight: 6.9990 chunk 1720 optimal weight: 9.9990 chunk 1583 optimal weight: 3.9990 chunk 1370 optimal weight: 0.9990 chunk 142 optimal weight: 7.9990 chunk 1058 optimal weight: 0.0270 chunk 840 optimal weight: 2.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2 165 ASN F2 67 GLN F2 138 HIS H2 70 HIS K2 75 ASN L2 7 ASN ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 98 ASN ** T2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U2 51 ASN ** X2 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y2 92 ASN ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A3 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B3 275 HIS ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D3 203 ASN E3 185 ASN ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 282 ASN ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 77 ASN R3 143 HIS Z3 76 ASN ** Z3 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN i3 36 HIS ** p3 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.8459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.835 235728 Z= 0.387 Angle : 0.695 88.581 346204 Z= 0.342 Chirality : 0.036 0.449 43162 Planarity : 0.006 0.155 22230 Dihedral : 16.582 179.982 82854 Min Nonbonded Distance : 1.076 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.03 % Favored : 91.79 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.23 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.07), residues: 11645 helix: -1.79 (0.09), residues: 3004 sheet: -1.47 (0.13), residues: 1527 loop : -2.28 (0.07), residues: 7114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23290 Ramachandran restraints generated. 11645 Oldfield, 0 Emsley, 11645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1906 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1855 time to evaluate : 11.266 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: 51 outliers final: 34 residues processed: 1873 average time/residue: 1.8303 time to fit residues: 6021.2776 Evaluate side-chains 1867 residues out of total 10150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1833 time to evaluate : 9.921 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 1.7286 time to fit residues: 116.5052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1727 random chunks: chunk 1088 optimal weight: 3.9990 chunk 1459 optimal weight: 5.9990 chunk 419 optimal weight: 10.0000 chunk 1263 optimal weight: 2.9990 chunk 202 optimal weight: 8.9990 chunk 380 optimal weight: 8.9990 chunk 1372 optimal weight: 0.6980 chunk 574 optimal weight: 7.9990 chunk 1409 optimal weight: 2.9990 chunk 173 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C2 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F2 67 GLN F2 138 HIS H2 70 HIS K2 75 ASN ** Q2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 98 ASN S2 127 ASN ** T2 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X2 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y2 92 ASN ** a2 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h2 191 HIS ** A3 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B3 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E3 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E3 282 ASN ** F3 240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G3 212 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P3 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q3 77 ASN R3 143 HIS ** Z3 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b3 61 ASN i3 36 HIS ** p3 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r3 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w3 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.164406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.125459 restraints weight = 310958.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.124127 restraints weight = 309143.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.126863 restraints weight = 211798.623| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 50 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.8460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.834 235728 Z= 0.426 Angle : 0.720 106.091 346204 Z= 0.353 Chirality : 0.037 0.628 43162 Planarity : 0.006 0.186 22230 Dihedral : 16.582 179.964 82854 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.10 % Favored : 91.73 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.21 % Cis-general : 0.03 % Twisted Proline : 1.44 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.07), residues: 11645 helix: -1.79 (0.09), residues: 2999 sheet: -1.47 (0.13), residues: 1527 loop : -2.28 (0.07), residues: 7119 =============================================================================== Job complete usr+sys time: 84232.73 seconds wall clock time: 1450 minutes 15.24 seconds (87015.24 seconds total)